├── nipype ├── external │ └── __init__.py ├── scripts │ └── __init__.py ├── testing │ └── data │ │ ├── A.scheme │ │ ├── NWARP │ │ ├── PD.mgz │ │ ├── SPM.mat │ │ ├── T1.mgz │ │ ├── T1.nii │ │ ├── T2.nii │ │ ├── TPM.nii │ │ ├── aseg.mgz │ │ ├── b0.nii │ │ ├── bvals │ │ ├── bvecs │ │ ├── c1s1.nii │ │ ├── c1s3.nii │ │ ├── csd.mif │ │ ├── db.xml │ │ ├── dirs.txt │ │ ├── dofrun1 │ │ ├── dofrun2 │ │ ├── dti.mif │ │ ├── dwi.mif │ │ ├── epi.nii │ │ ├── f1.1D │ │ ├── f2.1D │ │ ├── fods.mif │ │ ├── grad.b │ │ ├── im1.nii │ │ ├── im2.nii │ │ ├── im3.nii │ │ ├── image.v │ │ ├── lh.pial │ │ ├── lh.white │ │ ├── lta1.lta │ │ ├── lta2.lta │ │ ├── lut_file │ │ ├── maps.nii │ │ ├── mask.1D │ │ ├── mask.mif │ │ ├── mask.nii │ │ ├── mni.nii │ │ ├── norm.mgz │ │ ├── resp.1D │ │ ├── rh.pial │ │ ├── seed.1D │ │ ├── sh.mif │ │ ├── surf.txt │ │ ├── tac.nii │ │ ├── tdi.mif │ │ ├── vsm.nii │ │ ├── wm.mgz │ │ ├── 4d_dwi.nii │ │ ├── 5tt_in.mif │ │ ├── FLASH1.mgz │ │ ├── FLASH2.mgz │ │ ├── FLASH3.mgz │ │ ├── Fred+orig │ │ ├── T1.nii.gz │ │ ├── T1_brain.nii │ │ ├── T1map.nii.gz │ │ ├── TI4D.nii.gz │ │ ├── allFA.nii │ │ ├── all_FA.nii.gz │ │ ├── asl.nii.gz │ │ ├── atlas.nii.gz │ │ ├── b0.nii.gz │ │ ├── b0_b0rev.nii │ │ ├── brukerdir │ │ ├── fid │ │ └── pdata │ │ │ └── 1 │ │ │ └── 2dseq │ │ ├── bvals.scheme │ │ ├── bvecs.scheme │ │ ├── cmatrix.mat │ │ ├── complex.nii │ │ ├── cont1.nii │ │ ├── cont1a.nii │ │ ├── cont2.nii │ │ ├── cont2a.nii │ │ ├── converted.trk │ │ ├── cope.nii.gz │ │ ├── cope1.nii.gz │ │ ├── cortex.label │ │ ├── cov_split.mat │ │ ├── csffod.mif │ │ ├── data.Bfloat │ │ ├── degree.csv │ │ ├── degree.mat │ │ ├── design.con │ │ ├── diffusion.nii │ │ ├── dteig.Bdouble │ │ ├── dwi.nii.gz │ │ ├── dwi_FA.mif │ │ ├── dwi_evals.nii │ │ ├── elastix.txt │ │ ├── encoding.txt │ │ ├── epi_acqp.txt │ │ ├── epi_index.txt │ │ ├── epi_mask.nii │ │ ├── epi_rev.nii │ │ ├── fa.nii.gz │ │ ├── fdir00.nii │ │ ├── fdir01.nii │ │ ├── ffra00.nii │ │ ├── ffra01.nii │ │ ├── fixed1.nii │ │ ├── fixed2.nii │ │ ├── flash_05.mgz │ │ ├── flash_30.mgz │ │ ├── flirt.mat │ │ ├── gmfod.mif │ │ ├── grads.txt │ │ ├── gtmseg.mgz │ │ ├── gtmseg.nii │ │ ├── im_affine.aff │ │ ├── image.nii │ │ ├── indices.txt │ │ ├── input1.xfm │ │ ├── label.mgz │ │ ├── lh-pial.stl │ │ ├── lh.cope1.mgz │ │ ├── magnitude.nii │ │ ├── mask.nii.gz │ │ ├── minc_nlp.conf │ │ ├── mni2t1.nii │ │ ├── model.pklz │ │ ├── moving.csv │ │ ├── moving1.nii │ │ ├── moving2.nii │ │ ├── output.csv │ │ ├── pdfs.Bfloat │ │ ├── pet.nii.gz │ │ ├── phase.nii │ │ ├── rc1s1.nii │ │ ├── rc1s2.nii │ │ ├── rc2s1.nii │ │ ├── rc2s2.nii │ │ ├── ref_tac.dat │ │ ├── register.dat │ │ ├── register.mat │ │ ├── response.txt │ │ ├── resting.nii │ │ ├── rgb.nii.gz │ │ ├── rh-pial.stl │ │ ├── roi01.nii │ │ ├── roi01_idx.npz │ │ ├── roi02.nii │ │ ├── roi02_idx.npz │ │ ├── roi03.nii │ │ ├── roi03_idx.npz │ │ ├── roi04.nii │ │ ├── roi04_idx.npz │ │ ├── roi05.nii │ │ ├── roi05_idx.npz │ │ ├── run1+orig │ │ ├── run2+orig │ │ ├── seed_mask.nii │ │ ├── spmT_0001.img │ │ ├── subj1.cff │ │ ├── subj1.pck │ │ ├── subj2.cff │ │ ├── subj2.pck │ │ ├── surf1.vtk │ │ ├── surf2.vtk │ │ ├── timing.dat │ │ ├── track1.trk │ │ ├── track2.trk │ │ ├── tracks.tck │ │ ├── tracks.trk │ │ ├── trans.mat │ │ ├── warpfield.nii │ │ ├── weights.txt │ │ ├── wm_mask.mif │ │ ├── wmfod.mif │ │ ├── zstat1.nii.gz │ │ ├── A_qmat.Bdouble │ │ ├── Q25_warp+tlrc.HEAD │ │ ├── QSH_peaks.Bdouble │ │ ├── SubjectA.Bfloat │ │ ├── Template_6.nii │ │ ├── afni_output.3D │ │ ├── anat_coreg.mif │ │ ├── anatomical.nii │ │ ├── ants_Affine.txt │ │ ├── ants_Warp.nii.gz │ │ ├── aparc+aseg.nii │ │ ├── brain_mask.nii │ │ ├── clustering.mat │ │ ├── cope1run1.nii.gz │ │ ├── cope1run2.nii.gz │ │ ├── cope2run1.nii.gz │ │ ├── cope2run2.nii.gz │ │ ├── ds005 │ │ └── filler.txt │ │ ├── dwi_WMProb.mif │ │ ├── dwi_tensor.mif │ │ ├── epi_phasediff.nii │ │ ├── epi_slspec.txt │ │ ├── fieldmap_mag.nii │ │ ├── func_epi_1_1.nii │ │ ├── func_to_struct.mat │ │ ├── functional.HEAD │ │ ├── functional.nii │ │ ├── functional.par │ │ ├── functional.rms │ │ ├── functional2.nii │ │ ├── functional3.nii │ │ ├── functional_1.dcm │ │ ├── functional_2.dcm │ │ ├── im_warp.df.nii │ │ ├── indices-labels.txt │ │ ├── lh.area.structural │ │ ├── lh.cope1.nii.gz │ │ ├── lh.hippocampus.stl │ │ ├── lh.pbt.structural │ │ ├── mean_func.nii.gz │ │ ├── minc_initial.xfm │ │ ├── my_database.db │ │ ├── network0.gpickle │ │ ├── pet_resliced.nii │ │ ├── ref_class0.nii │ │ ├── ref_class1.nii │ │ ├── rh.pbt.structural │ │ ├── run1+orig_model │ │ ├── run1_categories.1D │ │ ├── run2_categories.1D │ │ ├── seed_source.nii.gz │ │ ├── seeds_to_M1.nii │ │ ├── seeds_to_M2.nii │ │ ├── session_info.npz │ │ ├── streamlines.trk │ │ ├── struct2mni.nii │ │ ├── struct_to_func.mat │ │ ├── structural.nii │ │ ├── subjectDesign.con │ │ ├── subjectDesign.mat │ │ ├── targets_MASK1.nii │ │ ├── targets_MASK2.nii │ │ ├── timeDesign.con │ │ ├── timeDesign.mat │ │ ├── timeseries.txt │ │ ├── tissue+air_map.nii │ │ ├── tissues.nii.gz │ │ ├── topup_encoding.txt │ │ ├── topup_movpar.txt │ │ ├── tract_data.Bfloat │ │ ├── tracts.Bdouble │ │ ├── tst_class0.nii │ │ ├── tst_class1.nii │ │ ├── varcope.nii.gz │ │ ├── A_recon_params.Bdouble │ │ ├── AffineTransform.mat │ │ ├── ROI_scale500.nii.gz │ │ ├── ants_deformed.nii.gz │ │ ├── brain_track.Bdouble │ │ ├── dicomdir │ │ └── 123456-1-1.dcm │ │ ├── diffusion_weighted.nii │ │ ├── dilated_wm_mask.nii │ │ ├── dwi2anat_Warp.nii.gz │ │ ├── dwi_CSD_tracked.tck │ │ ├── fieldmap_mag_brain.nii │ │ ├── first_merged.nii.gz │ │ ├── fitted_data1.Bfloat │ │ ├── fitted_data2.Bfloat │ │ ├── fsLUT_aparc+aseg.pck │ │ ├── lh.pial_converted.gii │ │ ├── merged_f1samples.nii.gz │ │ ├── merged_fsamples.nii │ │ ├── merged_phsamples.nii │ │ ├── merged_thsamples.nii │ │ ├── minc_test_2D_00.mnc │ │ ├── minc_test_2D_01.mnc │ │ ├── minc_test_2D_02.mnc │ │ ├── minc_test_2D_03.mnc │ │ ├── minc_test_2D_04.mnc │ │ ├── minc_test_2D_05.mnc │ │ ├── minc_test_2D_06.mnc │ │ ├── minc_test_2D_07.mnc │ │ ├── minc_test_2D_08.mnc │ │ ├── minc_test_2D_09.mnc │ │ ├── minc_test_3D_00.mnc │ │ ├── minc_test_3D_01.mnc │ │ ├── minc_test_3D_02.mnc │ │ ├── minc_test_3D_03.mnc │ │ ├── minc_test_3D_04.mnc │ │ ├── minc_test_3D_05.mnc │ │ ├── minc_test_3D_06.mnc │ │ ├── minc_test_3D_07.mnc │ │ ├── minc_test_3D_08.mnc │ │ ├── minc_test_3D_09.mnc │ │ ├── mrtrix3_labelconfig.txt │ │ ├── network0.aparc+aseg.nii │ │ ├── nodif_brain_mask.nii.gz │ │ ├── output_Composite.h5 │ │ ├── peak_directions.mif │ │ ├── rh.pial_converted.gii │ │ ├── skeleton_mask.nii.gz │ │ ├── struct_to_template.mat │ │ ├── study_template.nii.gz │ │ ├── topup_fieldcoef.nii.gz │ │ ├── u_rc1s1_Template.nii │ │ ├── u_rc1s2_Template.nii │ │ ├── u_rc1s3_Template.nii │ │ ├── varcope1run1.nii.gz │ │ ├── varcope1run2.nii.gz │ │ ├── varcope2run1.nii.gz │ │ ├── varcope2run2.nii.gz │ │ ├── voxel-order_data.Bfloat │ │ ├── voxeldisplacemap.vdm │ │ ├── wm_undersampled.nii │ │ ├── FreeSurferColorLUT.txt │ │ ├── MASK_average_thal_right.nii │ │ ├── Template_1_IXI550_MNI152.nii │ │ ├── TransformParameters.0.txt │ │ ├── ballstickfit_data.Bfloat │ │ ├── brain_study_template.nii.gz │ │ ├── dwi2anat_InverseWarp.nii.gz │ │ ├── dwi2anat_coreg_Affine.txt │ │ ├── func2anat_InverseWarp.nii.gz │ │ ├── func2anat_coreg_Affine.txt │ │ ├── lh.central.structural.gii │ │ ├── lh.sphere.reg.structural.gii │ │ ├── lh.sphere.structural.gii │ │ ├── merged_ph1samples.nii.gz │ │ ├── merged_th1samples.nii.gz │ │ ├── resting2anat_Warp.nii.gz │ │ ├── rh.central.structural.gii │ │ ├── rh.sphere.reg.structural.gii │ │ ├── rh.sphere.structural.gii │ │ ├── sub-01_dir-LR_epi.nii.gz │ │ ├── sub-01_dir-RL_epi.nii.gz │ │ ├── tensor_fitted_data.Bdouble │ │ ├── BrainSegmentationPrior01.nii.gz │ │ ├── BrainSegmentationPrior02.nii.gz │ │ ├── BrainSegmentationPrior03.nii.gz │ │ ├── BrainSegmentationPrior04.nii.gz │ │ ├── DisplacementFieldTransform.nii.gz │ │ ├── fieldmap_phase_fslprepared.nii │ │ ├── lh.aparc_a2009s.freesurfer.annot │ │ ├── resting2anat_coreg_Affine.txt │ │ ├── rh.aparc_a2009s.freesurfer.annot │ │ ├── sub-01_ses-baseline_pet.nii.gz │ │ ├── sub-01_task-rest.dtseries.nii │ │ ├── ProbabilityMaskOfStudyTemplate.nii.gz │ │ ├── func2anat_coreg_InverseWarp.nii.gz │ │ ├── sub-01_ses-baseline_pet_mean_reg.lta │ │ ├── config.ini │ │ ├── design.txt │ │ ├── sub-01.L.midthickness.32k_fs_LR.surf.gii │ │ ├── sub-01.R.midthickness.32k_fs_LR.surf.gii │ │ ├── FreeSurferColorLUT_adapted_aparc+aseg_out.pck │ │ ├── fs_LR.L.midthickness_va_avg.32k_fs_LR.shape.gii │ │ ├── fsaverage5_std_sphere.L.10k_fsavg_L.surf.gii │ │ ├── sub-01_task-rest_bold_space-fsaverage5.L.func.gii │ │ ├── fs_LR-deformed_to-fsaverage.L.sphere.32k_fs_LR.surf.gii │ │ ├── fsaverage5.L.midthickness_va_avg.10k_fsavg_L.shape.gii │ │ ├── jsongrabber.txt │ │ ├── design.mat │ │ ├── bedpostxout │ │ └── do_not_delete.txt │ │ ├── tbss_dir │ │ └── do_not_delete.txt │ │ ├── tpm_00.nii.gz │ │ ├── tpm_01.nii.gz │ │ ├── tpm_02.nii.gz │ │ ├── tpms_msk.nii.gz │ │ ├── segmentation0.nii.gz │ │ ├── segmentation1.nii.gz │ │ ├── ds003_sub-01_mc.nii.gz │ │ ├── ds003_sub-01_mc_brainmask.nii.gz │ │ ├── epi_param.txt │ │ ├── events.tsv │ │ ├── README │ │ ├── spminfo │ │ └── ds003_sub-01_mc.DVARS ├── tests │ └── __init__.py ├── caching │ ├── tests │ │ └── __init__.py │ └── __init__.py ├── interfaces │ ├── robex │ │ ├── __init__.py │ │ └── tests │ │ │ └── __init__.py │ ├── tests │ │ ├── __init__.py │ │ ├── test_auto_IOBase.py │ │ ├── test_auto_NiftiGeneratorBase.py │ │ ├── test_auto_NilearnBaseInterface.py │ │ ├── test_auto_SQLiteSink.py │ │ ├── test_auto_JSONFileGrabber.py │ │ ├── test_auto_RCommand.py │ │ ├── test_auto_LookupMeta.py │ │ ├── test_auto_MySQLSink.py │ │ ├── test_auto_SlicerCommandLine.py │ │ └── test_auto_SelectFiles.py │ ├── base │ │ └── tests │ │ │ ├── __init__.py │ │ │ ├── test_auto_BaseInterface.py │ │ │ ├── test_auto_SimpleInterface.py │ │ │ ├── test_auto_LibraryBaseInterface.py │ │ │ ├── test_auto_CommandLine.py │ │ │ ├── test_auto_SEMLikeCommandLine.py │ │ │ ├── test_auto_MpiCommandLine.py │ │ │ └── test_auto_StdOutCommandLine.py │ ├── cat12 │ │ ├── tests │ │ │ └── __init__.py │ │ ├── __init__.py │ │ └── base.py │ ├── cmtk │ │ ├── tests │ │ │ ├── __init__.py │ │ │ ├── test_auto_CFFBaseInterface.py │ │ │ └── test_auto_MergeCNetworks.py │ │ ├── __init__.py │ │ └── base.py │ ├── dipy │ │ ├── tests │ │ │ ├── __init__.py │ │ │ ├── test_auto_DipyBaseInterface.py │ │ │ └── test_auto_DipyDiffusionInterface.py │ │ ├── __init__.py │ │ ├── setup.py │ │ ├── stats.py │ │ └── registration.py │ ├── elastix │ │ ├── tests │ │ │ └── __init__.py │ │ ├── __init__.py │ │ └── base.py │ ├── fsl │ │ ├── tests │ │ │ ├── __init__.py │ │ │ └── test_auto_FSLCommand.py │ │ └── model_templates │ │ │ ├── feat_contrastmask_footer.tcl │ │ │ ├── feat_ev_ortho.tcl │ │ │ ├── feat_fe_featdirs.tcl │ │ │ ├── feat_contrast_ftest_element.tcl │ │ │ ├── feat_fe_copes.tcl │ │ │ ├── feat_contrastmask_header.tcl │ │ │ ├── feat_contrast_element.tcl │ │ │ ├── feat_contrastmask_element.tcl │ │ │ ├── feat_contrast_header.tcl │ │ │ ├── feat_fe_ev_element.tcl │ │ │ ├── feat_contrast_prolog.tcl │ │ │ ├── feat_nongui.tcl │ │ │ ├── feat_ev_none.tcl │ │ │ ├── feat_ev_hrf.tcl │ │ │ ├── feat_ev_gamma.tcl │ │ │ └── feat_fe_ev_header.tcl │ ├── minc │ │ ├── tests │ │ │ └── __init__.py │ │ └── testdata.py │ ├── mipav │ │ ├── tests │ │ │ └── __init__.py │ │ └── __init__.py │ ├── mixins │ │ ├── tests │ │ │ ├── __init__.py │ │ │ ├── test_auto_CopyHeaderInterface.py │ │ │ └── test_auto_ReportCapableInterface.py │ │ └── __init__.py │ ├── mne │ │ ├── tests │ │ │ └── __init__.py │ │ └── __init__.py │ ├── mrtrix │ │ ├── tests │ │ │ └── __init__.py │ │ └── defhdr.mat │ ├── mrtrix3 │ │ └── tests │ │ │ ├── __init__.py │ │ │ └── test_auto_MRTrix3Base.py │ ├── nipy │ │ ├── tests │ │ │ ├── __init__.py │ │ │ └── test_auto_NipyBaseInterface.py │ │ ├── __init__.py │ │ └── base.py │ ├── nitime │ │ ├── tests │ │ │ ├── __init__.py │ │ │ └── test_auto_NitimeBaseInterface.py │ │ ├── base.py │ │ └── __init__.py │ ├── slicer │ │ ├── tests │ │ │ ├── __init__.py │ │ │ └── test_auto_SlicerCommandLine.py │ │ ├── diffusion │ │ │ ├── tests │ │ │ │ └── __init__.py │ │ │ └── __init__.py │ │ ├── filtering │ │ │ ├── tests │ │ │ │ └── __init__.py │ │ │ └── __init__.py │ │ ├── legacy │ │ │ ├── tests │ │ │ │ └── __init__.py │ │ │ ├── diffusion │ │ │ │ ├── tests │ │ │ │ │ └── __init__.py │ │ │ │ └── __init__.py │ │ │ └── __init__.py │ │ ├── quantification │ │ │ ├── tests │ │ │ │ └── __init__.py │ │ │ └── __init__.py │ │ ├── registration │ │ │ ├── tests │ │ │ │ └── __init__.py │ │ │ └── __init__.py │ │ ├── segmentation │ │ │ ├── tests │ │ │ │ └── __init__.py │ │ │ └── __init__.py │ │ ├── base.py │ │ └── __init__.py │ ├── spm │ │ └── tests │ │ │ ├── __init__.py │ │ │ └── test_auto_SPMCommand.py │ ├── utility │ │ ├── tests │ │ │ ├── __init__.py │ │ │ ├── test_auto_AssertEqual.py │ │ │ ├── test_auto_IdentityInterface.py │ │ │ ├── test_auto_Function.py │ │ │ ├── test_auto_Select.py │ │ │ ├── test_auto_Split.py │ │ │ ├── test_auto_Merge.py │ │ │ └── test_auto_CSVReader.py │ │ └── __init__.py │ ├── vista │ │ ├── tests │ │ │ └── __init__.py │ │ └── __init__.py │ ├── brainsuite │ │ ├── tests │ │ │ ├── __init__.py │ │ │ └── test_auto_ThicknessPVC.py │ │ └── __init__.py │ ├── freesurfer │ │ └── tests │ │ │ ├── __init__.py │ │ │ ├── test_auto_FSCommand.py │ │ │ ├── test_auto_FSScriptCommand.py │ │ │ └── test_auto_FSCommandOpenMP.py │ ├── niftyfit │ │ ├── tests │ │ │ ├── __init__.py │ │ │ └── test_auto_NiftyFitCommand.py │ │ └── __init__.py │ ├── niftyreg │ │ ├── tests │ │ │ ├── __init__.py │ │ │ └── test_auto_NiftyRegCommand.py │ │ └── __init__.py │ ├── niftyseg │ │ ├── tests │ │ │ ├── __init__.py │ │ │ └── test_auto_NiftySegCommand.py │ │ └── __init__.py │ ├── semtools │ │ ├── tests │ │ │ └── __init__.py │ │ ├── brains │ │ │ ├── tests │ │ │ │ └── __init__.py │ │ │ └── __init__.py │ │ ├── legacy │ │ │ ├── tests │ │ │ │ └── __init__.py │ │ │ └── __init__.py │ │ ├── diffusion │ │ │ ├── tests │ │ │ │ └── __init__.py │ │ │ ├── tractography │ │ │ │ ├── tests │ │ │ │ │ └── __init__.py │ │ │ │ └── __init__.py │ │ │ └── __init__.py │ │ ├── filtering │ │ │ ├── tests │ │ │ │ └── __init__.py │ │ │ └── __init__.py │ │ ├── registration │ │ │ ├── tests │ │ │ │ └── __init__.py │ │ │ └── __init__.py │ │ ├── segmentation │ │ │ ├── tests │ │ │ │ └── __init__.py │ │ │ └── __init__.py │ │ ├── utilities │ │ │ ├── tests │ │ │ │ └── __init__.py │ │ │ └── __init__.py │ │ ├── testing │ │ │ └── __init__.py │ │ ├── generated.sh │ │ └── __init__.py │ ├── workbench │ │ ├── tests │ │ │ ├── __init__.py │ │ │ └── test_auto_WBCommand.py │ │ └── __init__.py │ ├── camino2trackvis │ │ ├── tests │ │ │ └── __init__.py │ │ └── __init__.py │ ├── diffusion_toolkit │ │ ├── tests │ │ │ └── __init__.py │ │ └── __init__.py │ ├── afni │ │ └── tests │ │ │ ├── __init__.py │ │ │ ├── test_extra_Deconvolve.py │ │ │ ├── test_auto_AFNICommandBase.py │ │ │ ├── test_auto_AFNICommand.py │ │ │ └── test_auto_AFNIPythonCommand.py │ ├── ants │ │ └── tests │ │ │ ├── __init__.py │ │ │ ├── test_base.py │ │ │ ├── test_auto_ANTSCommand.py │ │ │ └── test_extra_Registration.py │ ├── dtitk │ │ ├── tests │ │ │ ├── __init__.py │ │ │ └── test_auto_CommandLineDtitk.py │ │ └── __init__.py │ ├── camino │ │ ├── tests │ │ │ └── __init__.py │ │ └── __init__.py │ └── __init__.py ├── pipeline │ ├── plugins │ │ ├── semaphore_singleton.py │ │ ├── tests │ │ │ └── __init__.py │ │ └── __init__.py │ ├── engine │ │ ├── tests │ │ │ └── __init__.py │ │ └── __init__.py │ └── __init__.py ├── utils │ ├── __init__.py │ ├── README.txt │ ├── datetime.py │ ├── imagemanip.py │ ├── spm_get_doc.m │ └── tests │ │ └── use_resources ├── algorithms │ ├── tests │ │ ├── __init__.py │ │ ├── test_auto_TVTKBaseInterface.py │ │ ├── test_icc_anova.py │ │ ├── test_auto_CalculateMedian.py │ │ ├── test_auto_MergeROIs.py │ │ ├── test_auto_ModifyAffine.py │ │ ├── test_auto_Gzip.py │ │ ├── test_auto_Matlab2CSV.py │ │ ├── test_auto_SimpleThreshold.py │ │ ├── test_auto_NonSteadyStateDetector.py │ │ ├── test_auto_NormalizeProbabilityMapSet.py │ │ ├── test_auto_Gunzip.py │ │ ├── test_auto_AddCSVRow.py │ │ ├── test_auto_SplitROIs.py │ │ └── test_splitmerge.py │ └── __init__.py ├── sphinxext │ └── __init__.py ├── pytest.ini ├── COMMIT_INFO.txt └── refs.py ├── .coveragerc ├── setup.cfg ├── .gitattributes ├── doc ├── .gitignore ├── version.rst ├── _static │ └── nipype-banner-bg.png ├── devel │ ├── gitwash │ │ ├── branch_list.png │ │ ├── pull_button.png │ │ ├── forking_button.png │ │ ├── branch_list_compare.png │ │ ├── links.inc │ │ ├── this_project.inc │ │ ├── git_development.rst │ │ ├── index.rst │ │ ├── git_intro.rst │ │ ├── git_install.rst │ │ └── following_latest.rst │ ├── writing_custom_interfaces.rst │ ├── index.rst │ ├── provenance.rst │ └── matlab_interface_devel.rst ├── images │ └── nipype_architecture_overview2.png ├── requirements.txt ├── developers.rst ├── changes.rst ├── examples.rst ├── _templates │ └── navbar.html └── searchresults.rst ├── .github ├── release-drafter.yml ├── dependabot.yml ├── workflows │ └── codespell.yml ├── ISSUE_TEMPLATE.md └── PULL_REQUEST_TEMPLATE.md ├── .et ├── INSTALL ├── .circleci └── test_pytest.sh ├── docker ├── prune_dockerfile.sh └── files │ └── run_builddocs.sh ├── tools ├── ci │ ├── activate.sh │ ├── install_deb_dependencies.sh │ ├── create_venv.sh │ ├── install_dependencies.sh │ ├── env.sh │ ├── check.sh │ ├── build_archive.sh │ └── install.sh ├── run_examples.py ├── update_mailmap.sh ├── update_requirements.py ├── retry_cmd.sh └── install_spm_mcr.sh ├── MANIFEST.in ├── requirements.txt ├── examples └── README.md ├── .dockerignore ├── .codespellrc ├── .pre-commit-config.yaml ├── .gitignore ├── LICENSE ├── codecov.yml ├── pyproject.toml └── .readthedocs.yml /nipype/external/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/scripts/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/A.scheme: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/NWARP: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/PD.mgz: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/SPM.mat: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/T1.mgz: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/T1.nii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/T2.nii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/TPM.nii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/aseg.mgz: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/b0.nii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/bvals: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/bvecs: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/c1s1.nii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/c1s3.nii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/csd.mif: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/db.xml: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/dirs.txt: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/dofrun1: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/dofrun2: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/dti.mif: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/dwi.mif: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/epi.nii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/f1.1D: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/f2.1D: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/fods.mif: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/grad.b: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/im1.nii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/im2.nii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/im3.nii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/image.v: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/lh.pial: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/lh.white: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/lta1.lta: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/lta2.lta: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/lut_file: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/maps.nii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/mask.1D: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/mask.mif: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/mask.nii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/mni.nii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/norm.mgz: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/resp.1D: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/rh.pial: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/seed.1D: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/sh.mif: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/surf.txt: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/tac.nii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/tdi.mif: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/vsm.nii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/wm.mgz: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/tests/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/caching/tests/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/4d_dwi.nii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/5tt_in.mif: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/FLASH1.mgz: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/FLASH2.mgz: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/FLASH3.mgz: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/Fred+orig: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/T1.nii.gz: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/T1_brain.nii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/T1map.nii.gz: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/TI4D.nii.gz: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/allFA.nii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/all_FA.nii.gz: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/asl.nii.gz: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/atlas.nii.gz: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/b0.nii.gz: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/b0_b0rev.nii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/brukerdir/fid: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/bvals.scheme: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/bvecs.scheme: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/cmatrix.mat: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/complex.nii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/cont1.nii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/cont1a.nii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/cont2.nii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/cont2a.nii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/converted.trk: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/cope.nii.gz: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/cope1.nii.gz: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/cortex.label: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/cov_split.mat: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/csffod.mif: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/data.Bfloat: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/degree.csv: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/degree.mat: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/design.con: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/diffusion.nii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/dteig.Bdouble: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/dwi.nii.gz: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/dwi_FA.mif: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/dwi_evals.nii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/elastix.txt: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/encoding.txt: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/epi_acqp.txt: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/epi_index.txt: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/epi_mask.nii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/epi_rev.nii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/fa.nii.gz: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/fdir00.nii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/fdir01.nii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/ffra00.nii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/ffra01.nii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/fixed1.nii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/fixed2.nii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/flash_05.mgz: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/flash_30.mgz: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/flirt.mat: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/gmfod.mif: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/grads.txt: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/gtmseg.mgz: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/gtmseg.nii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/im_affine.aff: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/image.nii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/indices.txt: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/input1.xfm: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/label.mgz: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/lh-pial.stl: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/lh.cope1.mgz: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/magnitude.nii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/mask.nii.gz: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/minc_nlp.conf: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/mni2t1.nii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/model.pklz: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/moving.csv: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/moving1.nii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/moving2.nii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/output.csv: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/pdfs.Bfloat: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/pet.nii.gz: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/phase.nii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/rc1s1.nii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/rc1s2.nii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/rc2s1.nii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/rc2s2.nii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/ref_tac.dat: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/register.dat: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/register.mat: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/response.txt: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/resting.nii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/rgb.nii.gz: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/rh-pial.stl: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/roi01.nii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/roi01_idx.npz: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/roi02.nii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/roi02_idx.npz: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/roi03.nii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/roi03_idx.npz: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/roi04.nii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/roi04_idx.npz: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/roi05.nii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/roi05_idx.npz: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/run1+orig: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/run2+orig: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/seed_mask.nii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/spmT_0001.img: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/subj1.cff: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/subj1.pck: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/subj2.cff: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/subj2.pck: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/surf1.vtk: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/surf2.vtk: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/timing.dat: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/track1.trk: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/track2.trk: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/tracks.tck: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/tracks.trk: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/trans.mat: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/warpfield.nii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/weights.txt: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/wm_mask.mif: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/wmfod.mif: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/zstat1.nii.gz: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/interfaces/robex/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/interfaces/tests/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/A_qmat.Bdouble: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/Q25_warp+tlrc.HEAD: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/QSH_peaks.Bdouble: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/SubjectA.Bfloat: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/Template_6.nii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/afni_output.3D: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/anat_coreg.mif: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/anatomical.nii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/ants_Affine.txt: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/ants_Warp.nii.gz: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/aparc+aseg.nii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/brain_mask.nii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/clustering.mat: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/cope1run1.nii.gz: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/cope1run2.nii.gz: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/cope2run1.nii.gz: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/cope2run2.nii.gz: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/ds005/filler.txt: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/dwi_WMProb.mif: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/dwi_tensor.mif: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/epi_phasediff.nii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/epi_slspec.txt: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/fieldmap_mag.nii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/func_epi_1_1.nii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/func_to_struct.mat: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/functional.HEAD: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/functional.nii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/functional.par: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/functional.rms: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/functional2.nii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/functional3.nii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/functional_1.dcm: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/functional_2.dcm: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/im_warp.df.nii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/indices-labels.txt: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/lh.area.structural: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/lh.cope1.nii.gz: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/lh.hippocampus.stl: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/lh.pbt.structural: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/mean_func.nii.gz: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/minc_initial.xfm: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/my_database.db: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/network0.gpickle: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/pet_resliced.nii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/ref_class0.nii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/ref_class1.nii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/rh.pbt.structural: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/run1+orig_model: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/run1_categories.1D: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/run2_categories.1D: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/seed_source.nii.gz: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/seeds_to_M1.nii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/seeds_to_M2.nii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/session_info.npz: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/streamlines.trk: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/struct2mni.nii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/struct_to_func.mat: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/structural.nii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/subjectDesign.con: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/subjectDesign.mat: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/targets_MASK1.nii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/targets_MASK2.nii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/timeDesign.con: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/timeDesign.mat: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/timeseries.txt: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/tissue+air_map.nii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/tissues.nii.gz: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/topup_encoding.txt: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/topup_movpar.txt: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/tract_data.Bfloat: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/tracts.Bdouble: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/tst_class0.nii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/tst_class1.nii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/varcope.nii.gz: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /.coveragerc: -------------------------------------------------------------------------------- 1 | [run] 2 | branch = True 3 | -------------------------------------------------------------------------------- /nipype/interfaces/base/tests/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/interfaces/cat12/tests/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/interfaces/cmtk/tests/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/interfaces/dipy/tests/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/interfaces/elastix/tests/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/interfaces/fsl/tests/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/interfaces/minc/tests/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/interfaces/mipav/tests/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/interfaces/mixins/tests/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/interfaces/mne/tests/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/interfaces/mrtrix/tests/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/interfaces/mrtrix3/tests/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/interfaces/nipy/tests/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/interfaces/nitime/tests/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/interfaces/robex/tests/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/interfaces/slicer/tests/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/interfaces/spm/tests/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/interfaces/utility/tests/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/interfaces/vista/tests/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/A_recon_params.Bdouble: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/AffineTransform.mat: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/ROI_scale500.nii.gz: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/ants_deformed.nii.gz: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/brain_track.Bdouble: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/brukerdir/pdata/1/2dseq: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/dicomdir/123456-1-1.dcm: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/diffusion_weighted.nii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/dilated_wm_mask.nii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/dwi2anat_Warp.nii.gz: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/dwi_CSD_tracked.tck: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/fieldmap_mag_brain.nii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/first_merged.nii.gz: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/fitted_data1.Bfloat: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/fitted_data2.Bfloat: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/fsLUT_aparc+aseg.pck: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/lh.pial_converted.gii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/merged_f1samples.nii.gz: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/merged_fsamples.nii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/merged_phsamples.nii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/merged_thsamples.nii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/minc_test_2D_00.mnc: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/minc_test_2D_01.mnc: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/minc_test_2D_02.mnc: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/minc_test_2D_03.mnc: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/minc_test_2D_04.mnc: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/minc_test_2D_05.mnc: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/minc_test_2D_06.mnc: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/minc_test_2D_07.mnc: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/minc_test_2D_08.mnc: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/minc_test_2D_09.mnc: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/minc_test_3D_00.mnc: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/minc_test_3D_01.mnc: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/minc_test_3D_02.mnc: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/minc_test_3D_03.mnc: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/minc_test_3D_04.mnc: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/minc_test_3D_05.mnc: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/minc_test_3D_06.mnc: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/minc_test_3D_07.mnc: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/minc_test_3D_08.mnc: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/minc_test_3D_09.mnc: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/mrtrix3_labelconfig.txt: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/network0.aparc+aseg.nii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/nodif_brain_mask.nii.gz: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/output_Composite.h5: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/peak_directions.mif: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/rh.pial_converted.gii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/skeleton_mask.nii.gz: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/struct_to_template.mat: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/study_template.nii.gz: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/topup_fieldcoef.nii.gz: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/u_rc1s1_Template.nii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/u_rc1s2_Template.nii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/u_rc1s3_Template.nii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/varcope1run1.nii.gz: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/varcope1run2.nii.gz: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/varcope2run1.nii.gz: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/varcope2run2.nii.gz: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/voxel-order_data.Bfloat: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/voxeldisplacemap.vdm: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/wm_undersampled.nii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/interfaces/brainsuite/tests/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/interfaces/freesurfer/tests/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/interfaces/niftyfit/tests/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/interfaces/niftyreg/tests/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/interfaces/niftyseg/tests/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/interfaces/semtools/tests/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/interfaces/workbench/tests/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/FreeSurferColorLUT.txt: -------------------------------------------------------------------------------- 1 | 2 | -------------------------------------------------------------------------------- /nipype/testing/data/MASK_average_thal_right.nii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/Template_1_IXI550_MNI152.nii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/TransformParameters.0.txt: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/ballstickfit_data.Bfloat: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/brain_study_template.nii.gz: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/dwi2anat_InverseWarp.nii.gz: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/dwi2anat_coreg_Affine.txt: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/func2anat_InverseWarp.nii.gz: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/func2anat_coreg_Affine.txt: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/lh.central.structural.gii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/lh.sphere.reg.structural.gii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/lh.sphere.structural.gii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/merged_ph1samples.nii.gz: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/merged_th1samples.nii.gz: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/resting2anat_Warp.nii.gz: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/rh.central.structural.gii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/rh.sphere.reg.structural.gii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/rh.sphere.structural.gii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/sub-01_dir-LR_epi.nii.gz: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/sub-01_dir-RL_epi.nii.gz: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/tensor_fitted_data.Bdouble: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /setup.cfg: -------------------------------------------------------------------------------- 1 | [bdist_wheel] 2 | python-tag=py3 3 | -------------------------------------------------------------------------------- /nipype/interfaces/camino2trackvis/tests/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/interfaces/diffusion_toolkit/tests/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/interfaces/semtools/brains/tests/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/interfaces/semtools/legacy/tests/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/interfaces/slicer/diffusion/tests/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/interfaces/slicer/filtering/tests/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/interfaces/slicer/legacy/tests/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/BrainSegmentationPrior01.nii.gz: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/BrainSegmentationPrior02.nii.gz: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/BrainSegmentationPrior03.nii.gz: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/BrainSegmentationPrior04.nii.gz: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/DisplacementFieldTransform.nii.gz: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/fieldmap_phase_fslprepared.nii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/lh.aparc_a2009s.freesurfer.annot: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/resting2anat_coreg_Affine.txt: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/rh.aparc_a2009s.freesurfer.annot: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/sub-01_ses-baseline_pet.nii.gz: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/sub-01_task-rest.dtseries.nii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /.gitattributes: -------------------------------------------------------------------------------- 1 | nipype/COMMIT_INFO.txt export-subst 2 | -------------------------------------------------------------------------------- /doc/.gitignore: -------------------------------------------------------------------------------- 1 | /documentation.zip 2 | _static/python 3 | -------------------------------------------------------------------------------- /nipype/caching/__init__.py: -------------------------------------------------------------------------------- 1 | from .memory import Memory 2 | -------------------------------------------------------------------------------- /nipype/interfaces/semtools/diffusion/tests/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/interfaces/semtools/filtering/tests/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/interfaces/semtools/registration/tests/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/interfaces/semtools/segmentation/tests/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/interfaces/semtools/utilities/tests/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/interfaces/slicer/quantification/tests/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/interfaces/slicer/registration/tests/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/interfaces/slicer/segmentation/tests/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/ProbabilityMaskOfStudyTemplate.nii.gz: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/func2anat_coreg_InverseWarp.nii.gz: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/sub-01_ses-baseline_pet_mean_reg.lta: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/interfaces/slicer/legacy/diffusion/tests/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/config.ini: -------------------------------------------------------------------------------- 1 | [BOOL] 2 | ManualNIfTIConv=0 3 | -------------------------------------------------------------------------------- /nipype/testing/data/design.txt: -------------------------------------------------------------------------------- 1 | 0 0 0 2 | 0 0 0 3 | 0 0 0 4 | -------------------------------------------------------------------------------- /nipype/testing/data/sub-01.L.midthickness.32k_fs_LR.surf.gii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/sub-01.R.midthickness.32k_fs_LR.surf.gii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/interfaces/semtools/diffusion/tractography/tests/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/FreeSurferColorLUT_adapted_aparc+aseg_out.pck: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/fs_LR.L.midthickness_va_avg.32k_fs_LR.shape.gii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/fsaverage5_std_sphere.L.10k_fsavg_L.surf.gii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/sub-01_task-rest_bold_space-fsaverage5.L.func.gii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/fs_LR-deformed_to-fsaverage.L.sphere.32k_fs_LR.surf.gii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/fsaverage5.L.midthickness_va_avg.10k_fsavg_L.shape.gii: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nipype/testing/data/jsongrabber.txt: -------------------------------------------------------------------------------- 1 | {"param2": 4, "param1": "exampleStr"} 2 | -------------------------------------------------------------------------------- /.github/release-drafter.yml: -------------------------------------------------------------------------------- 1 | template: | 2 | ## What's Changed 3 | 4 | $CHANGES 5 | -------------------------------------------------------------------------------- /nipype/interfaces/semtools/legacy/__init__.py: -------------------------------------------------------------------------------- 1 | from .registration import scalartransform 2 | -------------------------------------------------------------------------------- /doc/version.rst: -------------------------------------------------------------------------------- 1 | :orphan: 2 | 3 | .. _version: 4 | 5 | :Release: |version| 6 | :Date: |today| 7 | -------------------------------------------------------------------------------- /nipype/testing/data/design.mat: -------------------------------------------------------------------------------- 1 | /NumWaves 3 2 | /NumPoints 3 3 | /Matrix 4 | 0 0 0 5 | 0 0 0 6 | 0 0 0 7 | -------------------------------------------------------------------------------- /.et: -------------------------------------------------------------------------------- 1 | { "bad_versions" : [ "1.2.1", 2 | "1.2.3", 3 | "1.3.0"] 4 | } 5 | -------------------------------------------------------------------------------- /doc/_static/nipype-banner-bg.