LICENSE
README.md
README_pypi.md
pyproject.toml
setup.py
scripts/parallelize
scripts/progress_bar_multi.sh
src/T1Prep.egg-info/PKG-INFO
src/T1Prep.egg-info/SOURCES.txt
src/T1Prep.egg-info/dependency_links.txt
src/T1Prep.egg-info/entry_points.txt
src/T1Prep.egg-info/requires.txt
src/T1Prep.egg-info/top_level.txt
src/t1prep/__init__.py
src/t1prep/_models.py
src/t1prep/_segment_utils.py
src/t1prep/dice.py
src/t1prep/metrics.py
src/t1prep/qa.py
src/t1prep/realign_longitudinal.py
src/t1prep/report.py
src/t1prep/segment.py
src/t1prep/surface_estimation.py
src/t1prep/t1prep.py
src/t1prep/utils.py
src/t1prep/cat_surf/__init__.py
src/t1prep/data/Names.tsv
src/t1prep/data/__init__.py
src/t1prep/data/cat_viewsurf_defaults.txt
src/t1prep/data/icon.png
src/t1prep/data/patches.csv
src/t1prep/data/atlases_surfaces_32k/atlases_surfaces_32k.md
src/t1prep/data/atlases_surfaces_32k/lh.Schaefer2018_100Parcels_17Networks_order.annot
src/t1prep/data/atlases_surfaces_32k/lh.Schaefer2018_100Parcels_17Networks_order.txt
src/t1prep/data/atlases_surfaces_32k/lh.Schaefer2018_200Parcels_17Networks_order.annot
src/t1prep/data/atlases_surfaces_32k/lh.Schaefer2018_200Parcels_17Networks_order.txt
src/t1prep/data/atlases_surfaces_32k/lh.Schaefer2018_400Parcels_17Networks_order.annot
src/t1prep/data/atlases_surfaces_32k/lh.Schaefer2018_400Parcels_17Networks_order.txt
src/t1prep/data/atlases_surfaces_32k/lh.Schaefer2018_600Parcels_17Networks_order.annot
src/t1prep/data/atlases_surfaces_32k/lh.Schaefer2018_600Parcels_17Networks_order.txt
src/t1prep/data/atlases_surfaces_32k/lh.aparc_DK40.freesurfer.annot
src/t1prep/data/atlases_surfaces_32k/lh.aparc_DK40.freesurfer.txt
src/t1prep/data/atlases_surfaces_32k/lh.aparc_HCP_MMP1.freesurfer.annot
src/t1prep/data/atlases_surfaces_32k/lh.aparc_HCP_MMP1.freesurfer.txt
src/t1prep/data/atlases_surfaces_32k/lh.aparc_a2009s.freesurfer.annot
src/t1prep/data/atlases_surfaces_32k/lh.aparc_a2009s.freesurfer.txt
src/t1prep/data/atlases_surfaces_32k/rh.Schaefer2018_100Parcels_17Networks_order.annot
src/t1prep/data/atlases_surfaces_32k/rh.Schaefer2018_200Parcels_17Networks_order.annot
src/t1prep/data/atlases_surfaces_32k/rh.Schaefer2018_400Parcels_17Networks_order.annot
src/t1prep/data/atlases_surfaces_32k/rh.Schaefer2018_600Parcels_17Networks_order.annot
src/t1prep/data/atlases_surfaces_32k/rh.aparc_DK40.freesurfer.annot
src/t1prep/data/atlases_surfaces_32k/rh.aparc_HCP_MMP1.freesurfer.annot
src/t1prep/data/atlases_surfaces_32k/rh.aparc_a2009s.freesurfer.annot
src/t1prep/data/templates_MNI152NLin2009cAsym/AAL3.csv
src/t1prep/data/templates_MNI152NLin2009cAsym/AAL3.nii.gz
src/t1prep/data/templates_MNI152NLin2009cAsym/AAL3.txt
src/t1prep/data/templates_MNI152NLin2009cAsym/Anatomy3.csv
src/t1prep/data/templates_MNI152NLin2009cAsym/Anatomy3.nii.gz
src/t1prep/data/templates_MNI152NLin2009cAsym/Anatomy3.txt
src/t1prep/data/templates_MNI152NLin2009cAsym/CoBra.csv
