├── LICENSE ├── NIfTI_toolbox ├── FAQ.pdf ├── NIfTI_tools.pdf ├── UseANALYZE.pdf ├── affine.m ├── bipolar.m ├── bresenham_line3d.m ├── clip_nii.m ├── collapse_nii_scan.m ├── examples.txt ├── expand_nii_scan.m ├── extra_nii_hdr.m ├── flip_lr.m ├── get_nii_frame.m ├── license.txt ├── load_nii.m ├── load_nii_ext.m ├── load_nii_hdr.m ├── load_nii_img.m ├── load_untouch0_nii_hdr.m ├── load_untouch_header_only.m ├── load_untouch_nii.m ├── load_untouch_nii_hdr.m ├── load_untouch_nii_img.m ├── make_ana.m ├── make_nii.m ├── mat_into_hdr.m ├── pad_nii.m ├── reslice_nii.m ├── rri_file_menu.m ├── rri_orient.m ├── rri_orient_ui.m ├── rri_select_file.m ├── rri_xhair.m ├── rri_zoom_menu.m ├── save_nii.m ├── save_nii_ext.m ├── save_nii_hdr.m ├── save_untouch0_nii_hdr.m ├── save_untouch_header_only.m ├── save_untouch_nii.m ├── save_untouch_nii_hdr.m ├── save_untouch_slice.m ├── unxform_nii.m ├── verify_nii_ext.m ├── view_nii.m ├── view_nii_menu.m └── xform_nii.m ├── PCNN3D_matlab ├── PCNN2D.p ├── PCNN3D.p ├── addnoise_mri.p ├── border_comp.p ├── border_comp_implay.p ├── border_comp_series.p ├── drawborder.p ├── drawborderslice.p ├── findit.p ├── jaccard.p ├── jaccard_PCNN.p ├── make_nii.p ├── makenii_border.p ├── read_analyze.p ├── readsparse3d.p ├── resize_slice.p ├── resize_z.p ├── roc.p ├── save_nii.p ├── save_nii_ext.p ├── save_nii_hdr.p ├── scaledLoG.p ├── scaledgauss.p ├── showbrainvol.p └── showbrainvol_iso.p ├── PCNN3D_run_v1_3.m ├── README.md ├── SoftwareInstallation_fsl_afni_ants.txt ├── data_mouse1 ├── EPI0.nii.gz ├── EPI_forward0.nii ├── EPI_n4_csf_mask.nii.gz ├── EPI_n4_mask.nii.gz ├── EPI_reverse0.nii └── FCmap.tif ├── data_rat1 ├── EPI0.nii.gz ├── EPI_forward0.nii ├── EPI_n4_mask.nii.gz ├── EPI_reverse0.nii └── FCmap.tif ├── generateEPItmp.sh ├── lib ├── tmp │ ├── mouseEPIatlas.nii │ ├── mouseEPIatlas_labels.csv │ ├── mouseEPItmp.nii │ ├── mouseT2tmp.nii │ ├── mousebrainMask.nii │ ├── ratEPIatlas.nii │ ├── ratEPIatlas_labels.csv │ ├── ratEPItmp.nii │ ├── 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