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nipy/nipype/HEAD/doc/_static/nipype-banner-bg.png -------------------------------------------------------------------------------- /doc/devel/gitwash/branch_list.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nipy/nipype/HEAD/doc/devel/gitwash/branch_list.png -------------------------------------------------------------------------------- /doc/devel/gitwash/pull_button.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nipy/nipype/HEAD/doc/devel/gitwash/pull_button.png -------------------------------------------------------------------------------- /nipype/interfaces/slicer/legacy/diffusion/__init__.py: -------------------------------------------------------------------------------- 1 | from .denoising import DWIUnbiasedNonLocalMeansFilter 2 | -------------------------------------------------------------------------------- /nipype/pipeline/plugins/semaphore_singleton.py: -------------------------------------------------------------------------------- 1 | import threading 2 | 3 | semaphore = threading.Semaphore(0) 4 | -------------------------------------------------------------------------------- /nipype/testing/data/bedpostxout/do_not_delete.txt: -------------------------------------------------------------------------------- 1 | This file has to be here because git ignores empty folders. 2 | -------------------------------------------------------------------------------- /nipype/testing/data/tbss_dir/do_not_delete.txt: -------------------------------------------------------------------------------- 1 | This file has to be here because git ignores empty folders. 2 | -------------------------------------------------------------------------------- /nipype/testing/data/tpm_00.nii.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nipy/nipype/HEAD/nipype/testing/data/tpm_00.nii.gz -------------------------------------------------------------------------------- /nipype/testing/data/tpm_01.nii.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nipy/nipype/HEAD/nipype/testing/data/tpm_01.nii.gz -------------------------------------------------------------------------------- /nipype/testing/data/tpm_02.nii.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nipy/nipype/HEAD/nipype/testing/data/tpm_02.nii.gz -------------------------------------------------------------------------------- /nipype/interfaces/mrtrix/defhdr.mat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nipy/nipype/HEAD/nipype/interfaces/mrtrix/defhdr.mat -------------------------------------------------------------------------------- /nipype/testing/data/tpms_msk.nii.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nipy/nipype/HEAD/nipype/testing/data/tpms_msk.nii.gz -------------------------------------------------------------------------------- /doc/devel/gitwash/forking_button.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nipy/nipype/HEAD/doc/devel/gitwash/forking_button.png -------------------------------------------------------------------------------- /nipype/interfaces/fsl/model_templates/feat_contrastmask_footer.tcl: -------------------------------------------------------------------------------- 1 | # Do contrast masking at all? 2 | set fmri(conmask1_1) 0 3 | -------------------------------------------------------------------------------- /nipype/testing/data/segmentation0.nii.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nipy/nipype/HEAD/nipype/testing/data/segmentation0.nii.gz -------------------------------------------------------------------------------- /nipype/testing/data/segmentation1.nii.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nipy/nipype/HEAD/nipype/testing/data/segmentation1.nii.gz -------------------------------------------------------------------------------- /doc/devel/gitwash/branch_list_compare.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nipy/nipype/HEAD/doc/devel/gitwash/branch_list_compare.png -------------------------------------------------------------------------------- /nipype/interfaces/fsl/model_templates/feat_ev_ortho.tcl: -------------------------------------------------------------------------------- 1 | # Orthogonalise EV $c0 wrt EV $c1 2 | set fmri(ortho$c0.$c1) $orthogonal 3 | -------------------------------------------------------------------------------- /nipype/testing/data/ds003_sub-01_mc.nii.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nipy/nipype/HEAD/nipype/testing/data/ds003_sub-01_mc.nii.gz -------------------------------------------------------------------------------- /doc/images/nipype_architecture_overview2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nipy/nipype/HEAD/doc/images/nipype_architecture_overview2.png -------------------------------------------------------------------------------- /nipype/interfaces/fsl/model_templates/feat_fe_featdirs.tcl: -------------------------------------------------------------------------------- 1 | # 4D AVW data or FEAT directory ($runno) 2 | set feat_files($runno) "${rundir}" 3 | 4 | -------------------------------------------------------------------------------- /nipype/interfaces/slicer/base.py: -------------------------------------------------------------------------------- 1 | from ..base import SEMLikeCommandLine 2 | 3 | 4 | class SlicerCommandLine(SEMLikeCommandLine): 5 | pass 6 | -------------------------------------------------------------------------------- /nipype/utils/__init__.py: -------------------------------------------------------------------------------- 1 | from .onetime import OneTimeProperty, setattr_on_read 2 | from .tmpdirs import TemporaryDirectory, InTemporaryDirectory 3 | -------------------------------------------------------------------------------- /nipype/interfaces/fsl/model_templates/feat_contrast_ftest_element.tcl: -------------------------------------------------------------------------------- 1 | # F-test $cnum element $element 2 | set fmri(ftest_$ctype$cnum.$element) $val 3 | -------------------------------------------------------------------------------- /nipype/testing/data/ds003_sub-01_mc_brainmask.nii.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nipy/nipype/HEAD/nipype/testing/data/ds003_sub-01_mc_brainmask.nii.gz -------------------------------------------------------------------------------- /doc/devel/gitwash/links.inc: -------------------------------------------------------------------------------- 1 | .. compiling links file 2 | .. include:: known_projects.inc 3 | .. include:: this_project.inc 4 | .. include:: git_links.inc 5 | -------------------------------------------------------------------------------- /nipype/algorithms/tests/__init__.py: -------------------------------------------------------------------------------- 1 | # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- 2 | # vi: set ft=python sts=4 ts=4 sw=4 et: 3 | -------------------------------------------------------------------------------- /nipype/interfaces/fsl/model_templates/feat_fe_copes.tcl: -------------------------------------------------------------------------------- 1 | # Use lower-level cope $copeno for higher-level analysis 2 | set fmri(copeinput.${copeno}) 1 3 | 4 | -------------------------------------------------------------------------------- /nipype/interfaces/afni/tests/__init__.py: -------------------------------------------------------------------------------- 1 | # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- 2 | # vi: set ft=python sts=4 ts=4 sw=4 et: 3 | -------------------------------------------------------------------------------- /nipype/interfaces/ants/tests/__init__.py: -------------------------------------------------------------------------------- 1 | # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- 2 | # vi: set ft=python sts=4 ts=4 sw=4 et: 3 | -------------------------------------------------------------------------------- /nipype/interfaces/dtitk/tests/__init__.py: -------------------------------------------------------------------------------- 1 | # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- 2 | # vi: set ft=python sts=4 ts=4 sw=4 et: 3 | -------------------------------------------------------------------------------- /nipype/interfaces/fsl/model_templates/feat_contrastmask_header.tcl: -------------------------------------------------------------------------------- 1 | # Contrast masking - use >0 instead of thresholding? 2 | set fmri(conmask_zerothresh_yn) 0 3 | -------------------------------------------------------------------------------- /nipype/pipeline/engine/tests/__init__.py: -------------------------------------------------------------------------------- 1 | # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- 2 | # vi: set ft=python sts=4 ts=4 sw=4 et: 3 | -------------------------------------------------------------------------------- /nipype/pipeline/plugins/tests/__init__.py: -------------------------------------------------------------------------------- 1 | # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- 2 | # vi: set ft=python sts=4 ts=4 sw=4 et: 3 | -------------------------------------------------------------------------------- /nipype/interfaces/camino/tests/__init__.py: -------------------------------------------------------------------------------- 1 | # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- 2 | # vi: set ft=python sts=4 ts=4 sw=4 et: 3 | -------------------------------------------------------------------------------- /nipype/interfaces/fsl/model_templates/feat_contrast_element.tcl: -------------------------------------------------------------------------------- 1 | # Real contrast_$ctype vector $cnum element $element 2 | set fmri(con_$ctype$cnum.$element) $val 3 | -------------------------------------------------------------------------------- /nipype/interfaces/fsl/model_templates/feat_contrastmask_element.tcl: -------------------------------------------------------------------------------- 1 | # Mask real contrast/F-test $c1 with real contrast/F-test $c2? 2 | set fmri(conmask${c1}_${c2}) 0 3 | 4 | -------------------------------------------------------------------------------- /nipype/interfaces/mne/__init__.py: -------------------------------------------------------------------------------- 1 | """MNE is a software for exploring, visualizing, and analyzing human neurophysiological data.""" 2 | 3 | from .base import WatershedBEM 4 | -------------------------------------------------------------------------------- /nipype/sphinxext/__init__.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- 3 | # vi: set ft=python sts=4 ts=4 sw=4 et: 4 | -------------------------------------------------------------------------------- /doc/requirements.txt: -------------------------------------------------------------------------------- 1 | dipy 2 | ipython 3 | matplotlib 4 | nbsphinx 5 | sphinx-argparse 6 | sphinx>=2.1.2 7 | sphinxcontrib-apidoc 8 | sphinxcontrib-napoleon 9 | niflow-nipype1-workflows 10 | -------------------------------------------------------------------------------- /INSTALL: -------------------------------------------------------------------------------- 1 | .. -*- rst -*- rest mode for emacs 2 | .. _development-quickstart: 3 | 4 | For installation instructions see documentation: 5 | 6 | http://nipy.org/nipype/ 7 | 8 | or doc/users/install.rst 9 | -------------------------------------------------------------------------------- /nipype/interfaces/slicer/quantification/__init__.py: -------------------------------------------------------------------------------- 1 | from .changequantification import IntensityDifferenceMetric 2 | from .petstandarduptakevaluecomputation import PETStandardUptakeValueComputation 3 | -------------------------------------------------------------------------------- /nipype/interfaces/cat12/__init__.py: -------------------------------------------------------------------------------- 1 | from .preprocess import CAT12Segment, CAT12SANLMDenoising 2 | from .surface import ( 3 | ExtractAdditionalSurfaceParameters, 4 | ExtractROIBasedSurfaceMeasures, 5 | ) 6 | -------------------------------------------------------------------------------- /nipype/interfaces/fsl/model_templates/feat_contrast_header.tcl: -------------------------------------------------------------------------------- 1 | # Contrast & F-tests mode 2 | # real : control real EVs 3 | # orig : control original EVs 4 | set fmri(con_mode_old) orig 5 | set fmri(con_mode) orig 6 | -------------------------------------------------------------------------------- /nipype/interfaces/fsl/model_templates/feat_fe_ev_element.tcl: -------------------------------------------------------------------------------- 1 | # Higher-level EV value for EV 1 and input $input 2 | set fmri(evg${input}.1) 1 3 | 4 | # Group membership for input $input 5 | set fmri(groupmem.${input}) 1 6 | -------------------------------------------------------------------------------- /nipype/interfaces/slicer/segmentation/__init__.py: -------------------------------------------------------------------------------- 1 | from .specialized import RobustStatisticsSegmenter, EMSegmentCommandLine, BRAINSROIAuto 2 | from .simpleregiongrowingsegmentation import SimpleRegionGrowingSegmentation 3 | -------------------------------------------------------------------------------- /doc/devel/gitwash/this_project.inc: -------------------------------------------------------------------------------- 1 | .. nipype 2 | .. _nipype: http://nipy.org/nipype 3 | .. _`nipype github`: http://github.com/nipy/nipype 4 | 5 | .. _`nipype mailing list`: http://mail.scipy.org/mailman/listinfo/nipy-devel 6 | -------------------------------------------------------------------------------- /doc/devel/writing_custom_interfaces.rst: -------------------------------------------------------------------------------- 1 | .. _writing_custom_interfaces: 2 | .. toctree:: 3 | :maxdepth: 2 4 | 5 | interface_specs 6 | cmd_interface_devel 7 | matlab_interface_devel 8 | python_interface_devel 9 | -------------------------------------------------------------------------------- /nipype/interfaces/semtools/testing/__init__.py: -------------------------------------------------------------------------------- 1 | from .featuredetection import SphericalCoordinateGeneration 2 | from .landmarkscompare import LandmarksCompare 3 | from .generateaveragelmkfile import GenerateAverageLmkFile 4 | -------------------------------------------------------------------------------- /.circleci/test_pytest.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | docker run --rm=false -t -v $WORKDIR:/work -v $HOME/examples:/data/examples:ro -w /work -e CI_SKIP_TEST=1 -e NIPYPE_RESOURCE_MONITOR=1 "${DOCKER_IMAGE}:py38" /usr/bin/run_pytests.sh 4 | -------------------------------------------------------------------------------- /nipype/interfaces/fsl/model_templates/feat_contrast_prolog.tcl: -------------------------------------------------------------------------------- 1 | # Display images for contrast_$ctype $cnum 2 | set fmri(conpic_$ctype.$cnum) 1 3 | 4 | # Title for contrast_$ctype $cnum 5 | set fmri(conname_$ctype.$cnum) "$cname" 6 | -------------------------------------------------------------------------------- /nipype/interfaces/mixins/__init__.py: -------------------------------------------------------------------------------- 1 | from .reporting import ( 2 | ReportCapableInterface, 3 | ReportCapableInputSpec, 4 | ReportCapableOutputSpec, 5 | ) 6 | from .fixheader import CopyHeaderInputSpec, CopyHeaderInterface 7 | -------------------------------------------------------------------------------- /nipype/interfaces/semtools/diffusion/tractography/__init__.py: -------------------------------------------------------------------------------- 1 | from .commandlineonly import fiberstats 2 | from .fiberprocess import fiberprocess 3 | from .fibertrack import fibertrack 4 | from .ukftractography import UKFTractography 5 | -------------------------------------------------------------------------------- /nipype/pytest.ini: -------------------------------------------------------------------------------- 1 | [pytest] 2 | norecursedirs = .git build dist doc nipype/external tools examples src 3 | addopts = --doctest-modules 4 | doctest_optionflags = ALLOW_UNICODE NORMALIZE_WHITESPACE 5 | env = 6 | PYTHONHASHSEED=0 7 | junit_family=xunit2 8 | -------------------------------------------------------------------------------- /nipype/interfaces/semtools/registration/__init__.py: -------------------------------------------------------------------------------- 1 | from .specialized import VBRAINSDemonWarp, BRAINSDemonWarp, BRAINSTransformFromFiducials 2 | from .brainsresample import BRAINSResample 3 | from .brainsfit import BRAINSFit 4 | from .brainsresize import BRAINSResize 5 | -------------------------------------------------------------------------------- /nipype/interfaces/nipy/__init__.py: -------------------------------------------------------------------------------- 1 | """NIPY is a python project for analysis of structural and functional neuroimaging data.""" 2 | 3 | from .model import FitGLM, EstimateContrast 4 | from .preprocess import ComputeMask, SpaceTimeRealigner 5 | from .utils import Similarity 6 | -------------------------------------------------------------------------------- /nipype/interfaces/slicer/registration/__init__.py: -------------------------------------------------------------------------------- 1 | from .specialized import ( 2 | ACPCTransform, 3 | FiducialRegistration, 4 | VBRAINSDemonWarp, 5 | BRAINSDemonWarp, 6 | ) 7 | from .brainsresample import BRAINSResample 8 | from .brainsfit import BRAINSFit 9 | -------------------------------------------------------------------------------- /nipype/interfaces/vista/__init__.py: -------------------------------------------------------------------------------- 1 | # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- 2 | # vi: set ft=python sts=4 ts=4 sw=4 et: 3 | """VistaSoft contains Matlab code to perform a variety of analysis on MRI data.""" 4 | from .vista import Vnifti2Image, VtoMat 5 | -------------------------------------------------------------------------------- /doc/developers.rst: -------------------------------------------------------------------------------- 1 | :orphan: 2 | 3 | .. _developers: 4 | 5 | ================== 6 | Developer's Corner 7 | ================== 8 | 9 | .. toctree:: 10 | :maxdepth: 2 11 | 12 | devel/index 13 | 14 | .. toctree:: 15 | :maxdepth: 3 16 | 17 | api/generated/nipype 18 | -------------------------------------------------------------------------------- /docker/prune_dockerfile.sh: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env bash 2 | 3 | if [ -z "$1" ]; then 4 | echo "Usage: $(basename $0) " 5 | exit 1 6 | fi 7 | 8 | # Remove empty lines, comments, and timestamp. 9 | sed -e '/\s*#.*$/d' -e '/^\s*$/d' -e '/generation_timestamp/d' "$1" 10 | -------------------------------------------------------------------------------- /nipype/testing/data/epi_param.txt: -------------------------------------------------------------------------------- 1 | { 2 | "enc_dir": "y-", 3 | "echospacing": 7.800117313764398e-4, 4 | "delta_te": 2.46e-3, 5 | "epi_factor": 128, 6 | "epi_lines": 57, 7 | "acc_factor": 2, 8 | "field_strength": 3.0, 9 | "field_axis": "z" 10 | } 11 | -------------------------------------------------------------------------------- /doc/changes.rst: -------------------------------------------------------------------------------- 1 | :orphan: 2 | :tocdepth: 2 3 | 4 | .. _changes: 5 | 6 | ================= 7 | Changes in Nipype 8 | ================= 9 | 10 | .. include:: changelog/1.X.X-changelog.rst 11 | 12 | .. include:: changelog/0.X.X-changelog.rst 13 | 14 | .. include:: links_names.txt 15 | -------------------------------------------------------------------------------- /tools/ci/activate.sh: -------------------------------------------------------------------------------- 1 | if [ -e virtenv/bin/activate ]; then 2 | source virtenv/bin/activate 3 | elif [ -e virtenv/Scripts/activate ]; then 4 | source virtenv/Scripts/activate 5 | else 6 | echo Cannot activate virtual environment 7 | ls -R virtenv 8 | false 9 | fi 10 | -------------------------------------------------------------------------------- /MANIFEST.in: -------------------------------------------------------------------------------- 1 | include INSTALL 2 | include LICENSE 3 | include MANIFEST.in 4 | include README 5 | include THANKS 6 | include Makefile 7 | include setup_egg.py 8 | include doc/documentation.zip 9 | include nipype/COMMIT_INFO.txt 10 | 11 | recursive-include doc * 12 | recursive-include tools * 13 | -------------------------------------------------------------------------------- /nipype/interfaces/camino2trackvis/__init__.py: -------------------------------------------------------------------------------- 1 | # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- 2 | # vi: set ft=python sts=4 ts=4 sw=4 et: 3 | """Camino-Trackvis allows interoperability between Camino and TrackVis.""" 