src/t1prep/data/templates_MNI152NLin2009cAsym/CoBra.nii.gz
src/t1prep/data/templates_MNI152NLin2009cAsym/CoBra.txt
src/t1prep/data/templates_MNI152NLin2009cAsym/Hammers.csv
src/t1prep/data/templates_MNI152NLin2009cAsym/Hammers.nii.gz
src/t1prep/data/templates_MNI152NLin2009cAsym/Hammers.txt
src/t1prep/data/templates_MNI152NLin2009cAsym/Hypothalamus.csv
src/t1prep/data/templates_MNI152NLin2009cAsym/Hypothalamus.nii.gz
src/t1prep/data/templates_MNI152NLin2009cAsym/Hypothalamus.txt
src/t1prep/data/templates_MNI152NLin2009cAsym/IBSR.csv
src/t1prep/data/templates_MNI152NLin2009cAsym/IBSR.nii.gz
src/t1prep/data/templates_MNI152NLin2009cAsym/IBSR.txt
src/t1prep/data/templates_MNI152NLin2009cAsym/JulichBrain.csv
src/t1prep/data/templates_MNI152NLin2009cAsym/JulichBrain.nii.gz
src/t1prep/data/templates_MNI152NLin2009cAsym/JulichBrain.txt
src/t1prep/data/templates_MNI152NLin2009cAsym/LPBA40.csv
src/t1prep/data/templates_MNI152NLin2009cAsym/LPBA40.nii.gz
src/t1prep/data/templates_MNI152NLin2009cAsym/LPBA40.txt
src/t1prep/data/templates_MNI152NLin2009cAsym/Melbourne-Subcortex-Atlas-7T.csv
src/t1prep/data/templates_MNI152NLin2009cAsym/Melbourne-Subcortex-Atlas-7T.nii.gz
src/t1prep/data/templates_MNI152NLin2009cAsym/Melbourne-Subcortex-Atlas-7T.txt
src/t1prep/data/templates_MNI152NLin2009cAsym/Mori.csv
src/t1prep/data/templates_MNI152NLin2009cAsym/Mori.nii.gz
src/t1prep/data/templates_MNI152NLin2009cAsym/Mori.txt
src/t1prep/data/templates_MNI152NLin2009cAsym/Neuromorphometrics.csv
src/t1prep/data/templates_MNI152NLin2009cAsym/Neuromorphometrics.nii.gz
src/t1prep/data/templates_MNI152NLin2009cAsym/Neuromorphometrics.txt
src/t1prep/data/templates_MNI152NLin2009cAsym/SUIT.csv
src/t1prep/data/templates_MNI152NLin2009cAsym/SUIT.nii.gz
src/t1prep/data/templates_MNI152NLin2009cAsym/SUIT.txt
src/t1prep/data/templates_MNI152NLin2009cAsym/Schaefer2018_100Parcels_17Networks_order.csv
src/t1prep/data/templates_MNI152NLin2009cAsym/Schaefer2018_100Parcels_17Networks_order.nii.gz
src/t1prep/data/templates_MNI152NLin2009cAsym/Schaefer2018_100Parcels_17Networks_order.txt
src/t1prep/data/templates_MNI152NLin2009cAsym/Schaefer2018_200Parcels_17Networks_order.csv
src/t1prep/data/templates_MNI152NLin2009cAsym/Schaefer2018_200Parcels_17Networks_order.nii.gz
src/t1prep/data/templates_MNI152NLin2009cAsym/Schaefer2018_200Parcels_17Networks_order.txt
src/t1prep/data/templates_MNI152NLin2009cAsym/Schaefer2018_400Parcels_17Networks_order.csv
src/t1prep/data/templates_MNI152NLin2009cAsym/Schaefer2018_400Parcels_17Networks_order.nii.gz
src/t1prep/data/templates_MNI152NLin2009cAsym/Schaefer2018_400Parcels_17Networks_order.txt
src/t1prep/data/templates_MNI152NLin2009cAsym/Schaefer2018_600Parcels_17Networks_order.csv
src/t1prep/data/templates_MNI152NLin2009cAsym/Schaefer2018_600Parcels_17Networks_order.nii.gz
