Revert "initial attempt at moving all resources files to OSF"

This reverts commit 608eff6.

Author: Jordan DeKraker - B. Bernhardt Lab

hippunfold/config/nnunet_model_urls.yml

@@ -0,0 +1,8 @@
+T1w: 'https://zenodo.org/record/4508747/files/trained_model.3d_fullres.Task101_hcp1200_T1w.nnUNetTrainerV2.model_best.tar'
+T2w: 'https://zenodo.org/record/4508747/files/trained_model.3d_fullres.Task102_hcp1200_T2w.nnUNetTrainerV2.model_best.tar'
+neonateT1w: 'https://zenodo.org/record/5733556/files/trained_model.3d_fullres.Task205_hcp1200_b1000_finetuneround2_dhcp_T1w.nnUNetTrainerV2.model_best.tar'
+neonateT1w_v2: 'https://zenodo.org/record/8209029/files/trained_model.3d_fullres.Task301_dhcp_T1w_synthseg_manuallycorrected.nnUNetTrainer.model_best.tar'
+hippb500: 'https://zenodo.org/record/5732291/files/trained_model.3d_fullres.Task110_hcp1200_b1000crop.nnUNetTrainerV2.model_best.tar'
+T1T2w: 'https://zenodo.org/record/4508747/files/trained_model.3d_fullres.Task103_hcp1200_T1T2w.nnUNetTrainerV2.model_best.tar'
+synthseg_v0.1: 'https://dropbox.com/s/asoanq94ofersv3/trained_model.3d_fullres.Task102_synsegGenDetailed.nnUNetTrainerV2.model_best.tar'
+synthseg_v0.2: 'https://www.dropbox.com/scl/fi/69yvmo38gdn3dj8aupq9z/trained_model.3d_fullres.Task203_synthseg.nnUNetTrainerV2.model_best.tar?rlkey=90km7u4t0cw8t15akr5tawxyl&dl=0'

