MANIFEST.in
README.rst
setup.py
hippunfold/__init__.py
hippunfold/download_models.py
hippunfold/run.py
hippunfold.egg-info/PKG-INFO
hippunfold.egg-info/SOURCES.txt
hippunfold.egg-info/dependency_links.txt
hippunfold.egg-info/entry_points.txt
hippunfold.egg-info/requires.txt
hippunfold.egg-info/top_level.txt
hippunfold/config/nnunet_model_urls.yml
hippunfold/config/snakebids.yml
hippunfold/resources/Training_Instructions.md
hippunfold/resources/desc-flipLR_type-itk_xfm.txt
hippunfold/resources/desc-subfields_dseg.tsv
hippunfold/resources/dseg.tsv
hippunfold/resources/example_sbatch.sh
hippunfold/resources/fineTune_UNet.sh
hippunfold/resources/write_config_NiftyNet.py
hippunfold/resources/CITI168/CoronalOblique_rigid.txt
hippunfold/resources/CITI168/Mask_300umCoronalOblique_hemi-L.nii.gz
hippunfold/resources/CITI168/Mask_300umCoronalOblique_hemi-R.nii.gz
hippunfold/resources/CITI168/T1w_300umCoronalOblique_hemi-L.nii.gz
hippunfold/resources/CITI168/T1w_300umCoronalOblique_hemi-R.nii.gz
hippunfold/resources/CITI168/T1w_head_700um.nii.gz
hippunfold/resources/CITI168/T2w_300umCoronalOblique_hemi-L.nii.gz
hippunfold/resources/CITI168/T2w_300umCoronalOblique_hemi-R.nii.gz
hippunfold/resources/bigbrain/BigBrain_ManualSubfields.png
hippunfold/resources/bigbrain/BigBrain_ManualSubfieldsUnfolded.mat
hippunfold/resources/bigbrain/BigBrain_ManualSubfieldsUnfolded_254x126.border
hippunfold/resources/bigbrain/BigBrain_ManualSubfieldsUnfolded_254x126.label.gii
hippunfold/resources/bigbrain/BigBrain_ManualSubfieldsUnfolded_254x126.shape.gii
hippunfold/resources/bigbrain/sub-bigbrain_hemi-L_subfields.border
hippunfold/resources/bigbrain/sub-bigbrain_hemi-L_subfields.label.gii
hippunfold/resources/bigbrain/sub-bigbrain_hemi-R_subfields.border
hippunfold/resources/bigbrain/sub-bigbrain_hemi-R_subfields.label.gii
hippunfold/resources/bigbrain/sub-bigbrain_labellist.txt
hippunfold/resources/tpl-upenn/.gitignore
hippunfold/resources/tpl-upenn/Snakefile
hippunfold/resources/tpl-upenn/dag.pdf
hippunfold/resources/tpl-upenn/tpl-upenn_desc-hipptissue_dseg.nii.gz
hippunfold/resources/tpl-upenn/tpl-upenn_dir-AP_coords.nii.gz
hippunfold/resources/tpl-upenn/tpl-upenn_dir-IO_coords.nii.gz
hippunfold/resources/tpl-upenn/tpl-upenn_dir-PD_coords.nii.gz
hippunfold/resources/unfold_template/tpl-avg_space-unfold_den-2k_inner.surf.gii
hippunfold/resources/unfold_template/tpl-avg_space-unfold_den-2k_midthickness.surf.gii
hippunfold/resources/unfold_template/tpl-avg_space-unfold_den-2k_outer.surf.gii
hippunfold/resources/unfold_template/tpl-avg_space-unfold_den-32k_inner.surf.gii
hippunfold/resources/unfold_template/tpl-avg_space-unfold_den-32k_inner.surf.vtk
hippunfold/resources/unfold_template/tpl-avg_space-unfold_den-32k_midthickness.surf.gii
hippunfold/resources/unfold_template/tpl-avg_space-unfold_den-32k_midthickness.surf.vtk
hippunfold/resources/unfold_template/tpl-avg_space-unfold_den-32k_outer.surf.gii
hippunfold/resources/unfold_template/tpl-avg_space-unfold_den-32k_outer.surf.vtk
hippunfold/resources/unfold_template/tpl-avg_space-unfold_den-400_inner.surf.gii
hippunfold/resources/unfold_template/tpl-avg_space-unfold_den-400_midthickness.surf.gii
hippunfold/resources/unfold_template/tpl-avg_space-unfold_den-400_outer.surf.gii
hippunfold/resources/unfold_template/tpl-avg_space-unfold_den-7k_inner.surf.gii
hippunfold/resources/unfold_template/tpl-avg_space-unfold_den-7k_midthickness.surf.gii
hippunfold/resources/unfold_template/tpl-avg_space-unfold_den-7k_outer.surf.gii
hippunfold/workflow/Snakefile
hippunfold/workflow/report/nnunet_qc.rst
hippunfold/workflow/report/subfield_qc.rst
hippunfold/workflow/report/subj_volume_plot.rst
hippunfold/workflow/report/t1w_template_regqc.rst
hippunfold/workflow/rules/autotop.smk
hippunfold/workflow/rules/common.smk
hippunfold/workflow/rules/gifti.smk
hippunfold/workflow/rules/masking_bet_from-b0.smk
hippunfold/workflow/rules/nnunet.smk
hippunfold/workflow/rules/preproc_cropseg.smk
hippunfold/workflow/rules/preproc_dwi.smk
hippunfold/workflow/rules/preproc_hippb500.smk
hippunfold/workflow/rules/preproc_seg.smk
hippunfold/workflow/rules/preproc_t1.smk
hippunfold/workflow/rules/preproc_t2.smk
hippunfold/workflow/rules/resample_final_to_crop_t1.smk
hippunfold/workflow/rules/shape_inject.smk
hippunfold/workflow/rules/subfields.smk
hippunfold/workflow/scripts/constrain_surf_to_bbox.py
hippunfold/workflow/scripts/create_warps.py
hippunfold/workflow/scripts/dice.py
hippunfold/workflow/scripts/fillnanvertices.py
hippunfold/workflow/scripts/gen_volume_tsv.py
hippunfold/workflow/scripts/label_subfields_from_vol_coords.py
hippunfold/workflow/scripts/laplace_coords.py
hippunfold/workflow/scripts/laplace_coords_withinit.py
hippunfold/workflow/scripts/mapUnfoldToFullGrid.sh
hippunfold/workflow/scripts/plot_subj_subfields.py
hippunfold/workflow/scripts/resample_unfolded_label.py
hippunfold/workflow/scripts/vis_qc_dseg.py
hippunfold/workflow/scripts/vis_qc_surf.py
hippunfold/workflow/scripts/vis_regqc.py
hippunfold/workflow/scripts/preproc_dwi/concat_bv.py
hippunfold/workflow/scripts/preproc_dwi/concat_json.py
hippunfold/workflow/scripts/preproc_dwi/get_eddy_index_txt.py
hippunfold/workflow/scripts/preproc_dwi/get_phase_encode_txt.py
hippunfold/workflow/scripts/preproc_dwi/get_shell_avg.py
hippunfold/workflow/scripts/preproc_dwi/get_shell_avgs.py
hippunfold/workflow/scripts/preproc_dwi/get_shells_from_bvals.py
hippunfold/workflow/scripts/preproc_dwi/get_slspec_txt.py