Merge pull request #277 from khanlab/download-osf

Download resources from osf
khanlab · Feb 15, 2024 · f0d0d8e · f0d0d8e
2 parents bf4ca6b + 5f0c4a8
commit f0d0d8e
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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
@@ -337,43 +337,40 @@ cifti_metric_types:
 singularity:
   autotop: 'docker://khanlab/hippunfold_deps:v0.5.0'
 
-xfm_identity: resources/identity_xfm.txt
-template: CITI168
+xfm_identity: resources/etc/identity_xfm.txt
+
 template_files:
   CITI168:
-    T1w: resources/CITI168/T1w_head_700um.nii.gz
-    T2w: resources/CITI168/T2w_head_700um.nii.gz
-    xfm_corobl: resources/CITI168/CoronalOblique_rigid.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: T1w_head_700um.nii.gz
+    T2w: T2w_head_700um.nii.gz
+    xfm_corobl: CoronalOblique_rigid.txt
+    crop_ref: T2w_300umCoronalOblique_hemi-{hemi}.nii.gz
+    crop_refT1w: T1w_300umCoronalOblique_hemi-{hemi}.nii.gz
+    Mask_crop: 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
-
-atlas: 
-  - multihist7
+    T1w: tpl-dHCP_cohort-1_res-1_T1w.nii.gz
+    T2w: tpl-dHCP_cohort-1_res-1_T2w.nii.gz
+    xfm_corobl: tpl-dHCP_cohort-1_to-corobl_affine.txt
+    crop_ref: tpl-dHCP_cohort-1_res-1_space-corobl_hemi-{hemi}_T2w.nii.gz
+    crop_refT1w: tpl-dHCP_cohort-1_res-1_space-corobl_hemi-{hemi}_T1w.nii.gz
+    Mask_crop: tpl-dHCP_cohort-1_res-1_space-corobl_hemi-{hemi}_desc-hipp_mask.nii.gz
 
 atlas_files:
   multihist7:
-    label_nii: resources/multihist7/sub-maxprob_label-hipp_desc-manualsubfieldsunfoldaligned_dseg.nii.gz
-    label_list: resources/multihist7/labellist.txt
-    thick: resources/multihist7/thickness.nii.gz
-    curv: resources/multihist7/curvature.nii.gz
-    gyr: resources/multihist7/gyrification.nii.gz
+    label_nii: sub-maxprob_label-hipp_desc-manualsubfieldsunfoldaligned_dseg.nii.gz
+    label_list: labellist.txt
+    thickness: thickness.nii.gz
+    curvature: curvature.nii.gz
+    gyrification: gyrification.nii.gz
   bigbrain:
-    label_nii: resources/bigbrain/sub-bigbrain_hemi-{hemi}_label-hipp_desc-manualsubfields_dseg.nii.gz
-    label_list: resources/bigbrain/sub-bigbrain_labellist.txt
+    label_nii: sub-bigbrain_hemi-{hemi}_label-hipp_desc-manualsubfields_dseg.nii.gz
+    label_list: sub-bigbrain_labellist.txt
   magdeburg:
-    label_nii: resources/magdeburg/sub-all_hemi-{hemi}_label-hipp_desc-manualsubfields_maxprob.nii.gz
-    label_list: resources/magdeburg/magdeburg_labellist.txt
+    label_nii: sub-all_hemi-{hemi}_label-hipp_desc-manualsubfields_maxprob.nii.gz
+    label_list: magdeburg_labellist.txt
   freesurfer:
-    label_nii: resources/freesurfer/sub-all_hemi-{hemi}_space-unfold_label-hipp_desc-freesurfersubfields_dseg.nii.gz
-    label_list: resources/freesurfer/freesurfer_labellist.txt
+    label_nii: sub-all_hemi-{hemi}_space-unfold_label-hipp_desc-freesurfersubfields_dseg.nii.gz
+    label_list: freesurfer_labellist.txt
 
 
 #values to use for re-mapping tissue labels when combining with subfields.
@@ -407,18 +404,39 @@ no_reg_template: False
 