hippunfold/config/snakebids.yml

@@ -363,43 +363,44 @@ template: CITI168
 
 template_files:
   CITI168:
-    T1w: templates-3d/CITI168/T1w_head_700um.nii.gz
-    T2w: templates-3d/CITI168/T2w_head_700um.nii.gz
-    xfm_corobl: templates-3d/CITI168/CoronalOblique_rigid.txt
-    crop_ref: templates-3d/CITI168/T2w_300umCoronalOblique_hemi-{hemi}.nii.gz
-    crop_refT1w: templates-3d/CITI168/T1w_300umCoronalOblique_hemi-{hemi}.nii.gz
-    Mask_crop: templates-3d/CITI168/Mask_300umCoronalOblique_hemi-{hemi}.nii.gz
+    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
   dHCP:
-    T1w: templates-3d/tpl-dHCP/cohort-1/tpl-dHCP_cohort-1_res-1_T1w.nii.gz
-    xfm_corobl: templates-3d/tpl-dHCP/cohort-1/tpl-dHCP_cohort-1_to-corobl_affine.txt
-    crop_ref: templates-3d/CITI168/T2w_300umCoronalOblique_hemi-{hemi}.nii.gz
-    crop_refT1w: templates-3d/CITI168/T1w_300umCoronalOblique_hemi-{hemi}.nii.gz
-    Mask_crop: templates-3d/CITI168/Mask_300umCoronalOblique_hemi-{hemi}.nii.gz
+    T1w: resources/templates-3d/tpl-dHCP/cohort-1/tpl-dHCP_cohort-1_res-1_T1w.nii.gz
+    xfm_corobl: resources/templates-3d/tpl-dHCP/cohort-1/tpl-dHCP_cohort-1_to-corobl_affine.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
     upenn:
-    dseg: templates-3d/tpl-upenn/tpl-upenn_desc-hipptissue_dseg.nii.gz
-    coords: templates-3d/tpl-upenn/tpl-upenn_dir-{dir}_label-{autotop}_coords.nii.gz
+    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
   MBMv2:
-    T1w: templates-3d/tpl-MBMv2/Template_sym_MTR_80um.nii.gz
-    T2w: templates-3d/tpl-MBMv2/Template_sym_T2_80um.nii.gz
-    xfm_corobl: templates-3d/tpl-MBMv2/tpl-MBMv2_from-native_to-corobl_type-itk_affine.txt
-    crop_ref: templates-3d/tpl-MBMv2/tpl-MBMv2_hemi-{hemi}_space-corobl_T2w.nii.gz
-    crop_refT1w: templates-3d/tpl-MBMv2/tpl-MBMv2_hemi-{hemi}_space-corobl_MTR.nii.gz
-    Mask_crop: templates-3d/tpl-MBMv2/tpl-MBMv2_hemi-{hemi}_space-corobl_desc-hipp_mask.nii.gz
-    dseg: templates-3d/tpl-MBMv2/tpl-MBMv2_hemi-R_space-corobl_desc-tissuemanual_dseg.nii.gz
-    coords: templates-3d/tpl-MBMv2/tpl-MBMv2_dir-{dir}_hemi-R_space-corobl_label-{autotop}_desc-laplace_coords.nii.gz 
+    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 
   MBMv3:
-    T1w: templates-3d/tpl-MBMv3/tpl-MBMv3_T1w.nii.gz
-    T2w: templates-3d/tpl-MBMv3/tpl-MBMv3_T2w.nii.gz
-    xfm_corobl: templates-3d/tpl-MBMv3/tpl-MBMv3_from-native_to-corobl_type-itk_affine.txt
-    crop_ref: templates-3d/tpl-MBMv3/tpl-MBMv3_hemi-{hemi}_space-corobl_T2w.nii.gz
-    crop_refT1w: templates-3d/tpl-MBMv3/tpl-MBMv3_hemi-{hemi}_space-corobl_T1w.nii.gz
-    Mask_crop: templates-3d/tpl-MBMv3/tpl-MBMv3_hemi-{hemi}_space-corobl_desc-hipp_mask.nii.gz
-    dseg: templates-3d/tpl-MBMv3/tpl-MBMv3_hemi-R_space-corobl_desc-tissue_dseg.nii.gz
-    coords: templates-3d/tpl-MBMv3/tpl-MBMv3_dir-{dir}_hemi-R_space-corobl_label-{autotop}_desc-laplace_coords.nii.gz 
+    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 
   upenn:
-    T1w: templates-3d/tpl-upenn/tpl-upenn_desc-hipptissue_dseg.nii.gz
-    dseg: templates-3d/tpl-upenn/tpl-upenn_desc-hipptissue_dseg.nii.gz
-    coords: templates-3d/tpl-upenn/tpl-upenn_dir-{dir}_label-{autotop}_coords.nii.gz
+    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
+
+
 
 
 
@@ -408,20 +409,20 @@ atlas:
 
 atlas_files:
   multihist7:
-    label_nii: atlases-unfolded/multihist7/sub-maxprob_label-hipp_desc-manualsubfieldsunfoldaligned_dseg.nii.gz
-    label_list: atlases-unfolded/multihist7/labellist.txt
-    thick: atlases-unfolded/multihist7/thickness.nii.gz
-    curv: atlases-unfolded/multihist7/curvature.nii.gz
-    gyr: atlases-unfolded/multihist7/gyrification.nii.gz
+    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
   bigbrain:
-    label_nii: atlases-unfolded/bigbrain/sub-bigbrain_hemi-{hemi}_label-hipp_desc-manualsubfields_dseg.nii.gz
-    label_list: atlases-unfolded/bigbrain/sub-bigbrain_labellist.txt
+    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
   magdeburg:
-    label_nii: atlases-unfolded/magdeburg/sub-all_hemi-{hemi}_label-hipp_desc-manualsubfields_maxprob.nii.gz
-    label_list: atlases-unfolded/magdeburg/magdeburg_labellist.txt
+    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
   freesurfer:
-    label_nii: atlases-unfolded/freesurfer/sub-all_hemi-{hemi}_space-unfold_label-hipp_desc-freesurfersubfields_dseg.nii.gz
-    label_list: atlases-unfolded/freesurfer/freesurfer_labellist.txt
+    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
 
 
 inject_template: upenn
@@ -460,7 +461,7 @@ modality: T2w
 
 
 