4 | from .convert import Camino2Trackvis, Trackvis2Camino 5 | -------------------------------------------------------------------------------- /nipype/COMMIT_INFO.txt: -------------------------------------------------------------------------------- 1 | # This is an ini file that may contain information about the code state 2 | [commit hash] 3 | # The line below may contain a valid hash if it has been substituted during 'git archive' 4 | archive_subst_hash=%h 5 | # This line may be modified by the install process 6 | install_hash= 7 | -------------------------------------------------------------------------------- /nipype/algorithms/__init__.py: -------------------------------------------------------------------------------- 1 | # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- 2 | # vi: set ft=python sts=4 ts=4 sw=4 et: 3 | """ 4 | Package contains pure python neuroimaging algorithms 5 | 6 | Examples: artifactdetect 7 | 8 | """ 9 | __docformat__ = "restructuredtext" 10 | -------------------------------------------------------------------------------- /doc/devel/gitwash/git_development.rst: -------------------------------------------------------------------------------- 1 | .. _git-development: 2 | 3 | ===================== 4 | Git for development 5 | ===================== 6 | 7 | Contents: 8 | 9 | .. toctree:: 10 | :maxdepth: 2 11 | 12 | forking_hell 13 | set_up_fork 14 | configure_git 15 | development_workflow 16 | -------------------------------------------------------------------------------- /nipype/interfaces/semtools/brains/__init__.py: -------------------------------------------------------------------------------- 1 | from .segmentation import SimilarityIndex, BRAINSTalairach, BRAINSTalairachMask 2 | from .utilities import ( 3 | HistogramMatchingFilter, 4 | GenerateEdgeMapImage, 5 | GeneratePurePlugMask, 6 | ) 7 | from .classify import BRAINSPosteriorToContinuousClass 8 | -------------------------------------------------------------------------------- /nipype/interfaces/diffusion_toolkit/__init__.py: -------------------------------------------------------------------------------- 1 | """Diffusion Toolkit performs data reconstruction and fiber tracking on diffusion MR images.""" 2 | 3 | from .base import Info 4 | from .postproc import SplineFilter, TrackMerge 5 | from .dti import DTIRecon, DTITracker 6 | from .odf import HARDIMat, ODFRecon, ODFTracker 7 | -------------------------------------------------------------------------------- /nipype/utils/README.txt: -------------------------------------------------------------------------------- 1 | ================== 2 | Nipype Utilities 3 | ================== 4 | 5 | This directory contains various utilities used in nipype. Some of 6 | them have been copied from nipy. Any changes to these should be done 7 | upstream. 8 | 9 | * From nipy: 10 | * onetime.py 11 | * tmpdirs.py 12 | -------------------------------------------------------------------------------- /nipype/interfaces/semtools/segmentation/__init__.py: -------------------------------------------------------------------------------- 1 | from .specialized import ( 2 | BRAINSCut, 3 | BRAINSROIAuto, 4 | BRAINSConstellationDetector, 5 | BRAINSCreateLabelMapFromProbabilityMaps, 6 | BinaryMaskEditorBasedOnLandmarks, 7 | BRAINSMultiSTAPLE, 8 | BRAINSABC, 9 | ESLR, 10 | ) 11 | -------------------------------------------------------------------------------- /doc/devel/gitwash/index.rst: -------------------------------------------------------------------------------- 1 | .. _using-git: 2 | 3 | Working with *nipype* source code 4 | ====================================== 5 | 6 | Contents: 7 | 8 | .. toctree:: 9 | :maxdepth: 2 10 | 11 | git_intro 12 | git_install 13 | following_latest 14 | patching 15 | git_development 16 | git_resources 17 | -------------------------------------------------------------------------------- /nipype/interfaces/brainsuite/__init__.py: -------------------------------------------------------------------------------- 1 | from .brainsuite import ( 2 | Bse, 3 | Bfc, 4 | Pvc, 5 | Cerebro, 6 | Cortex, 7 | Scrubmask, 8 | Tca, 9 | Dewisp, 10 | Dfs, 11 | Pialmesh, 12 | Skullfinder, 13 | Hemisplit, 14 | SVReg, 15 | BDP, 16 | ThicknessPVC, 17 | ) 18 | -------------------------------------------------------------------------------- /nipype/interfaces/nitime/base.py: -------------------------------------------------------------------------------- 1 | # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- 2 | # vi: set ft=python sts=4 ts=4 sw=4 et: 3 | """Base interface for nitime""" 4 | 5 | from ..base import LibraryBaseInterface 6 | 7 | 8 | class NitimeBaseInterface(LibraryBaseInterface): 9 | _pkg = "nitime" 10 | -------------------------------------------------------------------------------- /nipype/interfaces/workbench/__init__.py: -------------------------------------------------------------------------------- 1 | # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- 2 | # vi: set ft=python sts=4 ts=4 sw=4 et: 3 | """Connectome Workbench is a visualization for neuroimaging data, esp. derived from HCP data.""" 4 | from .metric import MetricResample 5 | from .cifti import CiftiSmooth 6 | -------------------------------------------------------------------------------- /nipype/pipeline/__init__.py: -------------------------------------------------------------------------------- 1 | # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- 2 | # vi: set ft=python sts=4 ts=4 sw=4 et: 3 | """ 4 | Package contains modules for generating pipelines using interfaces 5 | 6 | """ 7 | __docformat__ = "restructuredtext" 8 | from .engine import Node, MapNode, JoinNode, Workflow 9 | -------------------------------------------------------------------------------- /nipype/testing/data/events.tsv: -------------------------------------------------------------------------------- 1 | onset duration frequency pulse_width amplitude 2 | 183.75 20.0 20.0 0.005 1.0 3 | 313.75 20.0 20.0 0.005 1.0 4 | 483.75 20.0 20.0 0.005 1.0 5 | 633.75 20.0 20.0 0.005 1.0 6 | 783.75 20.0 20.0 0.005 1.0 7 | 933.75 20.0 20.0 0.005 1.0 8 | 1083.75 20.0 20.0 0.005 1.0 9 | 1233.75 20.0 20.0 0.005 1.0 10 | -------------------------------------------------------------------------------- /nipype/interfaces/elastix/__init__.py: -------------------------------------------------------------------------------- 1 | # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- 2 | # vi: set ft=python sts=4 ts=4 sw=4 et: 3 | """elastix is a toolbox for rigid and nonrigid registration of images.""" 4 | from .registration import Registration, ApplyWarp, AnalyzeWarp, PointsWarp 5 | from .utils import EditTransform 6 | -------------------------------------------------------------------------------- /.github/dependabot.yml: -------------------------------------------------------------------------------- 1 | # Dependabot configuration file 2 | version: 2 3 | updates: 4 | - package-ecosystem: "github-actions" 5 | directory: "/" 6 | schedule: 7 | interval: "weekly" 8 | groups: 9 | actions-infrastructure: 10 | patterns: 11 | - "actions/*" 12 | -------------------------------------------------------------------------------- /nipype/interfaces/minc/testdata.py: -------------------------------------------------------------------------------- 1 | from ...testing import example_data 2 | 3 | minc2Dfile = example_data("minc_test_2D_00.mnc") 4 | minc3Dfile = example_data("minc_test_3D_00.mnc") 5 | 6 | nlp_config = example_data("minc_nlp.conf") 7 | 8 | 9 | def nonempty_minc_data(i, shape="2D"): 10 | return example_data("minc_test_%s_%.2d.mnc" % (shape, i)) 11 | -------------------------------------------------------------------------------- /docker/files/run_builddocs.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | set -e 3 | set -x 4 | set -u 5 | 6 | WORKDIR=${WORK:-/work} 7 | 8 | mkdir -p ${WORKDIR}/docs 9 | make html 2>&1 | tee ${WORKDIR}/builddocs.log 10 | cp -r /src/nipype/doc/_build/html/* ${WORKDIR}/docs/ 11 | cat ${WORKDIR}/builddocs.log && if grep -q "ERROR" ${WORKDIR}/builddocs.log; then false; else true; fi 12 | -------------------------------------------------------------------------------- /nipype/interfaces/slicer/diffusion/__init__.py: -------------------------------------------------------------------------------- 1 | from .diffusion import ( 2 | ResampleDTIVolume, 3 | DWIRicianLMMSEFilter, 4 | TractographyLabelMapSeeding, 5 | DWIJointRicianLMMSEFilter, 6 | DiffusionWeightedVolumeMasking, 7 | DTIimport, 8 | DWIToDTIEstimation, 9 | DiffusionTensorScalarMeasurements, 10 | DTIexport, 11 | ) 12 | -------------------------------------------------------------------------------- /requirements.txt: -------------------------------------------------------------------------------- 1 | # Auto-generated by tools/update_requirements.py 2 | click>=6.6.0 3 | networkx>=2.0 4 | nibabel>=2.1.0 5 | numpy>=1.17 6 | packaging 7 | prov>=1.5.2 8 | pydot>=1.2.3 9 | python-dateutil>=2.2 10 | rdflib>=5.0.0 11 | scipy>=0.14 12 | simplejson>=3.8.0 13 | traits>=4.6,<6.4,!=5.0 14 | filelock>=3.0.0 15 | etelemetry>=0.2.0 16 | looseversion 17 | -------------------------------------------------------------------------------- /nipype/interfaces/cmtk/__init__.py: -------------------------------------------------------------------------------- 1 | """CMP implements a full processing pipeline for creating connectomes with dMRI data.""" 2 | 3 | from .cmtk import ROIGen, CreateMatrix, CreateNodes 4 | from .nx import NetworkXMetrics, AverageNetworks 5 | from .parcellation import Parcellate 6 | from .convert import CFFConverter, MergeCNetworks 7 | from .nbs import NetworkBasedStatistic 8 | -------------------------------------------------------------------------------- /nipype/interfaces/nitime/__init__.py: -------------------------------------------------------------------------------- 1 | # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- 2 | # vi: set ft=python sts=4 ts=4 sw=4 et: 3 | """Nitime is a library for time-series analysis of data from neuroscience experiments.""" 4 | from .analysis import ( 5 | CoherenceAnalyzerInputSpec, 6 | CoherenceAnalyzerOutputSpec, 7 | CoherenceAnalyzer, 8 | ) 9 | -------------------------------------------------------------------------------- /nipype/interfaces/dipy/__init__.py: -------------------------------------------------------------------------------- 1 | """DIPY is a computational neuroimaging tool for diffusion MRI.""" 2 | 3 | from .tracks import StreamlineTractography, TrackDensityMap 4 | from .tensors import TensorMode, DTI 5 | from .preprocess import Resample, Denoise 6 | from .reconstruction import RESTORE, EstimateResponseSH, CSD 7 | from .simulate import SimulateMultiTensor 8 | from .anisotropic_power import APMQball 9 | -------------------------------------------------------------------------------- /nipype/interfaces/semtools/generated.sh: -------------------------------------------------------------------------------- 1 | local_generate_classes.py --python_paths=/scratch/johnsonhj/src/NEP-11/NIPYPE --program_paths=/scratch/johnsonhj/src/NEP-11/bin:/usr/local/bin:/opt/ogs/bin/darwin-x64:/bin:/sbin:/usr/local/bin:/usr/bin:/usr/sbin:/usr/texbin:/Shared/sinapse/sharedopt/20120722/Darwin_i386/vv/bin:/usr/texbin:/scratch/johnsonhj/bin --output_path=/scratch/johnsonhj/src/NEP-11/BRAINSTools/AutoWorkup 2 | -------------------------------------------------------------------------------- /nipype/interfaces/tests/test_auto_IOBase.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..io import IOBase 3 | 4 | 5 | def test_IOBase_inputs(): 6 | input_map = dict() 7 | inputs = IOBase.input_spec() 8 | 9 | for key, metadata in list(input_map.items()): 10 | for metakey, value in list(metadata.items()): 11 | assert getattr(inputs.traits()[key], metakey) == value 12 | -------------------------------------------------------------------------------- /nipype/interfaces/cat12/base.py: -------------------------------------------------------------------------------- 1 | class Cell: 2 | def __init__(self, arg): 3 | self.arg = arg 4 | 5 | def to_string(self): 6 | if isinstance(self.arg, list): 7 | v = "\n".join([f"'{el}'" for el in self.arg]) 8 | else: 9 | v = self.arg 10 | return v 11 | 12 | 13 | class NestedCell(Cell): 14 | def __str__(self): 15 | return "{{%s}}" % self.to_string() 16 | -------------------------------------------------------------------------------- /nipype/interfaces/afni/tests/test_extra_Deconvolve.py: -------------------------------------------------------------------------------- 1 | """Test afni deconvolve""" 2 | 3 | from ..model import Deconvolve 4 | 5 | 6 | def test_x1dstop(): 7 | deconv = Deconvolve() 8 | deconv.inputs.out_file = "file.nii" 9 | assert "out_file" in deconv._list_outputs() 10 | deconv.inputs.x1D_stop = True 11 | assert "out_file" not in deconv._list_outputs() 12 | assert "cbucket" not in deconv._list_outputs() 13 | -------------------------------------------------------------------------------- /.github/workflows/codespell.yml: -------------------------------------------------------------------------------- 1 | --- 2 | name: Codespell 3 | 4 | on: 5 | push: 6 | branches: [master] 7 | pull_request: 8 | branches: [master] 9 | 10 | jobs: 11 | codespell: 12 | name: Check for spelling errors 13 | runs-on: ubuntu-latest 14 | 15 | steps: 16 | - name: Checkout 17 | uses: actions/checkout@v4 18 | - name: Codespell 19 | uses: codespell-project/actions-codespell@v2 20 | -------------------------------------------------------------------------------- /examples/README.md: -------------------------------------------------------------------------------- 1 | The examples directory previously held a set of 2 | [literate programming](https://en.wikipedia.org/wiki/Literate_programming) documents that 3 | demonstrated solutions to various problems using Nipype. 4 | 5 | These examples have been moved to the 6 | [Nipype1 Examples Niflow](https://github.com/niflows/nipype1-examples). Please refer to 7 | that repository for more information, and report any issues with the examples there. 8 | -------------------------------------------------------------------------------- /nipype/testing/data/README: -------------------------------------------------------------------------------- 1 | This directory contains empty, dummy files which are meant to be used 2 | in the doctests of nipype. For version 0.3 of nipype, we're using 3 | Traits and for input files, the code checks to confirm the assigned 4 | files actually exist. It doesn't matter what the files are, or even 5 | if they contain "real data", only that they exist. Again, these files 6 | are only meant to serve as documentation in the doctests. 7 | -------------------------------------------------------------------------------- /nipype/pipeline/engine/__init__.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- 3 | # vi: set ft=python sts=4 ts=4 sw=4 et: 4 | """ 5 | Package contains modules for generating pipelines using interfaces 6 | 7 | """ 8 | 9 | __docformat__ = "restructuredtext" 10 | from .workflows import Workflow 11 | from .nodes import Node, MapNode, JoinNode 12 | from .utils import generate_expanded_graph 13 | -------------------------------------------------------------------------------- /nipype/interfaces/base/tests/test_auto_BaseInterface.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..core import BaseInterface 3 | 4 | 5 | def test_BaseInterface_inputs(): 6 | input_map = dict() 7 | inputs = BaseInterface.input_spec() 8 | 9 | for key, metadata in list(input_map.items()): 10 | for metakey, value in list(metadata.items()): 11 | assert getattr(inputs.traits()[key], metakey) == value 12 | -------------------------------------------------------------------------------- /nipype/interfaces/utility/__init__.py: -------------------------------------------------------------------------------- 1 | # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- 2 | # vi: set ft=python sts=4 ts=4 sw=4 et: 3 | """ 4 | Package contains interfaces for using existing functionality in other packages 5 | 6 | Requires Packages to be installed 7 | """ 8 | 9 | from .base import IdentityInterface, Rename, Select, Split, Merge, AssertEqual 10 | from .csv import CSVReader 11 | from .wrappers import Function 12 | -------------------------------------------------------------------------------- /nipype/interfaces/base/tests/test_auto_SimpleInterface.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..core import SimpleInterface 3 | 4 | 5 | def test_SimpleInterface_inputs(): 6 | input_map = dict() 7 | inputs = SimpleInterface.input_spec() 8 | 9 | for key, metadata in list(input_map.items()): 10 | for metakey, value in list(metadata.items()): 11 | assert getattr(inputs.traits()[key], metakey) == value 12 | -------------------------------------------------------------------------------- /nipype/algorithms/tests/test_auto_TVTKBaseInterface.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..mesh import TVTKBaseInterface 3 | 4 | 5 | def test_TVTKBaseInterface_inputs(): 6 | input_map = dict() 7 | inputs = TVTKBaseInterface.input_spec() 8 | 9 | for key, metadata in list(input_map.items()): 10 | for metakey, value in list(metadata.items()): 11 | assert getattr(inputs.traits()[key], metakey) == value 12 | -------------------------------------------------------------------------------- /nipype/interfaces/cmtk/tests/test_auto_CFFBaseInterface.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..base import CFFBaseInterface 3 | 4 | 5 | def test_CFFBaseInterface_inputs(): 6 | input_map = dict() 7 | inputs = CFFBaseInterface.input_spec() 8 | 9 | for key, metadata in list(input_map.items()): 10 | for metakey, value in list(metadata.items()): 11 | assert getattr(inputs.traits()[key], metakey) == value 12 | -------------------------------------------------------------------------------- /nipype/interfaces/dipy/tests/test_auto_DipyBaseInterface.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..base import DipyBaseInterface 3 | 4 | 5 | def test_DipyBaseInterface_inputs(): 6 | input_map = dict() 7 | inputs = DipyBaseInterface.input_spec() 8 | 9 | for key, metadata in list(input_map.items()): 10 | for metakey, value in list(metadata.items()): 11 | assert getattr(inputs.traits()[key], metakey) == value 12 | -------------------------------------------------------------------------------- /nipype/interfaces/nipy/tests/test_auto_NipyBaseInterface.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..base import NipyBaseInterface 3 | 4 | 5 | def test_NipyBaseInterface_inputs(): 6 | input_map = dict() 7 | inputs = NipyBaseInterface.input_spec() 8 | 9 | for key, metadata in list(input_map.items()): 10 | for metakey, value in list(metadata.items()): 11 | assert getattr(inputs.traits()[key], metakey) == value 12 | -------------------------------------------------------------------------------- /nipype/interfaces/semtools/__init__.py: -------------------------------------------------------------------------------- 1 | """SEM Tools are useful tools for Structural Equation Modeling.""" 2 | 3 | from .diffusion import * 4 | from .featurecreator import GenerateCsfClippedFromClassifiedImage 5 | from .segmentation import * 6 | from .filtering import * 7 | from .brains import * 8 | from .testing import * 9 | from .utilities import * 10 | from .legacy import * 11 | from .registration import * 12 | from .converters import DWISimpleCompare, DWICompare 13 | -------------------------------------------------------------------------------- /nipype/interfaces/tests/test_auto_NiftiGeneratorBase.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..dcmstack import NiftiGeneratorBase 3 | 4 | 5 | def test_NiftiGeneratorBase_inputs(): 6 | input_map = dict() 7 | inputs = NiftiGeneratorBase.input_spec() 8 | 9 | for key, metadata in list(input_map.items()): 10 | for metakey, value in list(metadata.items()): 11 | assert getattr(inputs.traits()[key], metakey) == value 12 | -------------------------------------------------------------------------------- /nipype/interfaces/__init__.py: -------------------------------------------------------------------------------- 1 | # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- 2 | # vi: set ft=python sts=4 ts=4 sw=4 et: 3 | """ 4 | Package contains interfaces for using existing functionality in other packages 5 | 6 | Requires Packages to be installed 7 | """ 8 | __docformat__ = "restructuredtext" 9 | 10 | from .io import DataGrabber, DataSink, SelectFiles, BIDSDataGrabber 11 | from .utility import IdentityInterface, Rename, Function, Select, Merge 12 | -------------------------------------------------------------------------------- /nipype/interfaces/base/tests/test_auto_LibraryBaseInterface.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..core import LibraryBaseInterface 3 | 4 | 5 | def test_LibraryBaseInterface_inputs(): 6 | input_map = dict() 7 | inputs = LibraryBaseInterface.input_spec() 8 | 9 | for key, metadata in list(input_map.items()): 10 | for metakey, value in list(metadata.items()): 11 | assert getattr(inputs.traits()[key], metakey) == value 12 | -------------------------------------------------------------------------------- /nipype/interfaces/nitime/tests/test_auto_NitimeBaseInterface.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..base import NitimeBaseInterface 3 | 4 | 5 | def test_NitimeBaseInterface_inputs(): 6 | input_map = dict() 7 | inputs = NitimeBaseInterface.input_spec() 8 | 9 | for key, metadata in list(input_map.items()): 10 | for metakey, value in list(metadata.items()): 11 | assert getattr(inputs.traits()[key], metakey) == value 12 | -------------------------------------------------------------------------------- /nipype/interfaces/tests/test_auto_NilearnBaseInterface.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..nilearn import NilearnBaseInterface 3 | 4 | 5 | def test_NilearnBaseInterface_inputs(): 6 | input_map = dict() 7 | inputs = NilearnBaseInterface.input_spec() 8 | 9 | for key, metadata in list(input_map.items()): 10 | for metakey, value in list(metadata.items()): 11 | assert getattr(inputs.traits()[key], metakey) == value 12 | -------------------------------------------------------------------------------- /tools/run_examples.py: -------------------------------------------------------------------------------- 1 | import sys 2 | from textwrap import dedent 3 | 4 | 5 | if __name__ == "__main__": 6 | print( 7 | dedent( 8 | """Nipype examples have been moved to niflow-nipype1-examples. 9 | 10 | Install with: pip install niflow-nipype1-examples""" 11 | ) 12 | ) 13 | if sys.argv[1:]: 14 | print( 15 | "Run this command with: niflow-nipype1-examples " + " ".join(sys.argv[1:]) 16 | ) 17 | sys.exit(1) 18 | -------------------------------------------------------------------------------- /nipype/interfaces/mixins/tests/test_auto_CopyHeaderInterface.