new branch for cleaner PR (#269)

* this branch moves templates and atlases to https://osf.io/v8acf/ * new branch for cleaner PR * downloads rule * only one allowable atlas input. This adds simplicity, and multiple are almost never used * removed multiple atlases tester --------- Co-authored-by: Jordan DeKraker - B. Bernhardt Lab <[email protected]>
khanlab · Nov 16, 2023 · 6df9888 · 6df9888
1 parent ccf04a6
commit 6df9888
Show file tree

Hide file tree

Showing 106 changed files with 244 additions and 1,107 deletions.
diff --git a/.github/workflows/python-testing.yml b/.github/workflows/python-testing.yml
@@ -182,11 +182,6 @@ jobs:
     - name: Test modality T1w with freesurfer atlas
       run: |
         poetry run hippunfold test_data/bids_T1w test_out participant -np --modality T1w --atlas freesurfer
-    - name: Test modality T1w with bigbrain and freesurfer atlas
-      run: |
-        poetry run hippunfold test_data/bids_T1w test_out participant -np --modality T1w --atlas bigbrain freesurfer
-
-
 
 
 

diff --git a/hippunfold/config/nnunet_model_urls.yml b/hippunfold/config/nnunet_model_urls.yml
diff --git a/hippunfold/config/snakebids.yml b/hippunfold/config/snakebids.yml
@@ -225,9 +225,7 @@ parse_args:
       - 'magdeburg'
       - 'freesurfer'
       - 'multihist7'
-    default: 
-      - 'multihist7'
-    nargs: '+'
+    default: 'multihist7'
     help: 'Select the atlas (unfolded space) to use for subfield labels. (default: %(default)s)'
 
   --no_unfolded_reg:
@@ -352,7 +350,6 @@ cifti_metric_types:
 
 
 
