├── .coveragerc ├── .gitignore ├── .travis.yml ├── AWSRunFile.py ├── License.txt ├── Nipype_workflow_charts ├── BASC_Colored_Nipype.png ├── BASC_Detailed_nipype.png ├── BASC_Flat_Nipype.png └── BASC_detailed_exec_Nipype.png ├── PyBASC ├── SimRunFile.py ├── Template.yaml ├── __init__.py ├── __main__.py ├── basc.py ├── basc_workflow_runner.py ├── data │ ├── sub_0corr_0.1_noise_2.5_TRs_100.nii.gz │ ├── sub_1corr_0.1_noise_2.5_TRs_100.nii.gz │ ├── sub_2corr_0.1_noise_2.5_TRs_100.nii.gz │ ├── sub_3corr_0.1_noise_2.5_TRs_100.nii.gz │ ├── sub_4corr_0.1_noise_2.5_TRs_100.nii.gz │ ├── sub_5corr_0.1_noise_2.5_TRs_100.nii.gz │ ├── sub_6corr_0.1_noise_2.5_TRs_100.nii.gz │ ├── sub_7corr_0.1_noise_2.5_TRs_100.nii.gz │ ├── sub_8corr_0.1_noise_2.5_TRs_100.nii.gz │ └── sub_9corr_0.1_noise_2.5_TRs_100.nii.gz ├── masks │ ├── BG_2mm.nii.gz │ ├── BG_HarvardOxford3mm.nii.gz │ ├── BG_SimTrueMat_HarvardOxford3mm.nii.gz │ ├── Bilateral_Thalamus3mm.nii.gz │ ├── MNI152_T1_3mm_brain_mask.nii.gz │ ├── MNI_152_4mm.nii.gz │ ├── MNI_152_4mm_brain.nii.gz │ ├── Striatum_HarvardOxford.nii.gz │ ├── Striatum_HarvardOxford3mm.nii.gz │ ├── Thalamus_HarvardOxford.nii.gz │ ├── Thalamus_HarvardOxford3mm.nii.gz │ ├── TrueBGClust.nii.gz │ ├── Yeo7_3mmMasks │ │ ├── BilateralStriatumThalamus_3mm.nii.gz │ │ ├── FPNStriatumThalamus_3mm.nii.gz │ │ ├── MotorStriatumThalamus_3mm.nii.gz │ │ ├── YeoTest.nii.gz │ │ ├── YeoTest2.nii.gz │ │ ├── YeoTest3.nii.gz │ │ ├── YeoWholeBrain.nii.gz │ │ ├── Yeo_1_3mm.nii.gz │ │ ├── Yeo_2Test.nii.gz │ │ ├── Yeo_2_3mm.nii.gz │ │ ├── Yeo_3_3mm.nii.gz │ │ ├── Yeo_4_3mm.nii.gz │ │ ├── Yeo_5_3mm.nii.gz │ │ ├── Yeo_6_3mm.nii.gz │ │ ├── Yeo_7_3mm.nii.gz │ │ ├── Yeo_All_7_3mm.nii.gz │ │ ├── Yeo_All_7_4mm.nii.gz │ │ ├── Yeo_All_7_4mm_updated.nii.gz │ │ └── Yeo_All_7_Tight_3mm.nii.gz │ ├── basc7_resized_4mm.nii.gz │ ├── cerebellum_3mm.nii.gz │ └── oldmasks │ │ ├── Bellec_BASC_7_3mm_mask_resized.nii.gz │ │ ├── Bellec_BASC_7_4mm_mask.nii.gz │ │ ├── Bellec_BASC_7_4mm_mask_resampled.nii.gz │ │ ├── LC_Quarter_Res.nii.gz │ │ ├── Left_Caud_Put_Pall_bin_thresh_3mm.nii.gz │ │ ├── MNI152_T1_3mm_brain_b.nii.gz │ │ ├── RC_Quarter_Res.nii.gz │ │ ├── Right_Caud_Put_Pall_bin_thresh_3mm.nii.gz │ │ ├── Striatum_2thirdsRes.nii.gz │ │ ├── True3ClustBG.nii.gz │ │ ├── True3ClustBG_mask.nii.gz │ │ ├── yeo2_3mm.nii.gz │ │ ├── yeo_2.nii.gz │ │ ├── yeo_2_2thirdsRes_bin.nii.gz │ │ └── yeo_3mm.nii.gz ├── pipeline.py ├── tests │ ├── test_basc.py │ └── test_smoke.py └── utils.py ├── README.md ├── SimRunFile 2.py ├── SimRunFile.py ├── after_basc.py ├── codecov.yml ├── gsm_nifti.py ├── ism_nifti.py ├── post_basc.py ├── sample_data ├── sub1 │ ├── .DS_Store │ └── Func_Quarter_Res.nii.gz ├── sub2 │ └── Func_Quarter_Res.nii.gz └── sub3 │ └── Func_Quarter_Res.nii.gz ├── scripts └── PyBASC ├── setup.cfg ├── setup.py ├── testdata ├── Reg1_True.npy └── Reg2_True.npy └── tests └── ism_test.npy /.coveragerc: 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