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..fixheader import CopyHeaderInterface 3 | 4 | 5 | def test_CopyHeaderInterface_inputs(): 6 | input_map = dict() 7 | inputs = CopyHeaderInterface.input_spec() 8 | 9 | for key, metadata in list(input_map.items()): 10 | for metakey, value in list(metadata.items()): 11 | assert getattr(inputs.traits()[key], metakey) == value 12 | -------------------------------------------------------------------------------- /nipype/interfaces/mixins/tests/test_auto_ReportCapableInterface.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..reporting import ReportCapableInterface 3 | 4 | 5 | def test_ReportCapableInterface_inputs(): 6 | input_map = dict() 7 | inputs = ReportCapableInterface.input_spec() 8 | 9 | for key, metadata in list(input_map.items()): 10 | for metakey, value in list(metadata.items()): 11 | assert getattr(inputs.traits()[key], metakey) == value 12 | -------------------------------------------------------------------------------- /nipype/interfaces/slicer/legacy/__init__.py: -------------------------------------------------------------------------------- 1 | from .diffusion import * 2 | from .segmentation import OtsuThresholdSegmentation 3 | from .filtering import OtsuThresholdImageFilter, ResampleScalarVolume 4 | from .converters import BSplineToDeformationField 5 | from .registration import ( 6 | BSplineDeformableRegistration, 7 | AffineRegistration, 8 | MultiResolutionAffineRegistration, 9 | RigidRegistration, 10 | LinearRegistration, 11 | ExpertAutomatedRegistration, 12 | ) 13 | -------------------------------------------------------------------------------- /nipype/interfaces/niftyfit/__init__.py: -------------------------------------------------------------------------------- 1 | # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- 2 | # vi: set ft=python sts=4 ts=4 sw=4 et: 3 | """ 4 | NiftyFit is a software package for multi-parametric model-fitting of 4D MRI. 5 | 6 | The niftyfit module provides classes for interfacing with the `NiftyFit 7 | `__ command line tools. 8 | 9 | """ 10 | from .asl import FitAsl 11 | from .dwi import FitDwi, DwiTool 12 | from .qt1 import FitQt1 13 | -------------------------------------------------------------------------------- /tools/ci/install_deb_dependencies.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | echo "Installing NeuroDebian dependencies" 4 | 5 | set -eu 6 | 7 | echo "INSTALL_DEB_DEPENDENCIES = $INSTALL_DEB_DEPENDENCIES" 8 | 9 | DEPS=( 10 | fsl 11 | # afni 12 | # elastix 13 | fsl-atlases 14 | xvfb 15 | fusefat 16 | graphviz 17 | ) 18 | 19 | if $INSTALL_DEB_DEPENDENCIES; then 20 | bash <(wget -q -O- http://neuro.debian.net/_files/neurodebian-travis.sh) 21 | sudo apt update 22 | sudo apt install -y -qq ${DEPS[@]} 23 | fi 24 | -------------------------------------------------------------------------------- /.dockerignore: -------------------------------------------------------------------------------- 1 | # python cache 2 | __pycache__ 3 | **/__pycache__ 4 | **/*.pyc 5 | *.pyc 6 | 7 | # python distribution 8 | build/**/* 9 | build 10 | dist/**/* 11 | dist 12 | nipype.egg-info/**/* 13 | nipype.egg-info 14 | .eggs/**/* 15 | .eggs 16 | src/**/* 17 | src/ 18 | 19 | # git 20 | .gitignore 21 | .git/**/* 22 | .git 23 | 24 | # other 25 | doc/**/* 26 | doc/ 27 | .cache/ 28 | .circle/**/* 29 | .circle/ 30 | circle.yml 31 | Vagrantfile 32 | .travis.yml 33 | .mailmap 34 | 35 | # Previous coverage results 36 | .coverage 37 | -------------------------------------------------------------------------------- /tools/ci/create_venv.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | echo Creating isolated virtual environment 4 | 5 | source tools/ci/env.sh 6 | 7 | set -eu 8 | 9 | # Required variables 10 | echo SETUP_REQUIRES = $SETUP_REQUIRES 11 | 12 | set -x 13 | 14 | python -m pip install --upgrade pip virtualenv 15 | virtualenv --python=python virtenv 16 | source tools/ci/activate.sh 17 | python --version 18 | python -m pip install -U $SETUP_REQUIRES 19 | which python 20 | which pip 21 | 22 | set +eux 23 | 24 | echo Done creating isolated virtual environment 25 | -------------------------------------------------------------------------------- /nipype/testing/data/spminfo: -------------------------------------------------------------------------------- 1 | fprintf(1,'Executing %s at %s:\n',mfilename,datestr(now)); 2 | ver, 3 | try, 4 | if isempty(which('spm')), 5 | throw(MException('SPMCheck:NotFound','SPM not in matlab path')); 6 | end; 7 | spm_path = spm('dir'); 8 | fprintf(1, 'NIPYPE %s', spm_path); 9 | 10 | ,catch ME, 11 | fprintf(2,'MATLAB code threw an exception:\n'); 12 | fprintf(2,'%s\n',ME.message); 13 | if length(ME.stack) ~= 0, fprintf(2,'File:%s\nName:%s\nLine:%d\n',ME.stack.file,ME.stack.name,ME.stack.line);, end; 14 | end; 15 | -------------------------------------------------------------------------------- /nipype/utils/datetime.py: -------------------------------------------------------------------------------- 1 | # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- 2 | # vi: set ft=python sts=4 ts=4 sw=4 et: 3 | """ 4 | Utilities for dates and time 5 | """ 6 | 7 | from datetime import datetime as dt 8 | import sys 9 | 10 | if sys.version_info >= (3, 11): 11 | from datetime import UTC 12 | 13 | def utcnow(): 14 | """Adapter since 3.12 prior utcnow is deprecated, 15 | but not EOLed 3.8 does not have datetime.UTC""" 16 | return dt.now(UTC) 17 | 18 | else: 19 | utcnow = dt.utcnow 20 | -------------------------------------------------------------------------------- /tools/update_mailmap.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | # usage -> bash update_mailmap.sh 4 | # by default, will use the latest tag 5 | 6 | set -ux 7 | 8 | ROOT=$( git rev-parse --show-toplevel ) 9 | MAILMAP=$ROOT/.mailmap 10 | 11 | LAST=$(git describe --tags `git rev-list --tags --max-count=1`) 12 | RELEASE=${1:-$LAST} 13 | 14 | IFS=$'\n' 15 | for NAME in $(git shortlog -nse $RELEASE.. | cut -f2-); do 16 | echo $NAME 17 | done 18 | 19 | # sort and write 20 | sort $MAILMAP > .tmpmailmap 21 | cp .tmpmailmap $MAILMAP 22 | rm .tmpmailmap 23 | -------------------------------------------------------------------------------- /tools/ci/install_dependencies.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | echo Installing dependencies 4 | 5 | source tools/ci/activate.sh 6 | source tools/ci/env.sh 7 | 8 | set -eu 9 | 10 | # Required variables 11 | echo EXTRA_PIP_FLAGS = $EXTRA_PIP_FLAGS 12 | echo DEPENDS = $DEPENDS 13 | 14 | set -x 15 | 16 | if [ -n "$EXTRA_PIP_FLAGS" ]; then 17 | EXTRA_PIP_FLAGS=${!EXTRA_PIP_FLAGS} 18 | fi 19 | 20 | if [ -n "$DEPENDS" ]; then 21 | pip install ${EXTRA_PIP_FLAGS} --prefer-binary ${!DEPENDS} 22 | fi 23 | 24 | set +eux 25 | 26 | echo Done installing dependencies 27 | -------------------------------------------------------------------------------- /nipype/interfaces/dipy/setup.py: -------------------------------------------------------------------------------- 1 | # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- 2 | # vi: set ft=python sts=4 ts=4 sw=4 et: 3 | 4 | 5 | def configuration(parent_package="", top_path=None): 6 | from numpy.distutils.misc_util import Configuration 7 | 8 | config = Configuration("dipy", parent_package, top_path) 9 | 10 | # config.add_data_dir('tests') 11 | return config 12 | 13 | 14 | if __name__ == "__main__": 15 | from numpy.distutils.core import setup 16 | 17 | setup(**configuration(top_path="").todict()) 18 | -------------------------------------------------------------------------------- /.codespellrc: -------------------------------------------------------------------------------- 1 | [codespell] 2 | skip = .git,*.pdf,*.svg,external 3 | # nd,nam - import module short 4 | # fith - oddness coming from AFNI 5 | # whos - smth used in matlab things 6 | # SMAL - Stanford CNI MRS Library 7 | # Suh - name 8 | # noo,crasher,afile - field/var name used 9 | # Reson - short journal name 10 | # ALS, FWE - neuroimaging specific abbrevs 11 | # Comision - foreign word used 12 | # expad - AFNI flag 13 | ignore-words-list = te,inport,objekt,jist,nd,hel,inout,fith,whos,fot,ue,shs,smal,nam,filetest,suh,noo,reson,als,fwe,crasher,comision,afile,expad,burnin 14 | -------------------------------------------------------------------------------- /tools/update_requirements.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python3 2 | from runpy import run_path 3 | from pathlib import Path 4 | 5 | repo_root = Path(__file__).parent.parent 6 | info_file = repo_root / "nipype" / "info.py" 7 | reqs = repo_root / "requirements.txt" 8 | 9 | info = run_path(info_file) 10 | requirements = info["REQUIRES"] 11 | 12 | script_name = Path(__file__).relative_to(repo_root) 13 | 14 | lines = [f"# Auto-generated by {script_name}", ""] 15 | 16 | # Write requirements 17 | lines[1:-1] = requirements 18 | reqs.write_text("\n".join(lines), encoding='utf-8') 19 | -------------------------------------------------------------------------------- /nipype/testing/data/ds003_sub-01_mc.DVARS: -------------------------------------------------------------------------------- 1 | 2.02915 5.2016 1.74221 2 | 1.54871 3.97002 1.18108 3 | 0.921419 2.362 0.784497 4 | 1.26058 3.23142 0.734119 5 | 1.00079 2.56548 0.787452 6 | 0.929074 2.38163 0.828835 7 | 0.741207 1.90004 0.746263 8 | 1.07913 2.7663 0.779829 9 | 1.2969 3.32452 0.73856 10 | 0.767387 1.96715 0.772047 11 | 0.847059 2.17138 0.774103 12 | 0.984061 2.52258 0.88097 13 | 0.852897 2.18635 0.794655 14 | 0.927778 2.3783 0.756786 15 | 0.857544 2.19826 0.796125 16 | 0.780098 1.99973 0.731265 17 | 1.05496 2.70434 0.788584 18 | 1.32099 3.38628 0.831803 19 | 0.691529 1.77269 0.738788 20 | -------------------------------------------------------------------------------- /.pre-commit-config.yaml: -------------------------------------------------------------------------------- 1 | # See https://pre-commit.com for more information 2 | # See https://pre-commit.com/hooks.html for more hooks 3 | repos: 4 | - repo: https://github.com/pre-commit/pre-commit-hooks 5 | rev: v4.5.0 6 | hooks: 7 | - id: trailing-whitespace 8 | - id: end-of-file-fixer 9 | - id: check-yaml 10 | - id: check-added-large-files 11 | - repo: https://github.com/psf/black 12 | rev: 24.2.0 13 | hooks: 14 | - id: black 15 | - repo: https://github.com/codespell-project/codespell 16 | rev: v2.2.6 17 | hooks: 18 | - id: codespell 19 | -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | /build 2 | /dist 3 | /nipype.egg-info 4 | /MANIFEST 5 | /nipype/build 6 | /nipype/nipype.egg-info 7 | /doc/_build 8 | /doc/preproc 9 | /doc/users/examples 10 | /doc/api/generated 11 | *.pyc 12 | *.so 13 | .project 14 | .settings 15 | .pydevproject 16 | .eggs 17 | .idea/ 18 | /documentation.zip 19 | .DS_Store 20 | nipype/testing/data/von-ray_errmap.nii.gz 21 | nipype/testing/data/von_errmap.nii.gz 22 | nipype/testing/data/.proc* 23 | crash*.pklz 24 | .coverage 25 | htmlcov/ 26 | __pycache__/ 27 | *~ 28 | .*.swp 29 | .ipynb_checkpoints/ 30 | .ruby-version 31 | .pytest_cache 32 | .vscode/ 33 | venv/ 34 | -------------------------------------------------------------------------------- /nipype/interfaces/nipy/base.py: -------------------------------------------------------------------------------- 1 | # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- 2 | # vi: set ft=python sts=4 ts=4 sw=4 et: 3 | """Base interface for nipy""" 4 | 5 | from ..base import LibraryBaseInterface 6 | from ...utils.misc import package_check 7 | 8 | # Originally set in model, preprocess and utils 9 | # Set here to be imported, in case anybody depends on its presence 10 | # Remove in 2.0 11 | have_nipy = True 12 | try: 13 | package_check("nipy") 14 | except: 15 | have_nipy = False 16 | 17 | 18 | class NipyBaseInterface(LibraryBaseInterface): 19 | _pkg = "nipy" 20 | -------------------------------------------------------------------------------- /nipype/interfaces/base/tests/test_auto_CommandLine.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..core import CommandLine 3 | 4 | 5 | def test_CommandLine_inputs(): 6 | input_map = dict( 7 | args=dict( 8 | argstr="%s", 9 | ), 10 | environ=dict( 11 | nohash=True, 12 | usedefault=True, 13 | ), 14 | ) 15 | inputs = CommandLine.input_spec() 16 | 17 | for key, metadata in list(input_map.items()): 18 | for metakey, value in list(metadata.items()): 19 | assert getattr(inputs.traits()[key], metakey) == value 20 | -------------------------------------------------------------------------------- /nipype/interfaces/workbench/tests/test_auto_WBCommand.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..base import WBCommand 3 | 4 | 5 | def test_WBCommand_inputs(): 6 | input_map = dict( 7 | args=dict( 8 | argstr="%s", 9 | ), 10 | environ=dict( 11 | nohash=True, 12 | usedefault=True, 13 | ), 14 | ) 15 | inputs = WBCommand.input_spec() 16 | 17 | for key, metadata in list(input_map.items()): 18 | for metakey, value in list(metadata.items()): 19 | assert getattr(inputs.traits()[key], metakey) == value 20 | -------------------------------------------------------------------------------- /nipype/interfaces/mrtrix3/tests/test_auto_MRTrix3Base.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..base import MRTrix3Base 3 | 4 | 5 | def test_MRTrix3Base_inputs(): 6 | input_map = dict( 7 | args=dict( 8 | argstr="%s", 9 | ), 10 | environ=dict( 11 | nohash=True, 12 | usedefault=True, 13 | ), 14 | ) 15 | inputs = MRTrix3Base.input_spec() 16 | 17 | for key, metadata in list(input_map.items()): 18 | for metakey, value in list(metadata.items()): 19 | assert getattr(inputs.traits()[key], metakey) == value 20 | -------------------------------------------------------------------------------- /nipype/interfaces/tests/test_auto_SQLiteSink.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..io import SQLiteSink 3 | 4 | 5 | def test_SQLiteSink_inputs(): 6 | input_map = dict( 7 | database_file=dict( 8 | extensions=None, 9 | mandatory=True, 10 | ), 11 | table_name=dict( 12 | mandatory=True, 13 | ), 14 | ) 15 | inputs = SQLiteSink.input_spec() 16 | 17 | for key, metadata in list(input_map.items()): 18 | for metakey, value in list(metadata.items()): 19 | assert getattr(inputs.traits()[key], metakey) == value 20 | -------------------------------------------------------------------------------- /nipype/interfaces/afni/tests/test_auto_AFNICommandBase.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..base import AFNICommandBase 3 | 4 | 5 | def test_AFNICommandBase_inputs(): 6 | input_map = dict( 7 | args=dict( 8 | argstr="%s", 9 | ), 10 | environ=dict( 11 | nohash=True, 12 | usedefault=True, 13 | ), 14 | ) 15 | inputs = AFNICommandBase.input_spec() 16 | 17 | for key, metadata in list(input_map.items()): 18 | for metakey, value in list(metadata.items()): 19 | assert getattr(inputs.traits()[key], metakey) == value 20 | -------------------------------------------------------------------------------- /doc/devel/gitwash/git_intro.rst: -------------------------------------------------------------------------------- 1 | ============== 2 | Introduction 3 | ============== 4 | 5 | These pages describe a git_ and github_ workflow for the nipype_ 6 | project. 7 | 8 | There are several different workflows here, for different ways of 9 | working with *nipype*. 10 | 11 | This is not a comprehensive git_ reference, it's just a workflow for our 12 | own project. It's tailored to the github_ hosting service. You may well 13 | find better or quicker ways of getting stuff done with git_, but these 14 | should get you started. 15 | 16 | For general resources for learning git_ see :ref:`git-resources`. 17 | 18 | .. include:: links.inc 19 | -------------------------------------------------------------------------------- /nipype/interfaces/dtitk/tests/test_auto_CommandLineDtitk.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..base import CommandLineDtitk 3 | 4 | 5 | def test_CommandLineDtitk_inputs(): 6 | input_map = dict( 7 | args=dict( 8 | argstr="%s", 9 | ), 10 | environ=dict( 11 | nohash=True, 12 | usedefault=True, 13 | ), 14 | ) 15 | inputs = CommandLineDtitk.input_spec() 16 | 17 | for key, metadata in list(input_map.items()): 18 | for metakey, value in list(metadata.items()): 19 | assert getattr(inputs.traits()[key], metakey) == value 20 | -------------------------------------------------------------------------------- /nipype/interfaces/niftyfit/tests/test_auto_NiftyFitCommand.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..base import NiftyFitCommand 3 | 4 | 5 | def test_NiftyFitCommand_inputs(): 6 | input_map = dict( 7 | args=dict( 8 | argstr="%s", 9 | ), 10 | environ=dict( 11 | nohash=True, 12 | usedefault=True, 13 | ), 14 | ) 15 | inputs = NiftyFitCommand.input_spec() 16 | 17 | for key, metadata in list(input_map.items()): 18 | for metakey, value in list(metadata.items()): 19 | assert getattr(inputs.traits()[key], metakey) == value 20 | -------------------------------------------------------------------------------- /nipype/interfaces/niftyreg/__init__.py: -------------------------------------------------------------------------------- 1 | # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- 2 | # vi: set ft=python sts=4 ts=4 sw=4 et: 3 | """ 4 | NiftyReg is an open-source software for efficient medical image registration. 5 | 6 | The niftyreg module provides classes for interfacing with the `NiftyReg 7 | `_ command line tools. 8 | 9 | """ 10 | from .base import get_custom_path 11 | from .reg import RegAladin, RegF3D 12 | from .regutils import ( 13 | RegResample, 14 | RegJacobian, 15 | RegAverage, 16 | RegTools, 17 | RegTransform, 18 | RegMeasure, 19 | ) 20 | -------------------------------------------------------------------------------- /nipype/interfaces/niftyseg/tests/test_auto_NiftySegCommand.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..base import NiftySegCommand 3 | 4 | 5 | def test_NiftySegCommand_inputs(): 6 | input_map = dict( 7 | args=dict( 8 | argstr="%s", 9 | ), 10 | environ=dict( 11 | nohash=True, 12 | usedefault=True, 13 | ), 14 | ) 15 | inputs = NiftySegCommand.input_spec() 16 | 17 | for key, metadata in list(input_map.items()): 18 | for metakey, value in list(metadata.items()): 19 | assert getattr(inputs.traits()[key], metakey) == value 20 | -------------------------------------------------------------------------------- /nipype/interfaces/niftyseg/__init__.py: -------------------------------------------------------------------------------- 1 | # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- 2 | # vi: set ft=python sts=4 ts=4 sw=4 et: 3 | """ 4 | The niftyseg module provides classes for interfacing with the `NIFTYSEG 5 | `_ command line tools. 6 | 7 | Top-level namespace for niftyseg. 8 | """ 9 | 10 | from .em import EM 11 | from .label_fusion import LabelFusion, CalcTopNCC 12 | from .lesions import FillLesions 13 | from .maths import UnaryMaths, BinaryMaths, BinaryMathsInteger, TupleMaths, Merge 14 | from .patchmatch import PatchMatch 15 | from .stats import UnaryStats, BinaryStats 16 | -------------------------------------------------------------------------------- /nipype/interfaces/slicer/tests/test_auto_SlicerCommandLine.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..base import SlicerCommandLine 3 | 4 | 5 | def test_SlicerCommandLine_inputs(): 6 | input_map = dict( 7 | args=dict( 8 | argstr="%s", 9 | ), 10 | environ=dict( 11 | nohash=True, 12 | usedefault=True, 13 | ), 14 | ) 15 | inputs = SlicerCommandLine.input_spec() 16 | 17 | for key, metadata in list(input_map.items()): 18 | for metakey, value in list(metadata.items()): 19 | assert getattr(inputs.traits()[key], metakey) == value 20 | -------------------------------------------------------------------------------- /nipype/interfaces/base/tests/test_auto_SEMLikeCommandLine.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..core import SEMLikeCommandLine 3 | 4 | 5 | def test_SEMLikeCommandLine_inputs(): 6 | input_map = dict( 7 | args=dict( 8 | argstr="%s", 9 | ), 10 | environ=dict( 11 | nohash=True, 12 | usedefault=True, 13 | ), 14 | ) 15 | inputs = SEMLikeCommandLine.input_spec() 16 | 17 | for key, metadata in list(input_map.items()): 18 | for metakey, value in list(metadata.items()): 19 | assert getattr(inputs.traits()[key], metakey) == value 20 | -------------------------------------------------------------------------------- /nipype/interfaces/dtitk/__init__.py: -------------------------------------------------------------------------------- 1 | """ 2 | DTI-TK is a spatial normalization and atlas construction toolkit for DTI. 3 | 4 | Interfaces for the `Diffusion Tensor Imaging Toolkit (DTI-TK) 5 | `_ command line tools. 6 | 7 | """ 8 | 9 | from .registration import ( 10 | Rigid, 11 | Affine, 12 | Diffeo, 13 | ComposeXfm, 14 | DiffeoSymTensor3DVol, 15 | AffSymTensor3DVol, 16 | AffScalarVol, 17 | DiffeoScalarVol, 18 | ) 19 | from .utils import ( 20 | TVAdjustVoxSp, 21 | SVAdjustVoxSp, 22 | TVResample, 23 | SVResample, 24 | TVtool, 25 | BinThresh, 26 | ) 27 | -------------------------------------------------------------------------------- /nipype/interfaces/fsl/tests/test_auto_FSLCommand.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..base import FSLCommand 3 | 4 | 5 | def test_FSLCommand_inputs(): 6 | input_map = dict( 7 | args=dict( 8 | argstr="%s", 9 | ), 10 | environ=dict( 11 | nohash=True, 12 | usedefault=True, 13 | ), 14 | output_type=dict(), 15 | ) 16 | inputs = FSLCommand.input_spec() 17 | 18 | for key, metadata in list(input_map.items()): 19 | for metakey, value in list(metadata.items()): 20 | assert getattr(inputs.traits()[key], metakey) == value 21 | -------------------------------------------------------------------------------- /nipype/interfaces/freesurfer/tests/test_auto_FSCommand.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..base import FSCommand 3 | 4 | 5 | def test_FSCommand_inputs(): 6 | input_map = dict( 7 | args=dict( 8 | argstr="%s", 9 | ), 10 | environ=dict( 11 | nohash=True, 12 | usedefault=True, 13 | ), 14 | subjects_dir=dict(), 15 | ) 16 | inputs = FSCommand.input_spec() 17 | 18 | for key, metadata in list(input_map.items()): 19 | for metakey, value in list(metadata.items()): 20 | assert getattr(inputs.traits()[key], metakey) == value 21 | -------------------------------------------------------------------------------- /nipype/interfaces/utility/tests/test_auto_AssertEqual.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..base import AssertEqual 3 | 4 | 5 | def test_AssertEqual_inputs(): 6 | input_map = dict( 7 | volume1=dict( 8 | extensions=None, 9 | mandatory=True, 10 | ), 11 | volume2=dict( 12 | extensions=None, 13 | mandatory=True, 14 | ), 15 | ) 16 | inputs = AssertEqual.input_spec() 17 | 18 | for key, metadata in list(input_map.items()): 19 | for metakey, value in list(metadata.items()): 20 | assert getattr(inputs.traits()[key], metakey) == value 21 | -------------------------------------------------------------------------------- /doc/devel/index.rst: -------------------------------------------------------------------------------- 1 | .. _developers-guide-index: 2 | 3 | ================= 4 | Developer Guide 5 | ================= 6 | 7 | :Release: |version| 8 | :Date: |today| 9 | 10 | Since nipype is part of the NIPY_ project, we follow the same 11 | conventions documented in the `NIPY Developers Guide 12 | `_. For bleeding-edge version help see `Nightly documentation `_ 13 | 14 | .. toctree:: 15 | :maxdepth: 2 16 | 17 | writing_custom_interfaces 18 | gitwash/index 19 | architecture 20 | provenance 21 | software_using_nipype 22 | testing_nipype 23 | 24 | 25 | .. include:: ../links_names.txt 26 | -------------------------------------------------------------------------------- /doc/examples.rst: -------------------------------------------------------------------------------- 1 | :orphan: 2 | 3 | .. _examples: 4 | 5 | ======================= 6 | User Guide and Examples 7 | ======================= 8 | 9 | .. admonition:: Michael Notter's User Guide 10 | 11 | Be sure to read `Michael's excellent tutorials `__. 