-
 #--- workflow specific configuration -- 
 
 singularity:
@@ -363,67 +360,66 @@ template: CITI168
 
 template_files:
   CITI168:
-    T1w: resources/templates-3d/CITI168/T1w_head_700um.nii.gz
-    T2w: resources/templates-3d/CITI168/T2w_head_700um.nii.gz
-    xfm_corobl: resources/templates-3d/CITI168/CoronalOblique_rigid.txt
-    crop_ref: resources/templates-3d/CITI168/T2w_300umCoronalOblique_hemi-{hemi}.nii.gz
-    crop_refT1w: resources/templates-3d/CITI168/T1w_300umCoronalOblique_hemi-{hemi}.nii.gz
-    Mask_crop: resources/templates-3d/CITI168/Mask_300umCoronalOblique_hemi-{hemi}.nii.gz
+    T1w: CITI168/T1w_head_700um.nii.gz
+    T2w: CITI168/T2w_head_700um.nii.gz
+    xfm_corobl: CITI168/CoronalOblique_rigid.txt
+    crop_ref: CITI168/T2w_300umCoronalOblique_hemi-{hemi}.nii.gz
+    crop_refT1w: CITI168/T1w_300umCoronalOblique_hemi-{hemi}.nii.gz
+    Mask_crop: CITI168/Mask_300umCoronalOblique_hemi-{hemi}.nii.gz
   dHCP:
-    T1w: resources/tpl-dHCP/cohort-1/tpl-dHCP_cohort-1_res-1_T1w.nii.gz
-    T2w: resources/tpl-dHCP/cohort-1/tpl-dHCP_cohort-1_res-1_T2w.nii.gz
-    xfm_corobl: resources/tpl-dHCP/cohort-1/tpl-dHCP_cohort-1_to-corobl_affine.txt
-    crop_ref: resources/CITI168/T2w_300umCoronalOblique_hemi-{hemi}.nii.gz
-    crop_refT1w: resources/CITI168/T1w_300umCoronalOblique_hemi-{hemi}.nii.gz
-    Mask_crop: resources/CITI168/Mask_300umCoronalOblique_hemi-{hemi}.nii.gz
+    T1w: dHCP/cohort-1/tpl-dHCP_cohort-1_res-1_T1w.nii.gz
+    xfm_corobl: dHCP/cohort-1/tpl-dHCP_cohort-1_to-corobl_affine.txt
+    crop_ref: CITI168/T2w_300umCoronalOblique_hemi-{hemi}.nii.gz
+    crop_refT1w: CITI168/T1w_300umCoronalOblique_hemi-{hemi}.nii.gz
+    Mask_crop: CITI168/Mask_300umCoronalOblique_hemi-{hemi}.nii.gz
     upenn:
-    dseg: resources/templates-3d/tpl-upenn/tpl-upenn_desc-hipptissue_dseg.nii.gz
-    coords: resources/templates-3d/tpl-upenn/tpl-upenn_dir-{dir}_label-{autotop}_coords.nii.gz
+    dseg: upenn/tpl-upenn_desc-hipptissue_dseg.nii.gz
+    coords: upenn/tpl-upenn_dir-{dir}_label-{autotop}_coords.nii.gz
   MBMv2:
-    T1w: resources/templates-3d/tpl-MBMv2/Template_sym_MTR_80um.nii.gz
-    T2w: resources/templates-3d/tpl-MBMv2/Template_sym_T2_80um.nii.gz
-    xfm_corobl: resources/templates-3d/tpl-MBMv2/tpl-MBMv2_from-native_to-corobl_type-itk_affine.txt
-    crop_ref: resources/templates-3d/tpl-MBMv2/tpl-MBMv2_hemi-{hemi}_space-corobl_T2w.nii.gz
-    crop_refT1w: resources/templates-3d/tpl-MBMv2/tpl-MBMv2_hemi-{hemi}_space-corobl_MTR.nii.gz
-    Mask_crop: resources/templates-3d/tpl-MBMv2/tpl-MBMv2_hemi-{hemi}_space-corobl_desc-hipp_mask.nii.gz
-    dseg: resources/templates-3d/tpl-MBMv2/tpl-MBMv2_hemi-R_space-corobl_desc-tissuemanual_dseg.nii.gz
-    coords: resources/templates-3d/tpl-MBMv2/tpl-MBMv2_dir-{dir}_hemi-R_space-corobl_label-{autotop}_desc-laplace_coords.nii.gz 
+    T1w: MBMv2/Template_sym_MTR_80um.nii.gz
+    T2w: MBMv2/Template_sym_T2_80um.nii.gz
+    xfm_corobl: MBMv2/tpl-MBMv2_from-native_to-corobl_type-itk_affine.txt
+    crop_ref: MBMv2/tpl-MBMv2_hemi-{hemi}_space-corobl_T2w.nii.gz
+    crop_refT1w: MBMv2/tpl-MBMv2_hemi-{hemi}_space-corobl_MTR.nii.gz
+    Mask_crop: MBMv2/tpl-MBMv2_hemi-{hemi}_space-corobl_desc-hipp_mask.nii.gz
+    dseg: MBMv2/tpl-MBMv2_hemi-R_space-corobl_desc-tissuemanual_dseg.nii.gz
+    coords: MBMv2/tpl-MBMv2_dir-{dir}_hemi-R_space-corobl_label-{autotop}_desc-laplace_coords.nii.gz 
   MBMv3:
-    T1w: resources/templates-3d/tpl-MBMv3/tpl-MBMv3_T1w.nii.gz
-    T2w: resources/templates-3d/tpl-MBMv3/tpl-MBMv3_T2w.nii.gz
-    xfm_corobl: resources/templates-3d/tpl-MBMv3/tpl-MBMv3_from-native_to-corobl_type-itk_affine.txt
-    crop_ref: resources/templates-3d/tpl-MBMv3/tpl-MBMv3_hemi-{hemi}_space-corobl_T2w.nii.gz
-    crop_refT1w: resources/templates-3d/tpl-MBMv3/tpl-MBMv3_hemi-{hemi}_space-corobl_T1w.nii.gz
-    Mask_crop: resources/templates-3d/tpl-MBMv3/tpl-MBMv3_hemi-{hemi}_space-corobl_desc-hipp_mask.nii.gz
-    dseg: resources/templates-3d/tpl-MBMv3/tpl-MBMv3_hemi-R_space-corobl_desc-tissue_dseg.nii.gz
-    coords: resources/templates-3d/tpl-MBMv3/tpl-MBMv3_dir-{dir}_hemi-R_space-corobl_label-{autotop}_desc-laplace_coords.nii.gz 
+    T1w: MBMv3/tpl-MBMv3_T1w.nii.gz
+    T2w: MBMv3/tpl-MBMv3_T2w.nii.gz
+    xfm_corobl: MBMv3/tpl-MBMv3_from-native_to-corobl_type-itk_affine.txt
+    crop_ref: MBMv3/tpl-MBMv3_hemi-{hemi}_space-corobl_T2w.nii.gz
+    crop_refT1w: MBMv3/tpl-MBMv3_hemi-{hemi}_space-corobl_T1w.nii.gz
+    Mask_crop: MBMv3/tpl-MBMv3_hemi-{hemi}_space-corobl_desc-hipp_mask.nii.gz
+    dseg: MBMv3/tpl-MBMv3_hemi-R_space-corobl_desc-tissue_dseg.nii.gz
+    coords: MBMv3/tpl-MBMv3_dir-{dir}_hemi-R_space-corobl_label-{autotop}_desc-laplace_coords.nii.gz 
   upenn:
-    dseg: resources/templates-3d/tpl-upenn/tpl-upenn_desc-hipptissue_dseg.nii.gz
-    coords: resources/templates-3d/tpl-upenn/tpl-upenn_dir-{dir}_label-{autotop}_coords.nii.gz
-
+    T1w: upenn/tpl-upenn_desc-hipptissue_dseg.nii.gz
+    dseg: upenn/tpl-upenn_desc-hipptissue_dseg.nii.gz
+    coords: upenn/tpl-upenn_dir-{dir}_label-{autotop}_coords.nii.gz
 