src/t1prep/data/templates_MNI152NLin2009cAsym/Schaefer2018_600Parcels_17Networks_order.txt
src/t1prep/data/templates_MNI152NLin2009cAsym/Template_05mm_bet.nii.gz
src/t1prep/data/templates_MNI152NLin2009cAsym/Template_4_GS.nii.gz
src/t1prep/data/templates_MNI152NLin2009cAsym/Thalamic-Nuclei.csv
src/t1prep/data/templates_MNI152NLin2009cAsym/Thalamic-Nuclei.nii.gz
src/t1prep/data/templates_MNI152NLin2009cAsym/Thalamic-Nuclei.txt
src/t1prep/data/templates_MNI152NLin2009cAsym/Thalamus.csv
src/t1prep/data/templates_MNI152NLin2009cAsym/Thalamus.nii.gz
src/t1prep/data/templates_MNI152NLin2009cAsym/Thalamus.txt
src/t1prep/data/templates_MNI152NLin2009cAsym/cat_bloodvessels.nii.gz
src/t1prep/data/templates_MNI152NLin2009cAsym/cat_wmh.nii.gz
src/t1prep/data/templates_MNI152NLin2009cAsym/cat_wmh_miccai2017.nii.gz
src/t1prep/data/templates_MNI152NLin2009cAsym/csf_TPM.nii.gz
src/t1prep/data/templates_surfaces_32k/fsavg.index2D_256x128.txt
src/t1prep/data/templates_surfaces_32k/lh.central.Template_T1.gii
src/t1prep/data/templates_surfaces_32k/lh.central.freesurfer.gii
src/t1prep/data/templates_surfaces_32k/lh.inflated.freesurfer.gii
src/t1prep/data/templates_surfaces_32k/lh.mask
src/t1prep/data/templates_surfaces_32k/lh.mc.freesurfer.gii
src/t1prep/data/templates_surfaces_32k/lh.patch.freesurfer.gii
src/t1prep/data/templates_surfaces_32k/lh.sphere.freesurfer.gii
src/t1prep/data/templates_surfaces_32k/lh.sqrtsulc.freesurfer.gii
src/t1prep/data/templates_surfaces_32k/lh.thickness.Template_T1
src/t1prep/data/templates_surfaces_32k/mesh.central.Template_T1.gii
src/t1prep/data/templates_surfaces_32k/mesh.central.freesurfer.gii
src/t1prep/data/templates_surfaces_32k/mesh.inflated.freesurfer.gii
src/t1prep/data/templates_surfaces_32k/rh.central.Template_T1.gii
src/t1prep/data/templates_surfaces_32k/rh.central.freesurfer.gii
src/t1prep/data/templates_surfaces_32k/rh.inflated.freesurfer.gii
src/t1prep/data/templates_surfaces_32k/rh.mask
src/t1prep/data/templates_surfaces_32k/rh.mc.freesurfer.gii
src/t1prep/data/templates_surfaces_32k/rh.patch.freesurfer.gii
src/t1prep/data/templates_surfaces_32k/rh.sphere.freesurfer.gii
src/t1prep/data/templates_surfaces_32k/rh.sqrtsulc.freesurfer.gii
src/t1prep/data/templates_surfaces_32k/rh.thickness.Template_T1
src/t1prep/data/templates_surfaces_32k/templates_surfaces_32k.md
src/t1prep/data/templates_surfaces_4k/lh.central.freesurfer.gii
src/t1prep/data/templates_surfaces_4k/lh.inflated.freesurfer.gii
src/t1prep/data/templates_surfaces_4k/lh.mask
src/t1prep/data/templates_surfaces_4k/lh.sphere.freesurfer.gii
src/t1prep/data/templates_surfaces_4k/rh.central.freesurfer.gii
src/t1prep/data/templates_surfaces_4k/rh.inflated.freesurfer.gii
src/t1prep/data/templates_surfaces_4k/rh.mask
src/t1prep/data/templates_surfaces_4k/rh.sphere.freesurfer.gii
src/t1prep/gui/__init__.py
src/t1prep/gui/cat_viewimage.py
src/t1prep/gui/cat_viewsurf.py
tests/test_utils.py