12 | 13 | Examples 14 | ~~~~~~~~ 15 | The following examples are `literate programming `__ 16 | documents which solve specific problems using Nipype. 17 | In some cases, the same problem is solved with multiple underlying tools. 18 | 19 | .. toctree:: 20 | :maxdepth: 1 21 | :glob: 22 | 23 | users/examples/* 24 | -------------------------------------------------------------------------------- /nipype/interfaces/semtools/filtering/__init__.py: -------------------------------------------------------------------------------- 1 | from .denoising import UnbiasedNonLocalMeans 2 | from .featuredetection import ( 3 | GenerateSummedGradientImage, 4 | CannySegmentationLevelSetImageFilter, 5 | DilateImage, 6 | TextureFromNoiseImageFilter, 7 | FlippedDifference, 8 | ErodeImage, 9 | GenerateBrainClippedImage, 10 | NeighborhoodMedian, 11 | GenerateTestImage, 12 | NeighborhoodMean, 13 | HammerAttributeCreator, 14 | TextureMeasureFilter, 15 | DilateMask, 16 | DumpBinaryTrainingVectors, 17 | DistanceMaps, 18 | STAPLEAnalysis, 19 | GradientAnisotropicDiffusionImageFilter, 20 | CannyEdge, 21 | ) 22 | -------------------------------------------------------------------------------- /nipype/interfaces/freesurfer/tests/test_auto_FSScriptCommand.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..base import FSScriptCommand 3 | 4 | 5 | def test_FSScriptCommand_inputs(): 6 | input_map = dict( 7 | args=dict( 8 | argstr="%s", 9 | ), 10 | environ=dict( 11 | nohash=True, 12 | usedefault=True, 13 | ), 14 | subjects_dir=dict(), 15 | ) 16 | inputs = FSScriptCommand.input_spec() 17 | 18 | for key, metadata in list(input_map.items()): 19 | for metakey, value in list(metadata.items()): 20 | assert getattr(inputs.traits()[key], metakey) == value 21 | -------------------------------------------------------------------------------- /nipype/utils/imagemanip.py: -------------------------------------------------------------------------------- 1 | """Image manipulation utilities (mostly, NiBabel manipulations).""" 2 | 3 | import nibabel as nb 4 | 5 | 6 | def copy_header(header_file, in_file, keep_dtype=True): 7 | """Copy header from a reference image onto another image.""" 8 | hdr_img = nb.load(header_file) 9 | out_img = nb.load(in_file, mmap=False) 10 | hdr = hdr_img.header.copy() 11 | if keep_dtype: 12 | hdr.set_data_dtype(out_img.get_data_dtype()) 13 | 14 | new_img = out_img.__class__(out_img.dataobj, None, hdr) 15 | if not keep_dtype: 16 | new_img.set_data_dtype(hdr_img.get_data_dtype()) 17 | 18 | new_img.to_filename(in_file) 19 | return in_file 20 | -------------------------------------------------------------------------------- /tools/ci/env.sh: -------------------------------------------------------------------------------- 1 | SETUP_REQUIRES="pip setuptools>=30.3.0 wheel" 2 | 3 | # Minimum requirements 4 | REQUIREMENTS="-r requirements.txt" 5 | # Minimum versions of minimum requirements 6 | MIN_REQUIREMENTS="-r min-requirements.txt" 7 | 8 | # Numpy and scipy upload nightly/weekly/intermittent wheels 9 | NIGHTLY_WHEELS="https://pypi.anaconda.org/scipy-wheels-nightly/simple" 10 | STAGING_WHEELS="https://pypi.anaconda.org/multibuild-wheels-staging/simple" 11 | PRE_PIP_FLAGS="--pre --extra-index-url $NIGHTLY_WHEELS --extra-index-url $STAGING_WHEELS" 12 | 13 | for CONF in /etc/fsl/fsl.sh /etc/afni/afni.sh; do 14 | if [ -r $CONF ]; then source $CONF; fi 15 | done 16 | 17 | FSLOUTPUTTYPE=NIFTI_GZ 18 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | Copyright (c) 2009-2016, Nipype developers 2 | 3 | Licensed under the Apache License, Version 2.0 (the "License"); 4 | you may not use this file except in compliance with the License. 5 | You may obtain a copy of the License at 6 | 7 | http://www.apache.org/licenses/LICENSE-2.0 8 | 9 | Unless required by applicable law or agreed to in writing, software 10 | distributed under the License is distributed on an "AS IS" BASIS, 11 | WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 12 | See the License for the specific language governing permissions and 13 | limitations under the License. 14 | 15 | Prior to release 0.12, Nipype was licensed under a BSD license. 16 | -------------------------------------------------------------------------------- /nipype/interfaces/ants/tests/test_base.py: -------------------------------------------------------------------------------- 1 | from nipype.interfaces.ants.base import Info 2 | 3 | import pytest 4 | 5 | # fmt: off 6 | ANTS_VERSIONS = [("""\ 7 | ANTs Version: 2.3.3.dev168-g29bdf 8 | Compiled: Jun 9 2020 03:44:55 9 | 10 | """, "2.3.3"), ("""\ 11 | ANTs Version: v2.3.5.post76-g28dd25c 12 | Compiled: Nov 16 2021 14:57:48 13 | 14 | """, "2.3.5"), ("""\ 15 | ANTs Version: v2.1.0.post789-g0740f 16 | Compiled: I don't still have this so not going to pretend 17 | 18 | """, "2.2.0"), 19 | ] 20 | # fmt: on 21 | 22 | 23 | @pytest.mark.parametrize("raw_info, version", ANTS_VERSIONS) 24 | def test_version_parser(raw_info, version): 25 | assert Info.parse_version(raw_info) == version 26 | -------------------------------------------------------------------------------- /.github/ISSUE_TEMPLATE.md: -------------------------------------------------------------------------------- 1 | ### Summary 2 | 3 | ### Actual behavior 4 | 5 | ### Expected behavior 6 | 7 | ### How to replicate the behavior 8 | 9 | ### Script/Workflow details 10 | 11 | Please put URL to code or code here (if not too long). 12 | 13 | ### Platform details: 14 | 15 | 18 | 19 | ``` 20 | 21 | ``` 22 | 23 | ### Execution environment 24 | 25 | Choose one 26 | - Container [Tag: ???] 27 | - My python environment inside container [Base Tag: ???] 28 | - My python environment outside container 29 | -------------------------------------------------------------------------------- /nipype/interfaces/freesurfer/tests/test_auto_FSCommandOpenMP.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..base import FSCommandOpenMP 3 | 4 | 5 | def test_FSCommandOpenMP_inputs(): 6 | input_map = dict( 7 | args=dict( 8 | argstr="%s", 9 | ), 10 | environ=dict( 11 | nohash=True, 12 | usedefault=True, 13 | ), 14 | num_threads=dict(), 15 | subjects_dir=dict(), 16 | ) 17 | inputs = FSCommandOpenMP.input_spec() 18 | 19 | for key, metadata in list(input_map.items()): 20 | for metakey, value in list(metadata.items()): 21 | assert getattr(inputs.traits()[key], metakey) == value 22 | -------------------------------------------------------------------------------- /nipype/interfaces/semtools/utilities/__init__.py: -------------------------------------------------------------------------------- 1 | from .brains import ( 2 | BRAINSConstellationModeler, 3 | landmarksConstellationWeights, 4 | BRAINSTrimForegroundInDirection, 5 | BRAINSLmkTransform, 6 | BRAINSMush, 7 | BRAINSTransformConvert, 8 | landmarksConstellationAligner, 9 | BRAINSEyeDetector, 10 | BRAINSLinearModelerEPCA, 11 | BRAINSInitializedControlPoints, 12 | CleanUpOverlapLabels, 13 | BRAINSClipInferior, 14 | GenerateLabelMapFromProbabilityMap, 15 | BRAINSAlignMSP, 16 | BRAINSLandmarkInitializer, 17 | insertMidACPCpoint, 18 | BRAINSSnapShotWriter, 19 | JointHistogram, 20 | ShuffleVectorsModule, 21 | ImageRegionPlotter, 22 | ) 23 | -------------------------------------------------------------------------------- /nipype/interfaces/spm/tests/test_auto_SPMCommand.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..base import SPMCommand 3 | 4 | 5 | def test_SPMCommand_inputs(): 6 | input_map = dict( 7 | matlab_cmd=dict(), 8 | mfile=dict( 9 | usedefault=True, 10 | ), 11 | paths=dict(), 12 | use_mcr=dict(), 13 | use_v8struct=dict( 14 | min_ver="8", 15 | usedefault=True, 16 | ), 17 | ) 18 | inputs = SPMCommand.input_spec() 19 | 20 | for key, metadata in list(input_map.items()): 21 | for metakey, value in list(metadata.items()): 22 | assert getattr(inputs.traits()[key], metakey) == value 23 | -------------------------------------------------------------------------------- /codecov.yml: -------------------------------------------------------------------------------- 1 | coverage: 2 | range: "0...100" 3 | status: 4 | patch: 5 | default: 6 | target: 0 7 | threshold: 100 8 | project: 9 | default: 10 | target: 0 11 | threshold: 100 12 | patch: 13 | target: 0 14 | threshold: 100 15 | unittests: 16 | target: 0 17 | threshold: 100 18 | flags: 19 | - "unittests" 20 | smoketests: 21 | target: 0 22 | threshold: 100 23 | flags: 24 | - "smoketests" 25 | ignore: # files and folders that will be removed during processing 26 | - "nipype/external" 27 | - "tools" 28 | - "doc" 29 | - "**/tests" 30 | - "examples" 31 | -------------------------------------------------------------------------------- /doc/devel/gitwash/git_install.rst: -------------------------------------------------------------------------------- 1 | .. _install-git: 2 | 3 | ============= 4 | Install git 5 | ============= 6 | 7 | Overview 8 | ======== 9 | 10 | ================ ============= 11 | Debian / Ubuntu ``sudo apt-get install git-core`` 12 | Fedora ``sudo yum install git-core`` 13 | Windows Download and install msysGit_ 14 | OS X Use the git-osx-installer_ 15 | ================ ============= 16 | 17 | In detail 18 | ========= 19 | 20 | See the git_ page for the most recent information. 21 | 22 | Have a look at the github_ install help pages available from `github help`_ 23 | 24 | There are good instructions here: http://book.git-scm.com/2_installing_git.html 25 | 26 | .. include:: links.inc 27 | -------------------------------------------------------------------------------- /doc/_templates/navbar.html: -------------------------------------------------------------------------------- 1 | 2 | 8 | 9 | Home · 10 | Quickstart · 11 | User Guide and Examples · 12 | Interfaces Index · 13 | Developers · 14 | About · 15 | Nipy 16 | -------------------------------------------------------------------------------- /nipype/interfaces/ants/tests/test_auto_ANTSCommand.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..base import ANTSCommand 3 | 4 | 5 | def test_ANTSCommand_inputs(): 6 | input_map = dict( 7 | args=dict( 8 | argstr="%s", 9 | ), 10 | environ=dict( 11 | nohash=True, 12 | usedefault=True, 13 | ), 14 | num_threads=dict( 15 | nohash=True, 16 | usedefault=True, 17 | ), 18 | ) 19 | inputs = ANTSCommand.input_spec() 20 | 21 | for key, metadata in list(input_map.items()): 22 | for metakey, value in list(metadata.items()): 23 | assert getattr(inputs.traits()[key], metakey) == value 24 | -------------------------------------------------------------------------------- /nipype/utils/spm_get_doc.m: -------------------------------------------------------------------------------- 1 | function doc = spm_get_doc(docname) 2 | % Get the documentation from SPM for the functionality named 3 | % docname. 4 | % 5 | % This will search through the spm_config() object and grab the 6 | % documentation whose name matches docname. 7 | cfgstruct = spm_flat_config(0); 8 | [rows, cols] = size(cfgstruct); 9 | docstruct.help={'None'}; 10 | % Loop over cell array and search for the docname 11 | for i = 1:cols 12 | if strcmp(cfgstruct{i}.name, docname) 13 | docstruct = cfgstruct{i}; 14 | break 15 | end 16 | end 17 | % Add a tag so we can strip off the Matlab header information and 18 | % only print out the SPM documentation. 19 | tag = 'NIPYPE\n'; 20 | doc = strcat(tag, docstruct.help{:}); 21 | end 22 | -------------------------------------------------------------------------------- /pyproject.toml: -------------------------------------------------------------------------------- 1 | [build-system] 2 | requires = ["setuptools >= 30.3.0"] 3 | build-backend = "setuptools.build_meta" 4 | 5 | [tool.black] 6 | skip-string-normalization = true 7 | 8 | [tool.pytest.ini_options] 9 | minversion = "6" 10 | testpaths = ["nipype"] 11 | log_cli_level = "INFO" 12 | xfail_strict = true 13 | norecursedirs = [".git"] 14 | addopts = [ 15 | "-svx", 16 | "-ra", 17 | "--strict-config", 18 | "--strict-markers", 19 | "--doctest-modules", 20 | "--cov=nipype", 21 | "--cov-report=xml", 22 | "--cov-config=pyproject.toml", 23 | ] 24 | doctest_optionflags = "ALLOW_UNICODE NORMALIZE_WHITESPACE ELLIPSIS" 25 | env = "PYTHONHASHSEED=0" 26 | filterwarnings = ["ignore::DeprecationWarning"] 27 | junit_family = "xunit2" 28 | -------------------------------------------------------------------------------- /nipype/interfaces/base/tests/test_auto_MpiCommandLine.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..core import MpiCommandLine 3 | 4 | 5 | def test_MpiCommandLine_inputs(): 6 | input_map = dict( 7 | args=dict( 8 | argstr="%s", 9 | ), 10 | environ=dict( 11 | nohash=True, 12 | usedefault=True, 13 | ), 14 | n_procs=dict(), 15 | use_mpi=dict( 16 | usedefault=True, 17 | ), 18 | ) 19 | inputs = MpiCommandLine.input_spec() 20 | 21 | for key, metadata in list(input_map.items()): 22 | for metakey, value in list(metadata.items()): 23 | assert getattr(inputs.traits()[key], metakey) == value 24 | -------------------------------------------------------------------------------- /doc/searchresults.rst: -------------------------------------------------------------------------------- 1 | :orphan: 2 | 3 | .. This displays the search results from the Google Custom Search engine. 4 | Don't link to it directly. 5 | 6 | Search results 7 | ============== 8 | 9 | .. raw:: html 10 | 11 |
Loading 12 | 23 | 24 |
25 | -------------------------------------------------------------------------------- /tools/ci/check.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | echo Running tests 4 | 5 | source tools/ci/activate.sh 6 | source tools/ci/env.sh 7 | 8 | set -eu 9 | 10 | # Required variables 11 | echo CHECK_TYPE = $CHECK_TYPE 12 | 13 | set -x 14 | 15 | if [ "${CHECK_TYPE}" == "test" ]; then 16 | pytest --capture=no --verbose --doctest-modules -c nipype/pytest.ini \ 17 | --cov-config .coveragerc --cov nipype --cov-report xml \ 18 | --junitxml=test-results.xml nipype 19 | elif [ "$CHECK_TYPE" = "specs" ]; then 20 | make specs 21 | git status -s 22 | test -z "$(git status -s)" 23 | elif [ "$CHECK_TYPE" = "style" ]; then 24 | black --check nipype setup.py 25 | else 26 | false 27 | fi 28 | 29 | set +eux 30 | 31 | echo Done running tests 32 | -------------------------------------------------------------------------------- /nipype/interfaces/brainsuite/tests/test_auto_ThicknessPVC.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..brainsuite import ThicknessPVC 3 | 4 | 5 | def test_ThicknessPVC_inputs(): 6 | input_map = dict( 7 | args=dict( 8 | argstr="%s", 9 | ), 10 | environ=dict( 11 | nohash=True, 12 | usedefault=True, 13 | ), 14 | subjectFilePrefix=dict( 15 | argstr="%s", 16 | mandatory=True, 17 | ), 18 | ) 19 | inputs = ThicknessPVC.input_spec() 20 | 21 | for key, metadata in list(input_map.items()): 22 | for metakey, value in list(metadata.items()): 23 | assert getattr(inputs.traits()[key], metakey) == value 24 | -------------------------------------------------------------------------------- /nipype/interfaces/dipy/stats.py: -------------------------------------------------------------------------------- 1 | from looseversion import LooseVersion 2 | from ... import logging 3 | from .base import HAVE_DIPY, dipy_version, dipy_to_nipype_interface, get_dipy_workflows 4 | 5 | IFLOGGER = logging.getLogger("nipype.interface") 6 | 7 | if HAVE_DIPY and LooseVersion(dipy_version()) >= LooseVersion("0.16"): 8 | from dipy.workflows import stats 9 | 10 | l_wkflw = get_dipy_workflows(stats) 11 | for name, obj in l_wkflw: 12 | new_name = name.replace("Flow", "") 13 | globals()[new_name] = dipy_to_nipype_interface(new_name, obj) 14 | del l_wkflw 15 | 16 | else: 17 | IFLOGGER.info( 18 | "We advise you to upgrade DIPY version. This upgrade will" 19 | " open access to more function" 20 | ) 21 | -------------------------------------------------------------------------------- /tools/ci/build_archive.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | echo "Building archive" 4 | 5 | source tools/ci/activate.sh 6 | 7 | set -eu 8 | 9 | # Required dependencies 10 | echo "INSTALL_TYPE = $INSTALL_TYPE" 11 | 12 | set -x 13 | 14 | if [ "$INSTALL_TYPE" == "sdist" ]; then 15 | python setup.py egg_info # check egg_info while we're here 16 | python setup.py sdist 17 | export ARCHIVE=$( ls dist/*.tar.gz ) 18 | elif [ "$INSTALL_TYPE" == "wheel" ]; then 19 | python setup.py bdist_wheel 20 | export ARCHIVE=$( ls dist/*.whl ) 21 | elif [ "$INSTALL_TYPE" == "archive" ]; then 22 | export ARCHIVE="package.tar.gz" 23 | git archive -o $ARCHIVE HEAD 24 | elif [ "$INSTALL_TYPE" == "pip" ]; then 25 | export ARCHIVE="." 26 | fi 27 | 28 | set +eux 29 | -------------------------------------------------------------------------------- /nipype/interfaces/niftyreg/tests/test_auto_NiftyRegCommand.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..base import NiftyRegCommand 3 | 4 | 5 | def test_NiftyRegCommand_inputs(): 6 | input_map = dict( 7 | args=dict( 8 | argstr="%s", 9 | ), 10 | environ=dict( 11 | nohash=True, 12 | usedefault=True, 13 | ), 14 | omp_core_val=dict( 15 | argstr="-omp %i", 16 | usedefault=True, 17 | ), 18 | ) 19 | inputs = NiftyRegCommand.input_spec() 20 | 21 | for key, metadata in list(input_map.items()): 22 | for metakey, value in list(metadata.items()): 23 | assert getattr(inputs.traits()[key], metakey) == value 24 | -------------------------------------------------------------------------------- /nipype/refs.py: -------------------------------------------------------------------------------- 1 | # Use duecredit (duecredit.org) to provide a citation to relevant work to 2 | # be cited. This does nothing, unless the user has duecredit installed, 3 | # And calls this with duecredit (as in `python -m duecredit script.py`): 4 | from .external.due import due, Doi 5 | 6 | due.cite( 7 | Doi("10.3389/fninf.2011.00013"), 8 | description="A flexible, lightweight and extensible neuroimaging data" 9 | " processing framework in Python", 10 | path="nipype", 11 | tags=["implementation"], 12 | ) 13 | 14 | due.cite( 15 | Doi("10.5281/zenodo.50186"), 16 | description="A flexible, lightweight and extensible neuroimaging data" 17 | " processing framework in Python", 18 | path="nipype", 19 | tags=["implementation"], 20 | ) 21 | -------------------------------------------------------------------------------- /nipype/interfaces/dipy/registration.py: -------------------------------------------------------------------------------- 1 | from looseversion import LooseVersion 2 | from ... import logging 3 | from .base import HAVE_DIPY, dipy_version, dipy_to_nipype_interface, get_dipy_workflows 4 | 5 | IFLOGGER = logging.getLogger("nipype.interface") 6 | 7 | 8 | if HAVE_DIPY and LooseVersion(dipy_version()) >= LooseVersion("0.15"): 9 | from dipy.workflows import align 10 | 11 | l_wkflw = get_dipy_workflows(align) 12 | for name, obj in l_wkflw: 13 | new_name = name.replace("Flow", "") 14 | globals()[new_name] = dipy_to_nipype_interface(new_name, obj) 15 | del l_wkflw 16 | 17 | else: 18 | IFLOGGER.info( 19 | "We advise you to upgrade DIPY version. This upgrade will" 20 | " open access to more function" 21 | ) 22 | -------------------------------------------------------------------------------- /nipype/interfaces/fsl/model_templates/feat_nongui.tcl: -------------------------------------------------------------------------------- 1 | ########################################################## 2 | # Now options that don't appear in the GUI 3 | 4 | # Alternative example_func image (not derived from input 4D dataset) 5 | set fmri(alternative_example_func) "" 6 | 7 | # Alternative (to BETting) mask image 8 | set fmri(alternative_mask) "" 9 | 10 | # Initial structural space registration initialisation transform 11 | set fmri(init_initial_highres) "" 12 | 13 | # Structural space registration initialisation transform 14 | set fmri(init_highres) "" 15 | 16 | # Standard space registration initialisation transform 17 | set fmri(init_standard) "" 18 | 19 | # For full FEAT analysis: overwrite existing .feat output dir? 20 | set fmri(overwrite_yn) $overwrite 21 | -------------------------------------------------------------------------------- /nipype/interfaces/utility/tests/test_auto_IdentityInterface.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..base import IdentityInterface 3 | 4 | 5 | def test_IdentityInterface_inputs(): 6 | input_map = dict() 7 | inputs = IdentityInterface.input_spec() 8 | 9 | for key, metadata in list(input_map.items()): 10 | for metakey, value in list(metadata.items()): 11 | assert getattr(inputs.traits()[key], metakey) == value 12 | 13 | 14 | def test_IdentityInterface_outputs(): 15 | output_map = dict() 16 | outputs = IdentityInterface.output_spec() 17 | 18 | for key, metadata in list(output_map.items()): 19 | for metakey, value in list(metadata.items()): 20 | assert getattr(outputs.traits()[key], metakey) == value 21 | -------------------------------------------------------------------------------- /nipype/algorithms/tests/test_icc_anova.py: -------------------------------------------------------------------------------- 1 | import numpy as np 2 | from nipype.algorithms.icc import ICC_rep_anova 3 | 4 | 5 | def test_ICC_rep_anova(): 6 | # see table 2 in P. E. Shrout & Joseph L. Fleiss (1979). "Intraclass 7 | # Correlations: Uses in Assessing Rater Reliability". Psychological 8 | # Bulletin 86 (2): 420-428 9 | Y = np.array( 10 | [ 11 | [9, 2, 5, 8], 12 | [6, 1, 3, 2], 13 | [8, 4, 6, 8], 14 | [7, 1, 2, 6], 15 | [10, 5, 6, 9], 16 | [6, 2, 4, 7], 17 | ] 18 | ) 19 | 20 | icc, r_var, e_var, _, dfc, dfe = ICC_rep_anova(Y) 21 | # see table 4 22 | assert round(icc, 2) == 0.71 23 | assert dfc == 3 24 | assert dfe == 15 25 | assert np.isclose(r_var / (r_var + e_var), icc) 26 | -------------------------------------------------------------------------------- /nipype/interfaces/slicer/__init__.py: -------------------------------------------------------------------------------- 1 | """ 2 | 3D Slicer is a platform for medical image informatics processing and visualization. 3 | 4 | For an EXPERIMENTAL implementation of an interface for the ``3dSlicer`` full framework, 5 | please check `"dynamic" Slicer `__. 6 | """ 7 | 8 | from .diffusion import * 9 | from .segmentation import * 10 | from .filtering import * 11 | from .utilities import EMSegmentTransformToNewFormat 12 | from .surface import ( 13 | MergeModels, 14 | ModelToLabelMap, 15 | GrayscaleModelMaker, 16 | ProbeVolumeWithModel, 17 | LabelMapSmoothing, 18 | ModelMaker, 19 | ) 20 | from .quantification import * 21 | from .legacy import * 22 | from .registration import * 23 | from .converters import DicomToNrrdConverter, OrientScalarVolume 24 | -------------------------------------------------------------------------------- /nipype/interfaces/base/tests/test_auto_StdOutCommandLine.