-
-
-
-atlas: 
-  - multihist7
+atlas: multihist7
 
 atlas_files:
   multihist7:
-    label_nii: resources/atlases-unfolded/multihist7/sub-maxprob_label-hipp_desc-manualsubfieldsunfoldaligned_dseg.nii.gz
-    label_list: resources/atlases-unfolded/multihist7/labellist.txt
-    thick: resources/atlases-unfolded/multihist7/thickness.nii.gz
-    curv: resources/atlases-unfolded/multihist7/curvature.nii.gz
-    gyr: resources/atlases-unfolded/multihist7/gyrification.nii.gz
+    label_nii: multihist7/sub-maxprob_label-hipp_desc-manualsubfieldsunfoldaligned_dseg.nii.gz
+    label_list: multihist7/labellist.txt
+    subfields_list: multihist7/desc-subfields_atlas-multihist7_dseg.tsv
+    thick: multihist7/thickness.nii.gz
+    curv: multihist7/curvature.nii.gz
+    gyr: multihist7/gyrification.nii.gz
   bigbrain:
-    label_nii: resources/atlases-unfolded/bigbrain/sub-bigbrain_hemi-{hemi}_label-hipp_desc-manualsubfields_dseg.nii.gz
-    label_list: resources/atlases-unfolded/bigbrain/sub-bigbrain_labellist.txt
+    label_nii: bigbrain/sub-bigbrain_hemi-{hemi}_label-hipp_desc-manualsubfields_dseg.nii.gz
+    subfields_list: multihist7/desc-subfields_atlas-bigbrain_dseg.tsv
+    label_list: bigbrain/sub-bigbrain_labellist.txt
   magdeburg:
-    label_nii: resources/atlases-unfolded/magdeburg/sub-all_hemi-{hemi}_label-hipp_desc-manualsubfields_maxprob.nii.gz
-    label_list: resources/atlases-unfolded/magdeburg/magdeburg_labellist.txt
+    label_nii: magdeburg/sub-all_hemi-{hemi}_label-hipp_desc-manualsubfields_maxprob.nii.gz
+    subfields_list: multihist7/desc-subfields_atlas-magdeburg_dseg.tsv
+    label_list: magdeburg/magdeburg_labellist.txt
   freesurfer:
-    label_nii: resources/atlases-unfolded/freesurfer/sub-all_hemi-{hemi}_space-unfold_label-hipp_desc-freesurfersubfields_dseg.nii.gz
-    label_list: resources/atlases-unfolded/freesurfer/freesurfer_labellist.txt
+    label_nii: freesurfer/sub-all_hemi-{hemi}_space-unfold_label-hipp_desc-freesurfersubfields_dseg.nii.gz
+    subfields_list: multihist7/desc-subfields_atlas-freesurfer_dseg.tsv
+    label_list: freesurfer/freesurfer_labellist.txt
 
 
 inject_template: upenn
@@ -462,7 +458,7 @@ modality: T2w
 
 
 