 modality: T2w
 
+template: CITI168
+
+atlas: 
+  - multihist7
+
 
 
 #these will be downloaded to ~/.cache/hippunfold
-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'
-  hippb500: 'zenodo.org/record/5732291/files/trained_model.3d_fullres.Task110_hcp1200_b1000crop.nnUNetTrainerV2.model_best.tar'
-  neonateT1w: 'zenodo.org/record/5733556/files/trained_model.3d_fullres.Task205_hcp1200_b1000_finetuneround2_dhcp_T1w.nnUNetTrainerV2.model_best.tar'
-  neonateT1w_v2: 'zenodo.org/record/8209029/files/trained_model.3d_fullres.Task301_dhcp_T1w_synthseg_manuallycorrected.nnUNetTrainer.model_best.tar'
-  T1T2w: 'zenodo.org/record/4508747/files/trained_model.3d_fullres.Task103_hcp1200_T1T2w.nnUNetTrainerV2.model_best.tar'
-  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'
+resource_urls:
+  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'
+    hippb500: 'zenodo.org/record/5732291/files/trained_model.3d_fullres.Task110_hcp1200_b1000crop.nnUNetTrainerV2.model_best.tar'
+    neonateT1w: 'zenodo.org/record/5733556/files/trained_model.3d_fullres.Task205_hcp1200_b1000_finetuneround2_dhcp_T1w.nnUNetTrainerV2.model_best.tar'
+    neonateT1w_v2: 'zenodo.org/record/8209029/files/trained_model.3d_fullres.Task301_dhcp_T1w_synthseg_manuallycorrected.nnUNetTrainer.model_best.tar'
+    T1T2w: 'zenodo.org/record/4508747/files/trained_model.3d_fullres.Task103_hcp1200_T1T2w.nnUNetTrainerV2.model_best.tar'
+    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:
+    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='
+  template:
+    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/CITI168/CoronalOblique_rigid.txt b/hippunfold/resources/CITI168/CoronalOblique_rigid.txt
diff --git a/hippunfold/resources/CITI168/Mask_300umCoronalOblique_hemi-L.nii.gz b/hippunfold/resources/CITI168/Mask_300umCoronalOblique_hemi-L.nii.gz
diff --git a/hippunfold/resources/CITI168/Mask_300umCoronalOblique_hemi-R.nii.gz b/hippunfold/resources/CITI168/Mask_300umCoronalOblique_hemi-R.nii.gz
diff --git a/hippunfold/resources/CITI168/T1w_300umCoronalOblique_hemi-L.nii.gz b/hippunfold/resources/CITI168/T1w_300umCoronalOblique_hemi-L.nii.gz
diff --git a/hippunfold/resources/CITI168/T1w_300umCoronalOblique_hemi-R.nii.gz b/hippunfold/resources/CITI168/T1w_300umCoronalOblique_hemi-R.nii.gz
diff --git a/hippunfold/resources/CITI168/T1w_head_700um.nii.gz b/hippunfold/resources/CITI168/T1w_head_700um.nii.gz
diff --git a/hippunfold/resources/CITI168/T2w_300umCoronalOblique_hemi-L.nii.gz b/hippunfold/resources/CITI168/T2w_300umCoronalOblique_hemi-L.nii.gz
diff --git a/hippunfold/resources/CITI168/T2w_300umCoronalOblique_hemi-R.nii.gz b/hippunfold/resources/CITI168/T2w_300umCoronalOblique_hemi-R.nii.gz
diff --git a/hippunfold/resources/CITI168/T2w_head_700um.nii.gz b/hippunfold/resources/CITI168/T2w_head_700um.nii.gz
diff --git a/hippunfold/resources/Training_Instructions.md b/hippunfold/resources/Training_Instructions.md
diff --git a/hippunfold/resources/bigbrain/bigbrain_snaplabels.txt b/hippunfold/resources/bigbrain/bigbrain_snaplabels.txt
diff --git a/...unfold/resources/bigbrain/sub-bigbrain_hemi-L_label-hipp_desc-manualsubfields_dseg.nii.gz b/...unfold/resources/bigbrain/sub-bigbrain_hemi-L_label-hipp_desc-manualsubfields_dseg.nii.gz
diff --git a/...unfold/resources/bigbrain/sub-bigbrain_hemi-R_label-hipp_desc-manualsubfields_dseg.nii.gz b/...unfold/resources/bigbrain/sub-bigbrain_hemi-R_label-hipp_desc-manualsubfields_dseg.nii.gz
diff --git a/hippunfold/resources/bigbrain/sub-bigbrain_labellist.txt b/hippunfold/resources/bigbrain/sub-bigbrain_labellist.txt
diff --git a/hippunfold/resources/desc-flipLR_type-itk_xfm.txt b/hippunfold/resources/desc-flipLR_type-itk_xfm.txt
diff --git a/hippunfold/resources/identity_xfm.txt → hippunfold/resources/etc/identity_xfm.txt b/hippunfold/resources/identity_xfm.txt → hippunfold/resources/etc/identity_xfm.txt
diff --git a/hippunfold/resources/example_sbatch.sh b/hippunfold/resources/example_sbatch.sh
diff --git a/hippunfold/resources/fineTune_UNet.sh b/hippunfold/resources/fineTune_UNet.sh
diff --git a/hippunfold/resources/freesurfer/README.md b/hippunfold/resources/freesurfer/README.md