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..core import StdOutCommandLine 3 | 4 | 5 | def test_StdOutCommandLine_inputs(): 6 | input_map = dict( 7 | args=dict( 8 | argstr="%s", 9 | ), 10 | environ=dict( 11 | nohash=True, 12 | usedefault=True, 13 | ), 14 | out_file=dict( 15 | argstr="> %s", 16 | extensions=None, 17 | genfile=True, 18 | position=-1, 19 | ), 20 | ) 21 | inputs = StdOutCommandLine.input_spec() 22 | 23 | for key, metadata in list(input_map.items()): 24 | for metakey, value in list(metadata.items()): 25 | assert getattr(inputs.traits()[key], metakey) == value 26 | -------------------------------------------------------------------------------- /nipype/interfaces/mipav/__init__.py: -------------------------------------------------------------------------------- 1 | """MIPAV enables quantitative analysis and visualization of multimodal medical images.""" 2 | 3 | from .developer import ( 4 | JistLaminarVolumetricLayering, 5 | JistBrainMgdmSegmentation, 6 | JistLaminarProfileGeometry, 7 | JistLaminarProfileCalculator, 8 | MedicAlgorithmN3, 9 | JistLaminarROIAveraging, 10 | MedicAlgorithmLesionToads, 11 | JistBrainMp2rageSkullStripping, 12 | JistCortexSurfaceMeshInflation, 13 | RandomVol, 14 | MedicAlgorithmImageCalculator, 15 | JistBrainMp2rageDuraEstimation, 16 | JistLaminarProfileSampling, 17 | MedicAlgorithmMipavReorient, 18 | MedicAlgorithmSPECTRE2010, 19 | JistBrainPartialVolumeFilter, 20 | JistIntensityMp2rageMasking, 21 | MedicAlgorithmThresholdToBinaryMask, 22 | ) 23 | -------------------------------------------------------------------------------- /nipype/pipeline/plugins/__init__.py: -------------------------------------------------------------------------------- 1 | # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- 2 | # vi: set ft=python sts=4 ts=4 sw=4 et: 3 | 4 | from .debug import DebugPlugin 5 | from .linear import LinearPlugin 6 | from .pbs import PBSPlugin 7 | from .oar import OARPlugin 8 | from .sge import SGEPlugin 9 | from .condor import CondorPlugin 10 | from .dagman import CondorDAGManPlugin 11 | from .multiproc import MultiProcPlugin 12 | from .legacymultiproc import LegacyMultiProcPlugin 13 | from .ipython import IPythonPlugin 14 | from .somaflow import SomaFlowPlugin 15 | from .pbsgraph import PBSGraphPlugin 16 | from .sgegraph import SGEGraphPlugin 17 | from .lsf import LSFPlugin 18 | from .slurm import SLURMPlugin 19 | from .slurmgraph import SLURMGraphPlugin 20 | 21 | from . import semaphore_singleton 22 | -------------------------------------------------------------------------------- /nipype/interfaces/fsl/model_templates/feat_ev_none.tcl: -------------------------------------------------------------------------------- 1 | # EV title 2 | set fmri(evtitle$ev_num) "$ev_name" 3 | 4 | # Basic waveform shape 5 | # 0 : Square 6 | # 1 : Sinusoid 7 | # 2 : Custom (1 entry per volume) 8 | # 3 : Custom (3 column format) 9 | # 4 : Interaction 10 | # 10 : Empty (all zeros) 11 | set fmri(shape$ev_num) 2 12 | 13 | # Convolution 14 | # 0 : None 15 | # 1 : Gaussian 16 | # 2 : Gamma 17 | # 3 : Double-Gamma HRF 18 | # 4 : Gamma basis functions 19 | # 5 : Sine basis functions 20 | # 6 : FIR basis functions 21 | # 7 : Optimal/custom basis functions 22 | set fmri(convolve$ev_num) 0 23 | 24 | # Apply temporal filtering 25 | set fmri(tempfilt_yn$ev_num) $tempfilt_yn 26 | 27 | # Add temporal derivative 28 | set fmri(deriv_yn$ev_num) 0 29 | 30 | # Custom EV file 31 | set fmri(custom$ev_num) "$cond_file" 32 | -------------------------------------------------------------------------------- /tools/retry_cmd.sh: -------------------------------------------------------------------------------- 1 | #!/bin/sh 2 | # 3 | # retry_cmd.sh [-n NLOOPS] [-s SLEEP] CMD 4 | # 5 | # Retry command until success or pre-specified number of failures 6 | # 7 | # 2018 Chris Markiewicz 8 | # Released into public domain 9 | 10 | NLOOPS=3 11 | TOSLEEP=5 12 | 13 | while true; do 14 | case "$1" in 15 | -n ) NLOOPS="$2"; shift 2 ;; 16 | -s ) TOSLEEP="$2"; shift 2 ;; 17 | -- ) shift; break ;; 18 | * ) break ;; 19 | esac 20 | done 21 | 22 | # Normalize whitespace in command, preserving quotes 23 | CMD="" 24 | for ARG; do 25 | CMD="$CMD \"$ARG\""; 26 | done 27 | 28 | RET=0 29 | for i in `seq $NLOOPS`; do 30 | sh -c "$CMD" 31 | RET="$?" 32 | if [ "$RET" -eq 0 ]; then break; fi 33 | if [ "$i" -ne "$NLOOPS" ]; then sleep $TOSLEEP; fi 34 | done 35 | 36 | exit $RET 37 | -------------------------------------------------------------------------------- /nipype/interfaces/utility/tests/test_auto_Function.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..wrappers import Function 3 | 4 | 5 | def test_Function_inputs(): 6 | input_map = dict( 7 | function_str=dict( 8 | mandatory=True, 9 | ), 10 | ) 11 | inputs = Function.input_spec() 12 | 13 | for key, metadata in list(input_map.items()): 14 | for metakey, value in list(metadata.items()): 15 | assert getattr(inputs.traits()[key], metakey) == value 16 | 17 | 18 | def test_Function_outputs(): 19 | output_map = dict() 20 | outputs = Function.output_spec() 21 | 22 | for key, metadata in list(output_map.items()): 23 | for metakey, value in list(metadata.items()): 24 | assert getattr(outputs.traits()[key], metakey) == value 25 | -------------------------------------------------------------------------------- /.github/PULL_REQUEST_TEMPLATE.md: -------------------------------------------------------------------------------- 1 | 12 | ## Summary 13 | 15 | 16 | Fixes # . 17 | 18 | ## List of changes proposed in this PR (pull-request) 19 | 20 | -------------------------------------------------------------------------------- /nipype/interfaces/cmtk/base.py: -------------------------------------------------------------------------------- 1 | # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- 2 | # vi: set ft=python sts=4 ts=4 sw=4 et: 3 | """Base interface for cmtk""" 4 | 5 | from ..base import LibraryBaseInterface 6 | from ...utils.misc import package_check 7 | 8 | 9 | class CFFBaseInterface(LibraryBaseInterface): 10 | _pkg = "cfflib" 11 | 12 | 13 | # Originally set in convert, nbs, nx, parcellation 14 | # Set here to be imported, in case anybody depends on its presence 15 | # Remove in 2.0 16 | have_cmp = True 17 | try: 18 | package_check("cmp") 19 | except ImportError: 20 | have_cmp = False 21 | 22 | have_cfflib = True 23 | try: 24 | package_check("cfflib") 25 | except ImportError: 26 | have_cfflib = False 27 | 28 | have_cv = True 29 | try: 30 | package_check("cviewer") 31 | except ImportError: 32 | have_cv = False 33 | -------------------------------------------------------------------------------- /tools/ci/install.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | echo Installing nipype 4 | 5 | source tools/ci/activate.sh 6 | source tools/ci/env.sh 7 | 8 | set -eu 9 | 10 | # Required variables 11 | echo INSTALL_TYPE = $INSTALL_TYPE 12 | echo CHECK_TYPE = $CHECK_TYPE 13 | echo NIPYPE_EXTRAS = $NIPYPE_EXTRAS 14 | echo EXTRA_PIP_FLAGS = $EXTRA_PIP_FLAGS 15 | 16 | set -x 17 | 18 | if [ -n "$EXTRA_PIP_FLAGS" ]; then 19 | EXTRA_PIP_FLAGS=${!EXTRA_PIP_FLAGS} 20 | fi 21 | 22 | if [ "$INSTALL_TYPE" == "setup" ]; then 23 | python setup.py install 24 | else 25 | pip install $EXTRA_PIP_FLAGS $ARCHIVE 26 | fi 27 | 28 | # Basic import check 29 | python -c 'import nipype; print(nipype.__version__)' 30 | 31 | if [ "$CHECK_TYPE" == "skiptests" ]; then 32 | exit 0 33 | fi 34 | 35 | pip install $EXTRA_PIP_FLAGS "nipype[$NIPYPE_EXTRAS]" 36 | 37 | set +eux 38 | 39 | echo Done installing nipype 40 | -------------------------------------------------------------------------------- /nipype/interfaces/ants/tests/test_extra_Registration.py: -------------------------------------------------------------------------------- 1 | # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- 2 | # vi: set ft=python sts=4 ts=4 sw=4 et: 3 | from nipype.interfaces.ants import registration 4 | import os 5 | import pytest 6 | 7 | 8 | def test_ants_mand(tmpdir): 9 | tmpdir.chdir() 10 | filepath = os.path.dirname(os.path.realpath(__file__)) 11 | datadir = os.path.realpath(os.path.join(filepath, "../../../testing/data")) 12 | 13 | ants = registration.ANTS() 14 | ants.inputs.transformation_model = "SyN" 15 | ants.inputs.moving_image = [os.path.join(datadir, "resting.nii")] 16 | ants.inputs.fixed_image = [os.path.join(datadir, "T1.nii")] 17 | ants.inputs.metric = ["MI"] 18 | 19 | with pytest.raises(ValueError) as er: 20 | ants.run() 21 | assert "ANTS requires a value for input 'radius'" in str(er.value) 22 | -------------------------------------------------------------------------------- /nipype/interfaces/tests/test_auto_JSONFileGrabber.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..io import JSONFileGrabber 3 | 4 | 5 | def test_JSONFileGrabber_inputs(): 6 | input_map = dict( 7 | defaults=dict(), 8 | in_file=dict( 9 | extensions=None, 10 | ), 11 | ) 12 | inputs = JSONFileGrabber.input_spec() 13 | 14 | for key, metadata in list(input_map.items()): 15 | for metakey, value in list(metadata.items()): 16 | assert getattr(inputs.traits()[key], metakey) == value 17 | 18 | 19 | def test_JSONFileGrabber_outputs(): 20 | output_map = dict() 21 | outputs = JSONFileGrabber.output_spec() 22 | 23 | for key, metadata in list(output_map.items()): 24 | for metakey, value in list(metadata.items()): 25 | assert getattr(outputs.traits()[key], metakey) == value 26 | -------------------------------------------------------------------------------- /.readthedocs.yml: -------------------------------------------------------------------------------- 1 | # Read the Docs configuration file 2 | # See https://docs.readthedocs.io/en/stable/config-file/v2.html for details 3 | 4 | # Required 5 | version: 2 6 | 7 | # Set the OS, Python version and other tools you might need 8 | build: 9 | os: ubuntu-22.04 10 | tools: 11 | python: "3.10" 12 | 13 | # Build documentation in the docs/ directory with Sphinx 14 | sphinx: 15 | configuration: doc/conf.py 16 | 17 | # Optionally build your docs in additional formats such as PDF and ePub 18 | formats: 19 | - htmlzip 20 | 21 | # Optional but recommended, declare the Python requirements required 22 | # to build your documentation 23 | # See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html 24 | python: 25 | install: 26 | - requirements: doc/requirements.txt 27 | - method: pip 28 | path: . 29 | extra_requirements: 30 | - doc 31 | -------------------------------------------------------------------------------- /nipype/interfaces/utility/tests/test_auto_Select.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..base import Select 3 | 4 | 5 | def test_Select_inputs(): 6 | input_map = dict( 7 | index=dict( 8 | mandatory=True, 9 | ), 10 | inlist=dict( 11 | mandatory=True, 12 | ), 13 | ) 14 | inputs = Select.input_spec() 15 | 16 | for key, metadata in list(input_map.items()): 17 | for metakey, value in list(metadata.items()): 18 | assert getattr(inputs.traits()[key], metakey) == value 19 | 20 | 21 | def test_Select_outputs(): 22 | output_map = dict( 23 | out=dict(), 24 | ) 25 | outputs = Select.output_spec() 26 | 27 | for key, metadata in list(output_map.items()): 28 | for metakey, value in list(metadata.items()): 29 | assert getattr(outputs.traits()[key], metakey) == value 30 | -------------------------------------------------------------------------------- /nipype/interfaces/dipy/tests/test_auto_DipyDiffusionInterface.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..base import DipyDiffusionInterface 3 | 4 | 5 | def test_DipyDiffusionInterface_inputs(): 6 | input_map = dict( 7 | b0_thres=dict( 8 | usedefault=True, 9 | ), 10 | in_bval=dict( 11 | extensions=None, 12 | mandatory=True, 13 | ), 14 | in_bvec=dict( 15 | extensions=None, 16 | mandatory=True, 17 | ), 18 | in_file=dict( 19 | extensions=None, 20 | mandatory=True, 21 | ), 22 | out_prefix=dict(), 23 | ) 24 | inputs = DipyDiffusionInterface.input_spec() 25 | 26 | for key, metadata in list(input_map.items()): 27 | for metakey, value in list(metadata.items()): 28 | assert getattr(inputs.traits()[key], metakey) == value 29 | -------------------------------------------------------------------------------- /nipype/interfaces/tests/test_auto_RCommand.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..r import RCommand 3 | 4 | 5 | def test_RCommand_inputs(): 6 | input_map = dict( 7 | args=dict( 8 | argstr="%s", 9 | ), 10 | environ=dict( 11 | nohash=True, 12 | usedefault=True, 13 | ), 14 | rfile=dict( 15 | usedefault=True, 16 | ), 17 | script=dict( 18 | argstr='-e "%s"', 19 | mandatory=True, 20 | position=-1, 21 | ), 22 | script_file=dict( 23 | extensions=None, 24 | usedefault=True, 25 | ), 26 | ) 27 | inputs = RCommand.input_spec() 28 | 29 | for key, metadata in list(input_map.items()): 30 | for metakey, value in list(metadata.items()): 31 | assert getattr(inputs.traits()[key], metakey) == value 32 | -------------------------------------------------------------------------------- /nipype/interfaces/tests/test_auto_LookupMeta.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..dcmstack import LookupMeta 3 | 4 | 5 | def test_LookupMeta_inputs(): 6 | input_map = dict( 7 | in_file=dict( 8 | extensions=None, 9 | mandatory=True, 10 | ), 11 | meta_keys=dict( 12 | mandatory=True, 13 | ), 14 | ) 15 | inputs = LookupMeta.input_spec() 16 | 17 | for key, metadata in list(input_map.items()): 18 | for metakey, value in list(metadata.items()): 19 | assert getattr(inputs.traits()[key], metakey) == value 20 | 21 | 22 | def test_LookupMeta_outputs(): 23 | output_map = dict() 24 | outputs = LookupMeta.output_spec() 25 | 26 | for key, metadata in list(output_map.items()): 27 | for metakey, value in list(metadata.items()): 28 | assert getattr(outputs.traits()[key], metakey) == value 29 | -------------------------------------------------------------------------------- /nipype/interfaces/utility/tests/test_auto_Split.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..base import Split 3 | 4 | 5 | def test_Split_inputs(): 6 | input_map = dict( 7 | inlist=dict( 8 | mandatory=True, 9 | ), 10 | splits=dict( 11 | mandatory=True, 12 | ), 13 | squeeze=dict( 14 | usedefault=True, 15 | ), 16 | ) 17 | inputs = Split.input_spec() 18 | 19 | for key, metadata in list(input_map.items()): 20 | for metakey, value in list(metadata.items()): 21 | assert getattr(inputs.traits()[key], metakey) == value 22 | 23 | 24 | def test_Split_outputs(): 25 | output_map = dict() 26 | outputs = Split.output_spec() 27 | 28 | for key, metadata in list(output_map.items()): 29 | for metakey, value in list(metadata.items()): 30 | assert getattr(outputs.traits()[key], metakey) == value 31 | -------------------------------------------------------------------------------- /nipype/interfaces/afni/tests/test_auto_AFNICommand.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..base import AFNICommand 3 | 4 | 5 | def test_AFNICommand_inputs(): 6 | input_map = dict( 7 | args=dict( 8 | argstr="%s", 9 | ), 10 | environ=dict( 11 | nohash=True, 12 | usedefault=True, 13 | ), 14 | num_threads=dict( 15 | nohash=True, 16 | usedefault=True, 17 | ), 18 | out_file=dict( 19 | argstr="-prefix %s", 20 | extensions=None, 21 | name_source=["in_file"], 22 | name_template="%s_afni", 23 | ), 24 | outputtype=dict(), 25 | ) 26 | inputs = AFNICommand.input_spec() 27 | 28 | for key, metadata in list(input_map.items()): 29 | for metakey, value in list(metadata.items()): 30 | assert getattr(inputs.traits()[key], metakey) == value 31 | -------------------------------------------------------------------------------- /nipype/algorithms/tests/test_auto_CalculateMedian.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..misc import CalculateMedian 3 | 4 | 5 | def test_CalculateMedian_inputs(): 6 | input_map = dict( 7 | in_files=dict(), 8 | median_file=dict(), 9 | median_per_file=dict( 10 | usedefault=True, 11 | ), 12 | ) 13 | inputs = CalculateMedian.input_spec() 14 | 15 | for key, metadata in list(input_map.items()): 16 | for metakey, value in list(metadata.items()): 17 | assert getattr(inputs.traits()[key], metakey) == value 18 | 19 | 20 | def test_CalculateMedian_outputs(): 21 | output_map = dict( 22 | median_files=dict(), 23 | ) 24 | outputs = CalculateMedian.output_spec() 25 | 26 | for key, metadata in list(output_map.items()): 27 | for metakey, value in list(metadata.items()): 28 | assert getattr(outputs.traits()[key], metakey) == value 29 | -------------------------------------------------------------------------------- /tools/install_spm_mcr.sh: -------------------------------------------------------------------------------- 1 | if [ ! -d $HOME/mcr ] 2 | then 3 | echo "destinationFolder=$HOME/mcr" > $HOME/mcr_options.txt 4 | echo "agreeToLicense=yes" >> $HOME/mcr_options.txt 5 | echo "outputFile=/tmp/matlabinstall_log" >> $HOME/mcr_options.txt 6 | echo "mode=silent" >> $HOME/mcr_options.txt 7 | mkdir -p $HOME/matlab_installer 8 | wget -nc http://www.mathworks.com/supportfiles/downloads/R2015a/deployment_files/R2015a/installers/glnxa64/MCR_R2015a_glnxa64_installer.zip -O $HOME/matlab_installer/installer.zip 9 | unzip $HOME/matlab_installer/installer.zip -d $HOME/matlab_installer/ 10 | $HOME/matlab_installer/install -inputFile $HOME/mcr_options.txt 11 | rm -rf $HOME/matlab_installer $HOME/mcr_options.txt 12 | fi 13 | 14 | if [ ! -d $HOME/spm12 ] 15 | then 16 | wget http://www.fil.ion.ucl.ac.uk/spm/download/restricted/utopia/dev/spm12_r6472_Linux_R2015a.zip -O $HOME/spm12.zip 17 | unzip $HOME/spm12.zip -d $HOME 18 | rm -rf $HOME/spm12.zip 19 | fi 20 | -------------------------------------------------------------------------------- /nipype/algorithms/tests/test_auto_MergeROIs.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..misc import MergeROIs 3 | 4 | 5 | def test_MergeROIs_inputs(): 6 | input_map = dict( 7 | in_files=dict(), 8 | in_index=dict(), 9 | in_reference=dict( 10 | extensions=None, 11 | ), 12 | ) 13 | inputs = MergeROIs.input_spec() 14 | 15 | for key, metadata in list(input_map.items()): 16 | for metakey, value in list(metadata.items()): 17 | assert getattr(inputs.traits()[key], metakey) == value 18 | 19 | 20 | def test_MergeROIs_outputs(): 21 | output_map = dict( 22 | merged_file=dict( 23 | extensions=None, 24 | ), 25 | ) 26 | outputs = MergeROIs.output_spec() 27 | 28 | for key, metadata in list(output_map.items()): 29 | for metakey, value in list(metadata.items()): 30 | assert getattr(outputs.traits()[key], metakey) == value 31 | -------------------------------------------------------------------------------- /nipype/interfaces/fsl/model_templates/feat_ev_hrf.tcl: -------------------------------------------------------------------------------- 1 | # EV title 2 | set fmri(evtitle$ev_num) "$ev_name" 3 | 4 | # Basic waveform shape (EV $ev_num) 5 | # 0 : Square 6 | # 1 : Sinusoid 7 | # 2 : Custom (1 entry per volume) 8 | # 3 : Custom (3 column format) 9 | # 4 : Interaction 10 | # 10 : Empty (all zeros) 11 | set fmri(shape$ev_num) 3 12 | 13 | # Convolution (EV $ev_num) 14 | # 0 : None 15 | # 1 : Gaussian 16 | # 2 : Gamma 17 | # 3 : Double-Gamma HRF 18 | # 4 : Gamma basis functions 19 | # 5 : Sine basis functions 20 | # 6 : FIR basis functions 21 | # 7 : Optimal/custom basis functions 22 | set fmri(convolve$ev_num) 3 23 | 24 | # Convolve phase (EV $ev_num) 25 | set fmri(convolve_phase$ev_num) 0 26 | 27 | # Apply temporal filtering (EV $ev_num) 28 | set fmri(tempfilt_yn$ev_num) $tempfilt_yn 29 | 30 | # Add temporal derivative (EV $ev_num) 31 | set fmri(deriv_yn$ev_num) $temporalderiv 32 | 33 | # Custom EV file (EV $ev_num) 34 | set fmri(custom$ev_num) "$cond_file" 35 | -------------------------------------------------------------------------------- /nipype/algorithms/tests/test_auto_ModifyAffine.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..misc import ModifyAffine 3 | 4 | 5 | def test_ModifyAffine_inputs(): 6 | input_map = dict( 7 | transformation_matrix=dict( 8 | usedefault=True, 9 | ), 10 | volumes=dict( 11 | mandatory=True, 12 | ), 13 | ) 14 | inputs = ModifyAffine.input_spec() 15 | 16 | for key, metadata in list(input_map.items()): 17 | for metakey, value in list(metadata.items()): 18 | assert getattr(inputs.traits()[key], metakey) == value 19 | 20 | 21 | def test_ModifyAffine_outputs(): 22 | output_map = dict( 23 | transformed_volumes=dict(), 24 | ) 25 | outputs = ModifyAffine.output_spec() 26 | 27 | for key, metadata in list(output_map.items()): 28 | for metakey, value in list(metadata.items()): 29 | assert getattr(outputs.traits()[key], metakey) == value 30 | -------------------------------------------------------------------------------- /nipype/interfaces/elastix/base.py: -------------------------------------------------------------------------------- 1 | # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- 2 | # vi: set ft=python sts=4 ts=4 sw=4 et: 3 | """The :py:mod:`nipype.interfaces.elastix` provides the interface to 4 | the elastix registration software. 5 | 6 | .. note:: http://elastix.isi.uu.nl/ 7 | 8 | 9 | """ 10 | 11 | from ... import logging 12 | from ..base import CommandLineInputSpec, Directory, traits 13 | 14 | iflogger = logging.getLogger("nipype.interface") 15 | 16 | 17 | class ElastixBaseInputSpec(CommandLineInputSpec): 18 | output_path = Directory( 19 | "./", 20 | exists=True, 21 | mandatory=True, 22 | usedefault=True, 23 | argstr="-out %s", 24 | desc="output directory", 25 | ) 26 | num_threads = traits.Int( 27 | 1, 28 | usedefault=True, 29 | argstr="-threads %01d", 30 | nohash=True, 31 | desc="set the maximum number of threads of elastix", 32 | ) 33 | -------------------------------------------------------------------------------- /nipype/interfaces/slicer/filtering/__init__.py: -------------------------------------------------------------------------------- 1 | from .morphology import GrayscaleGrindPeakImageFilter, GrayscaleFillHoleImageFilter 2 | from .denoising import ( 3 | GradientAnisotropicDiffusion, 4 | CurvatureAnisotropicDiffusion, 5 | GaussianBlurImageFilter, 6 | MedianImageFilter, 7 | ) 8 | from .arithmetic import ( 9 | MultiplyScalarVolumes, 10 | MaskScalarVolume, 11 | SubtractScalarVolumes, 12 | AddScalarVolumes, 13 | CastScalarVolume, 14 | ) 15 | from .extractskeleton import ExtractSkeleton 16 | from .histogrammatching import HistogramMatching 17 | from .thresholdscalarvolume import ThresholdScalarVolume 18 | from .n4itkbiasfieldcorrection import N4ITKBiasFieldCorrection 19 | from .checkerboardfilter import CheckerBoardFilter 20 | from .imagelabelcombine import ImageLabelCombine 21 | from .votingbinaryholefillingimagefilter import VotingBinaryHoleFillingImageFilter 22 | from .resamplescalarvectordwivolume import ResampleScalarVectorDWIVolume 23 | -------------------------------------------------------------------------------- /nipype/interfaces/tests/test_auto_MySQLSink.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..io import MySQLSink 3 | 4 | 5 | def test_MySQLSink_inputs(): 6 | input_map = dict( 7 | config=dict( 8 | extensions=None, 9 | mandatory=True, 10 | xor=["host"], 11 | ), 12 | database_name=dict( 13 | mandatory=True, 14 | ), 15 | host=dict( 16 | mandatory=True, 17 | requires=["username", "password"], 18 | usedefault=True, 19 | xor=["config"], 20 | ), 21 | password=dict(), 22 | table_name=dict( 23 | mandatory=True, 24 | ), 25 | username=dict(), 26 | ) 27 | inputs = MySQLSink.input_spec() 28 | 29 | for key, metadata in list(input_map.items()): 30 | for metakey, value in list(metadata.items()): 31 | assert getattr(inputs.traits()[key], metakey) == value 32 | -------------------------------------------------------------------------------- /nipype/algorithms/tests/test_auto_Gzip.