-#these will be downloaded to ~/.cache/hippunfold
+#these will be downloaded to ~/.cache/hippunfold or $HIPPUNFOLD_CACHE_DIR
 nnunet_model:
   T1w: 'zenodo.org/record/4508747/files/trained_model.3d_fullres.Task101_hcp1200_T1w.nnUNetTrainerV2.model_best.tar'
   T2w: 'zenodo.org/record/4508747/files/trained_model.3d_fullres.Task102_hcp1200_T2w.nnUNetTrainerV2.model_best.tar'
@@ -473,6 +469,21 @@ nnunet_model:
   synthseg_v0.1: 'zenodo.org/record/8184230/files/trained_model.3d_fullres.Task102_synsegGenDetailed.nnUNetTrainerV2.model_best.tar'
   synthseg_v0.2: 'zenodo.org/record/8184230/files/trained_model.3d_fullres.Task203_synthseg.nnUNetTrainerV2.model_best.tar'
 
+atlas_links_osf:
+  multihist7: 'files.ca-1.osf.io/v1/resources/v8acf/providers/osfstorage/65395b782827451220b86dd8/?zip='
+  bigbrain: 'files.ca-1.osf.io/v1/resources/v8acf/providers/osfstorage/65395b8b13d27b123094c96f/?zip='
+  magdeburg: 'files.ca-1.osf.io/v1/resources/v8acf/providers/osfstorage/65395b8013d27b122f94c938/?zip='
+  freesurfer: 'files.ca-1.osf.io/v1/resources/v8acf/providers/osfstorage/65395b8513d27b123094c96a/?zip='
+#to get hash, see https://github.com/CenterForOpenScience/osf.io/issues/8256#issuecomment-379833911
+
+template_links_osf:
+  CITI168: 'files.ca-1.osf.io/v1/resources/v8acf/providers/osfstorage/65395bf0282745121fb86a93/?zip='
+  dHCP: 'files.ca-1.osf.io/v1/resources/v8acf/providers/osfstorage/65395bff13d27b123094c9b4/?zip='
+  MBMv2: 'files.ca-1.osf.io/v1/resources/v8acf/providers/osfstorage/65395c0887852d133ca597dd/?zip='
+  MBMv3: 'files.ca-1.osf.io/v1/resources/v8acf/providers/osfstorage/65395c0e8a28b11240ffc6e9/?zip='
+  upenn: 'files.ca-1.osf.io/v1/resources/v8acf/providers/osfstorage/65395c1613d27b122a94ca09/?zip='
+#to get hash, see https://github.com/CenterForOpenScience/osf.io/issues/8256#issuecomment-379833911
+
 crop_native_box: '256x256x256vox'
 crop_native_res: '0.2x0.2x0.2mm'
 

diff --git a/hippunfold/download_models.py b/hippunfold/download_models.py
diff --git a/hippunfold/resources/atlases-unfolded/bigbrain/bigbrain_snaplabels.txt b/hippunfold/resources/atlases-unfolded/bigbrain/bigbrain_snaplabels.txt
diff --git a/hippunfold/resources/atlases-unfolded/bigbrain/desc-subfields_atlas-bigbrain_dseg.tsv b/hippunfold/resources/atlases-unfolded/bigbrain/desc-subfields_atlas-bigbrain_dseg.tsv
diff --git a/...atlases-unfolded/bigbrain/sub-bigbrain_hemi-L_label-hipp_desc-manualsubfields_dseg.nii.gz b/...atlases-unfolded/bigbrain/sub-bigbrain_hemi-L_label-hipp_desc-manualsubfields_dseg.nii.gz
diff --git a/...atlases-unfolded/bigbrain/sub-bigbrain_hemi-R_label-hipp_desc-manualsubfields_dseg.nii.gz b/...atlases-unfolded/bigbrain/sub-bigbrain_hemi-R_label-hipp_desc-manualsubfields_dseg.nii.gz
diff --git a/hippunfold/resources/atlases-unfolded/bigbrain/sub-bigbrain_labellist.txt b/hippunfold/resources/atlases-unfolded/bigbrain/sub-bigbrain_labellist.txt
diff --git a/hippunfold/resources/atlases-unfolded/freesurfer/README.md b/hippunfold/resources/atlases-unfolded/freesurfer/README.md
diff --git a/hippunfold/resources/atlases-unfolded/freesurfer/desc-subfields_atlas-freesurfer_dseg.tsv b/hippunfold/resources/atlases-unfolded/freesurfer/desc-subfields_atlas-freesurfer_dseg.tsv
diff --git a/hippunfold/resources/atlases-unfolded/freesurfer/desc-subfields_freeview_desg.tsv b/hippunfold/resources/atlases-unfolded/freesurfer/desc-subfields_freeview_desg.tsv