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..misc import Gzip 3 | 4 | 5 | def test_Gzip_inputs(): 6 | input_map = dict( 7 | in_file=dict( 8 | extensions=None, 9 | mandatory=True, 10 | ), 11 | mode=dict( 12 | usedefault=True, 13 | ), 14 | ) 15 | inputs = Gzip.input_spec() 16 | 17 | for key, metadata in list(input_map.items()): 18 | for metakey, value in list(metadata.items()): 19 | assert getattr(inputs.traits()[key], metakey) == value 20 | 21 | 22 | def test_Gzip_outputs(): 23 | output_map = dict( 24 | out_file=dict( 25 | extensions=None, 26 | ), 27 | ) 28 | outputs = Gzip.output_spec() 29 | 30 | for key, metadata in list(output_map.items()): 31 | for metakey, value in list(metadata.items()): 32 | assert getattr(outputs.traits()[key], metakey) == value 33 | -------------------------------------------------------------------------------- /nipype/algorithms/tests/test_auto_Matlab2CSV.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..misc import Matlab2CSV 3 | 4 | 5 | def test_Matlab2CSV_inputs(): 6 | input_map = dict( 7 | in_file=dict( 8 | extensions=None, 9 | mandatory=True, 10 | ), 11 | reshape_matrix=dict( 12 | usedefault=True, 13 | ), 14 | ) 15 | inputs = Matlab2CSV.input_spec() 16 | 17 | for key, metadata in list(input_map.items()): 18 | for metakey, value in list(metadata.items()): 19 | assert getattr(inputs.traits()[key], metakey) == value 20 | 21 | 22 | def test_Matlab2CSV_outputs(): 23 | output_map = dict( 24 | csv_files=dict(), 25 | ) 26 | outputs = Matlab2CSV.output_spec() 27 | 28 | for key, metadata in list(output_map.items()): 29 | for metakey, value in list(metadata.items()): 30 | assert getattr(outputs.traits()[key], metakey) == value 31 | -------------------------------------------------------------------------------- /nipype/algorithms/tests/test_auto_SimpleThreshold.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..misc import SimpleThreshold 3 | 4 | 5 | def test_SimpleThreshold_inputs(): 6 | input_map = dict( 7 | threshold=dict( 8 | mandatory=True, 9 | ), 10 | volumes=dict( 11 | mandatory=True, 12 | ), 13 | ) 14 | inputs = SimpleThreshold.input_spec() 15 | 16 | for key, metadata in list(input_map.items()): 17 | for metakey, value in list(metadata.items()): 18 | assert getattr(inputs.traits()[key], metakey) == value 19 | 20 | 21 | def test_SimpleThreshold_outputs(): 22 | output_map = dict( 23 | thresholded_volumes=dict(), 24 | ) 25 | outputs = SimpleThreshold.output_spec() 26 | 27 | for key, metadata in list(output_map.items()): 28 | for metakey, value in list(metadata.items()): 29 | assert getattr(outputs.traits()[key], metakey) == value 30 | -------------------------------------------------------------------------------- /nipype/algorithms/tests/test_auto_NonSteadyStateDetector.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..confounds import NonSteadyStateDetector 3 | 4 | 5 | def test_NonSteadyStateDetector_inputs(): 6 | input_map = dict( 7 | in_file=dict( 8 | extensions=None, 9 | mandatory=True, 10 | ), 11 | ) 12 | inputs = NonSteadyStateDetector.input_spec() 13 | 14 | for key, metadata in list(input_map.items()): 15 | for metakey, value in list(metadata.items()): 16 | assert getattr(inputs.traits()[key], metakey) == value 17 | 18 | 19 | def test_NonSteadyStateDetector_outputs(): 20 | output_map = dict( 21 | n_volumes_to_discard=dict(), 22 | ) 23 | outputs = NonSteadyStateDetector.output_spec() 24 | 25 | for key, metadata in list(output_map.items()): 26 | for metakey, value in list(metadata.items()): 27 | assert getattr(outputs.traits()[key], metakey) == value 28 | -------------------------------------------------------------------------------- /nipype/interfaces/afni/tests/test_auto_AFNIPythonCommand.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..base import AFNIPythonCommand 3 | 4 | 5 | def test_AFNIPythonCommand_inputs(): 6 | input_map = dict( 7 | args=dict( 8 | argstr="%s", 9 | ), 10 | environ=dict( 11 | nohash=True, 12 | usedefault=True, 13 | ), 14 | num_threads=dict( 15 | nohash=True, 16 | usedefault=True, 17 | ), 18 | out_file=dict( 19 | argstr="-prefix %s", 20 | extensions=None, 21 | name_source=["in_file"], 22 | name_template="%s_afni", 23 | ), 24 | outputtype=dict(), 25 | ) 26 | inputs = AFNIPythonCommand.input_spec() 27 | 28 | for key, metadata in list(input_map.items()): 29 | for metakey, value in list(metadata.items()): 30 | assert getattr(inputs.traits()[key], metakey) == value 31 | -------------------------------------------------------------------------------- /nipype/algorithms/tests/test_auto_NormalizeProbabilityMapSet.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..misc import NormalizeProbabilityMapSet 3 | 4 | 5 | def test_NormalizeProbabilityMapSet_inputs(): 6 | input_map = dict( 7 | in_files=dict(), 8 | in_mask=dict( 9 | extensions=None, 10 | ), 11 | ) 12 | inputs = NormalizeProbabilityMapSet.input_spec() 13 | 14 | for key, metadata in list(input_map.items()): 15 | for metakey, value in list(metadata.items()): 16 | assert getattr(inputs.traits()[key], metakey) == value 17 | 18 | 19 | def test_NormalizeProbabilityMapSet_outputs(): 20 | output_map = dict( 21 | out_files=dict(), 22 | ) 23 | outputs = NormalizeProbabilityMapSet.output_spec() 24 | 25 | for key, metadata in list(output_map.items()): 26 | for metakey, value in list(metadata.items()): 27 | assert getattr(outputs.traits()[key], metakey) == value 28 | -------------------------------------------------------------------------------- /nipype/interfaces/semtools/diffusion/__init__.py: -------------------------------------------------------------------------------- 1 | from .diffusion import dtiaverage, dtiestim, dtiprocess, DWIConvert 2 | from .tractography import * 3 | from .gtract import ( 4 | gtractTransformToDisplacementField, 5 | gtractInvertBSplineTransform, 6 | gtractConcatDwi, 7 | gtractAverageBvalues, 8 | gtractCoregBvalues, 9 | gtractResampleAnisotropy, 10 | gtractResampleCodeImage, 11 | gtractCopyImageOrientation, 12 | gtractCreateGuideFiber, 13 | gtractAnisotropyMap, 14 | gtractClipAnisotropy, 15 | gtractResampleB0, 16 | gtractInvertRigidTransform, 17 | gtractImageConformity, 18 | compareTractInclusion, 19 | gtractFastMarchingTracking, 20 | gtractInvertDisplacementField, 21 | gtractCoRegAnatomy, 22 | gtractResampleDWIInPlace, 23 | gtractCostFastMarching, 24 | gtractFiberTracking, 25 | extractNrrdVectorIndex, 26 | gtractResampleFibers, 27 | gtractTensor, 28 | ) 29 | from .maxcurvature import maxcurvature 30 | -------------------------------------------------------------------------------- /nipype/algorithms/tests/test_auto_Gunzip.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..misc import Gunzip 3 | 4 | 5 | def test_Gunzip_inputs(): 6 | input_map = dict( 7 | in_file=dict( 8 | extensions=None, 9 | mandatory=True, 10 | ), 11 | mode=dict( 12 | usedefault=True, 13 | ), 14 | ) 15 | inputs = Gunzip.input_spec() 16 | 17 | for key, metadata in list(input_map.items()): 18 | for metakey, value in list(metadata.items()): 19 | assert getattr(inputs.traits()[key], metakey) == value 20 | 21 | 22 | def test_Gunzip_outputs(): 23 | output_map = dict( 24 | out_file=dict( 25 | extensions=None, 26 | ), 27 | ) 28 | outputs = Gunzip.output_spec() 29 | 30 | for key, metadata in list(output_map.items()): 31 | for metakey, value in list(metadata.items()): 32 | assert getattr(outputs.traits()[key], metakey) == value 33 | -------------------------------------------------------------------------------- /nipype/interfaces/utility/tests/test_auto_Merge.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..base import Merge 3 | 4 | 5 | def test_Merge_inputs(): 6 | input_map = dict( 7 | axis=dict( 8 | usedefault=True, 9 | ), 10 | no_flatten=dict( 11 | usedefault=True, 12 | ), 13 | ravel_inputs=dict( 14 | usedefault=True, 15 | ), 16 | ) 17 | inputs = Merge.input_spec() 18 | 19 | for key, metadata in list(input_map.items()): 20 | for metakey, value in list(metadata.items()): 21 | assert getattr(inputs.traits()[key], metakey) == value 22 | 23 | 24 | def test_Merge_outputs(): 25 | output_map = dict( 26 | out=dict(), 27 | ) 28 | outputs = Merge.output_spec() 29 | 30 | for key, metadata in list(output_map.items()): 31 | for metakey, value in list(metadata.items()): 32 | assert getattr(outputs.traits()[key], metakey) == value 33 | -------------------------------------------------------------------------------- /nipype/interfaces/tests/test_auto_SlicerCommandLine.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..dynamic_slicer import SlicerCommandLine 3 | 4 | 5 | def test_SlicerCommandLine_inputs(): 6 | input_map = dict( 7 | args=dict( 8 | argstr="%s", 9 | ), 10 | environ=dict( 11 | nohash=True, 12 | usedefault=True, 13 | ), 14 | module=dict(), 15 | ) 16 | inputs = SlicerCommandLine.input_spec() 17 | 18 | for key, metadata in list(input_map.items()): 19 | for metakey, value in list(metadata.items()): 20 | assert getattr(inputs.traits()[key], metakey) == value 21 | 22 | 23 | def test_SlicerCommandLine_outputs(): 24 | output_map = dict() 25 | outputs = SlicerCommandLine.output_spec() 26 | 27 | for key, metadata in list(output_map.items()): 28 | for metakey, value in list(metadata.items()): 29 | assert getattr(outputs.traits()[key], metakey) == value 30 | -------------------------------------------------------------------------------- /nipype/interfaces/utility/tests/test_auto_CSVReader.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..csv import CSVReader 3 | 4 | 5 | def test_CSVReader_inputs(): 6 | input_map = dict( 7 | delimiter=dict( 8 | usedefault=True, 9 | ), 10 | header=dict( 11 | usedefault=True, 12 | ), 13 | in_file=dict( 14 | extensions=None, 15 | mandatory=True, 16 | ), 17 | ) 18 | inputs = CSVReader.input_spec() 19 | 20 | for key, metadata in list(input_map.items()): 21 | for metakey, value in list(metadata.items()): 22 | assert getattr(inputs.traits()[key], metakey) == value 23 | 24 | 25 | def test_CSVReader_outputs(): 26 | output_map = dict() 27 | outputs = CSVReader.output_spec() 28 | 29 | for key, metadata in list(output_map.items()): 30 | for metakey, value in list(metadata.items()): 31 | assert getattr(outputs.traits()[key], metakey) == value 32 | -------------------------------------------------------------------------------- /nipype/algorithms/tests/test_auto_AddCSVRow.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..misc import AddCSVRow 3 | 4 | 5 | def test_AddCSVRow_inputs(): 6 | input_map = dict( 7 | _outputs=dict( 8 | usedefault=True, 9 | ), 10 | in_file=dict( 11 | extensions=None, 12 | mandatory=True, 13 | ), 14 | ) 15 | inputs = AddCSVRow.input_spec() 16 | 17 | for key, metadata in list(input_map.items()): 18 | for metakey, value in list(metadata.items()): 19 | assert getattr(inputs.traits()[key], metakey) == value 20 | 21 | 22 | def test_AddCSVRow_outputs(): 23 | output_map = dict( 24 | csv_file=dict( 25 | extensions=None, 26 | ), 27 | ) 28 | outputs = AddCSVRow.output_spec() 29 | 30 | for key, metadata in list(output_map.items()): 31 | for metakey, value in list(metadata.items()): 32 | assert getattr(outputs.traits()[key], metakey) == value 33 | -------------------------------------------------------------------------------- /doc/devel/gitwash/following_latest.rst: -------------------------------------------------------------------------------- 1 | .. _following-latest: 2 | 3 | ============================= 4 | Following the latest source 5 | ============================= 6 | 7 | These are the instructions if you just want to follow the latest 8 | *nipype* source, but you don't need to do any development for now. 9 | 10 | The steps are: 11 | 12 | * :ref:`install-git` 13 | * get local copy of the git repository from github_ 14 | * update local copy from time to time 15 | 16 | Get the local copy of the code 17 | ============================== 18 | 19 | From the command line:: 20 | 21 | git clone git://github.com/nipy/nipype.git 22 | 23 | You now have a copy of the code tree in the new ``nipype`` directory. 24 | 25 | Updating the code 26 | ================= 27 | 28 | From time to time you may want to pull down the latest code. Do this with:: 29 | 30 | cd nipype 31 | git pull 32 | 33 | The tree in ``nipype`` will now have the latest changes from the initial 34 | repository. 35 | 36 | .. include:: links.inc 37 | -------------------------------------------------------------------------------- /nipype/interfaces/fsl/model_templates/feat_ev_gamma.tcl: -------------------------------------------------------------------------------- 1 | # EV title 2 | set fmri(evtitle$ev_num) "$ev_name" 3 | 4 | # Basic waveform shape 5 | # 0 : Square 6 | # 1 : Sinusoid 7 | # 2 : Custom (1 entry per volume) 8 | # 3 : Custom (3 column format) 9 | # 4 : Interaction 10 | # 10 : Empty (all zeros) 11 | set fmri(shape$ev_num) 3 12 | 13 | # Convolution 14 | # 0 : None 15 | # 1 : Gaussian 16 | # 2 : Gamma 17 | # 3 : Double-Gamma HRF 18 | # 4 : Gamma basis functions 19 | # 5 : Sine basis functions 20 | # 6 : FIR basis functions 21 | # 7 : Optimal/custom basis functions 22 | set fmri(convolve$ev_num) 2 23 | 24 | # Convolve phase 25 | set fmri(convolve_phase$ev_num) 0 26 | 27 | # Apply temporal filtering 28 | set fmri(tempfilt_yn$ev_num) 1 29 | 30 | # Add temporal derivative 31 | set fmri(deriv_yn$ev_num) $temporalderiv 32 | 33 | # Custom EV file 34 | set fmri(custom$ev_num) "$cond_file" 35 | 36 | # Gamma sigma 37 | set fmri(gammasigma$ev_num) $gammasigma 38 | 39 | # Gamma delay 40 | set fmri(gammadelay$ev_num) $gammadelay 41 | -------------------------------------------------------------------------------- /doc/devel/provenance.rst: -------------------------------------------------------------------------------- 1 | ================ 2 | W3C PROV support 3 | ================ 4 | 5 | Overview 6 | -------- 7 | 8 | We're using the `W3C PROV data model `_ to 9 | capture and represent provenance in Nipype. 10 | 11 | For an overview see: 12 | 13 | `PROV-DM overview `_ 14 | 15 | Each interface writes out a provenance.json (currently prov-json) or 16 | provenance.rdf (if rdflib is available) file. The workflow engine can also 17 | write out a provenance of the workflow if instructed. 18 | 19 | This is very much an experimental feature as we continue to refine how exactly 20 | the provenance should be stored and how such information can be used for 21 | reporting or reconstituting workflows. By default provenance writing is disabled 22 | for the 0.9 release, to enable insert the following code at the top of your 23 | script:: 24 | 25 | >>> from nipype import config 26 | >>> config.enable_provenance() 27 | -------------------------------------------------------------------------------- /nipype/interfaces/camino/__init__.py: -------------------------------------------------------------------------------- 1 | # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- 2 | # vi: set ft=python sts=4 ts=4 sw=4 et: 3 | """Camino top level namespace""" 4 | 5 | from .connectivity import Conmat 6 | from .convert import ( 7 | Image2Voxel, 8 | FSL2Scheme, 9 | VtkStreamlines, 10 | ProcStreamlines, 11 | TractShredder, 12 | DT2NIfTI, 13 | NIfTIDT2Camino, 14 | AnalyzeHeader, 15 | Shredder, 16 | ) 17 | from .dti import ( 18 | DTIFit, 19 | ModelFit, 20 | DTLUTGen, 21 | PicoPDFs, 22 | Track, 23 | TrackPICo, 24 | TrackBayesDirac, 25 | TrackDT, 26 | TrackBallStick, 27 | TrackBootstrap, 28 | TrackBedpostxDeter, 29 | TrackBedpostxProba, 30 | ComputeFractionalAnisotropy, 31 | ComputeMeanDiffusivity, 32 | ComputeTensorTrace, 33 | ComputeEigensystem, 34 | DTMetric, 35 | ) 36 | from .calib import SFPICOCalibData, SFLUTGen 37 | from .odf import QBallMX, LinRecon, SFPeaks, MESD 38 | from .utils import ImageStats 39 | -------------------------------------------------------------------------------- /nipype/interfaces/tests/test_auto_SelectFiles.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..io import SelectFiles 3 | 4 | 5 | def test_SelectFiles_inputs(): 6 | input_map = dict( 7 | base_directory=dict(), 8 | force_lists=dict( 9 | usedefault=True, 10 | ), 11 | raise_on_empty=dict( 12 | usedefault=True, 13 | ), 14 | sort_filelist=dict( 15 | usedefault=True, 16 | ), 17 | ) 18 | inputs = SelectFiles.input_spec() 19 | 20 | for key, metadata in list(input_map.items()): 21 | for metakey, value in list(metadata.items()): 22 | assert getattr(inputs.traits()[key], metakey) == value 23 | 24 | 25 | def test_SelectFiles_outputs(): 26 | output_map = dict() 27 | outputs = SelectFiles.output_spec() 28 | 29 | for key, metadata in list(output_map.items()): 30 | for metakey, value in list(metadata.items()): 31 | assert getattr(outputs.traits()[key], metakey) == value 32 | -------------------------------------------------------------------------------- /doc/devel/matlab_interface_devel.rst: -------------------------------------------------------------------------------- 1 | .. matlab_interface_devel: 2 | 3 | =========================== 4 | How to wrap a MATLAB script 5 | =========================== 6 | 7 | 8 | Example 1 9 | +++++++++ 10 | 11 | This is a minimal script for wrapping MATLAB code. You should replace the MATLAB 12 | code template, and define appropriate inputs and outputs. 13 | 14 | .. literalinclude:: matlab_example1.py 15 | 16 | .. admonition:: Example source code 17 | 18 | You can download :download:`the source code of this example `. 19 | 20 | Example 2 21 | +++++++++ 22 | 23 | By subclassing :class:`nipype.interfaces.matlab.MatlabCommand` for your main 24 | class, and :class:`nipype.interfaces.matlab.MatlabInputSpec` for your input and 25 | output spec, you gain access to some useful MATLAB hooks 26 | 27 | .. literalinclude:: matlab_example2.py 28 | 29 | .. admonition:: Example source code 30 | 31 | You can download :download:`the source code of this example `. 32 | 33 | .. include:: ../links_names.txt 34 | -------------------------------------------------------------------------------- /nipype/interfaces/fsl/model_templates/feat_fe_ev_header.tcl: -------------------------------------------------------------------------------- 1 | # Add confound EVs text file 2 | set fmri(confoundevs) 0 3 | 4 | # EV 1 title 5 | set fmri(evtitle1) "" 6 | 7 | # Basic waveform shape (EV 1) 8 | # 0 : Square 9 | # 1 : Sinusoid 10 | # 2 : Custom (1 entry per volume) 11 | # 3 : Custom (3 column format) 12 | # 4 : Interaction 13 | # 10 : Empty (all zeros) 14 | set fmri(shape1) 2 15 | 16 | # Convolution (EV 1) 17 | # 0 : None 18 | # 1 : Gaussian 19 | # 2 : Gamma 20 | # 3 : Double-Gamma HRF 21 | # 4 : Gamma basis functions 22 | # 5 : Sine basis functions 23 | # 6 : FIR basis functions 24 | set fmri(convolve1) 0 25 | 26 | # Convolve phase (EV 1) 27 | set fmri(convolve_phase1) 0 28 | 29 | # Apply temporal filtering (EV 1) 30 | set fmri(tempfilt_yn1) 0 31 | 32 | # Add temporal derivative (EV 1) 33 | set fmri(deriv_yn1) 0 34 | 35 | # Custom EV file (EV 1) 36 | set fmri(custom1) "dummy" 37 | 38 | # Orthogonalise EV 1 wrt EV 0 39 | set fmri(ortho1.0) 0 40 | 41 | # Orthogonalise EV 1 wrt EV 1 42 | set fmri(ortho1.1) 0 43 | 44 | 45 | 46 | -------------------------------------------------------------------------------- /nipype/utils/tests/use_resources: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | # 3 | # use_resources 4 | ''' 5 | Python script to use a certain amount of RAM on disk and number of 6 | threads 7 | 8 | Usage: 9 | use_resources -g -p 10 | ''' 11 | 12 | # Make main executable 13 | if __name__ == '__main__': 14 | 15 | # Import packages 16 | import argparse 17 | from nipype.utils.profiler import _use_resources 18 | 19 | # Init argparser 20 | parser = argparse.ArgumentParser(description=__doc__) 21 | 22 | # Add arguments 23 | parser.add_argument( 24 | '-g', 25 | '--num_gb', 26 | required=True, 27 | type=float, 28 | help='Number of GB RAM to use, can be float or int') 29 | parser.add_argument( 30 | '-p', 31 | '--num_threads', 32 | required=True, 33 | type=int, 34 | help='Number of threads to run in parallel') 35 | 36 | # Parse args 37 | args = parser.parse_args() 38 | _use_resources(args.num_threads, args.num_gb) 39 | -------------------------------------------------------------------------------- /nipype/algorithms/tests/test_auto_SplitROIs.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..misc import SplitROIs 3 | 4 | 5 | def test_SplitROIs_inputs(): 6 | input_map = dict( 7 | in_file=dict( 8 | extensions=None, 9 | mandatory=True, 10 | ), 11 | in_mask=dict( 12 | extensions=None, 13 | ), 14 | roi_size=dict(), 15 | ) 16 | inputs = SplitROIs.input_spec() 17 | 18 | for key, metadata in list(input_map.items()): 19 | for metakey, value in list(metadata.items()): 20 | assert getattr(inputs.traits()[key], metakey) == value 21 | 22 | 23 | def test_SplitROIs_outputs(): 24 | output_map = dict( 25 | out_files=dict(), 26 | out_index=dict(), 27 | out_masks=dict(), 28 | ) 29 | outputs = SplitROIs.output_spec() 30 | 31 | for key, metadata in list(output_map.items()): 32 | for metakey, value in list(metadata.items()): 33 | assert getattr(outputs.traits()[key], metakey) == value 34 | -------------------------------------------------------------------------------- /nipype/algorithms/tests/test_splitmerge.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | 3 | from nipype.testing import example_data 4 | 5 | 6 | def test_split_and_merge(tmpdir): 7 | import numpy as np 8 | import nibabel as nb 9 | 10 | from nipype.algorithms.misc import split_rois, merge_rois 11 | 12 | in_mask = example_data("tpms_msk.nii.gz") 13 | dwfile = tmpdir.join("dwi.nii.gz").strpath 14 | mask_img = nb.load(in_mask) 15 | mskdata = np.asanyarray(mask_img.dataobj) 16 | aff = mask_img.affine 17 | 18 | dwshape = (mskdata.shape[0], mskdata.shape[1], mskdata.shape[2], 6) 19 | dwdata = np.random.normal(size=dwshape) 20 | tmpdir.chdir() 21 | nb.Nifti1Image(dwdata.astype(np.float32), aff, None).to_filename(dwfile) 22 | 23 | resdw, resmsk, resid = split_rois(dwfile, in_mask, roishape=(20, 20, 2)) 24 | merged = merge_rois(resdw, resid, in_mask) 25 | dwmerged = nb.load(merged).get_fdata(dtype=np.float32) 26 | 27 | dwmasked = dwdata * mskdata[:, :, :, np.newaxis] 28 | 29 | assert np.allclose(dwmasked, dwmerged) 30 | -------------------------------------------------------------------------------- /nipype/interfaces/cmtk/tests/test_auto_MergeCNetworks.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..convert import MergeCNetworks 3 | 4 | 5 | def test_MergeCNetworks_inputs(): 6 | input_map = dict( 7 | in_files=dict( 8 | mandatory=True, 9 | ), 10 | out_file=dict( 11 | extensions=None, 12 | usedefault=True, 13 | ), 14 | ) 15 | inputs = MergeCNetworks.input_spec() 16 | 17 | for key, metadata in list(input_map.items()): 18 | for metakey, value in list(metadata.items()): 19 | assert getattr(inputs.traits()[key], metakey) == value 20 | 21 | 22 | def test_MergeCNetworks_outputs(): 23 | output_map = dict( 24 | connectome_file=dict( 25 | extensions=None, 26 | ), 27 | ) 28 | outputs = MergeCNetworks.output_spec() 29 | 30 | for key, metadata in list(output_map.items()): 31 | for metakey, value in list(metadata.items()): 32 | assert getattr(outputs.traits()[key], metakey) == value 33 | --------------------------------------------------------------------------------