-#these will be downloaded to ~/.cache/hippunfold or $HIPPUNFOLD_CACHE_DIR
+#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'
@@ -471,21 +472,6 @@ 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_files_osf:
-  multihist7: 'https://files.ca-1.osf.io/v1/resources/v8acf/providers/osfstorage/65395b782827451220b86dd8/?zip='
-  bigbrain: 'https://files.ca-1.osf.io/v1/resources/v8acf/providers/osfstorage/65395b8b13d27b123094c96f/?zip='
-  magdeburg: 'https://files.ca-1.osf.io/v1/resources/v8acf/providers/osfstorage/65395b8013d27b122f94c938/?zip='
-  freesurfer: 'https://files.ca-1.osf.io/v1/resources/v8acf/providers/osfstorage/65395b8513d27b123094c96a/?zip='
-#https://github.com/CenterForOpenScience/osf.io/issues/8256#issuecomment-379833911
-
-template_files_osf:
-  CITI168: 'https://files.ca-1.osf.io/v1/resources/v8acf/providers/osfstorage/65395bf0282745121fb86a93/?zip='
-  dHCP: 'https://files.ca-1.osf.io/v1/resources/v8acf/providers/osfstorage/65395bff13d27b123094c9b4/?zip='
-  MBMv2: 'https://files.ca-1.osf.io/v1/resources/v8acf/providers/osfstorage/65395c0887852d133ca597dd/?zip='
-  MBMv3: 'https://files.ca-1.osf.io/v1/resources/v8acf/providers/osfstorage/65395c0e8a28b11240ffc6e9/?zip='
-  upenn: 'https://files.ca-1.osf.io/v1/resources/v8acf/providers/osfstorage/65395c1613d27b122a94ca09/?zip='
-#https://github.com/CenterForOpenScience/osf.io/issues/8256#issuecomment-379833911
-
 crop_native_box: '256x256x256vox'
 crop_native_res: '0.2x0.2x0.2mm'
 

hippunfold/download_models.py

@@ -0,0 +1,84 @@
+#!/usr/bin/env python3
+import argparse
+import errno
+import os
+
+import requests
+import yaml
+from appdirs import AppDirs
+
+
+def get_model_dict():
+    # get list of model urls
+    model_cfg = os.path.join(
+        os.path.dirname(__file__), "config", "nnunet_model_urls.yml"
+    )
+    with open(model_cfg, "r") as cfg:
+        model_dict = yaml.load(cfg, Loader=yaml.FullLoader)
+    return model_dict
+
+
+def parse_args(model_dict):
+    parser = argparse.ArgumentParser(
+        prog="hippunfold_download_models",
+        description="Tool for downloading U-net models for hippunfold",
+    )
+
+    parser.add_argument("--models", nargs="+", dest="models", choices=model_dict.keys())
+    args = parser.parse_args()
+    return args
+
+
+def main():
+
+    # get the model dict first, so we know what to parse
+    model_dict = get_model_dict()
+    inputs = parse_args(model_dict)
+
+    if "HIPPUNFOLD_CACHE_DIR" in os.environ.keys():
+        print(
+            f"HIPPUNFOLD_CACHE_DIR defined, using: {os.environ['HIPPUNFOLD_CACHE_DIR']}"
+        )
+        download_dir = os.environ["HIPPUNFOLD_CACHE_DIR"]
+    else:
+        print(f"HIPPUNFOLD_CACHE_DIR not defined, using default location")
+        # create local download dir if it doesn't exist
+        dirs = AppDirs("hippunfold", "khanlab")
+        download_dir = dirs.user_cache_dir
+
+    try:
+        os.mkdir(download_dir)
+    except OSError as exc:
+        if exc.errno != errno.EEXIST:
+            raise
+        pass
+
+    if inputs.models == None:
+        models = model_dict.keys()
+    else:
+        models = inputs.models
+
+    for modality in models:
+        url = model_dict[modality]
+        tarfile = url.split("/")[-1]
+        local_path = os.path.join(download_dir, tarfile)
+
+        # add ?dl=1 to url
+        url = "".join([url, "?dl=1"])
+
+        # if it doesn't exist, download the file
+        if not os.path.exists(local_path):
+            # download it:
+            print(f"Downloading {modality} model...")
+            print(f"   url = {url}")
+            print(f"   dest = {local_path}")
+            r = requests.get(url, allow_redirects=True, stream=True)
+            with open(local_path, "wb") as f:
+                f.write(r.content)
+            print("   Download complete")
+        else:
+            print(f"Skipping {modality} model: already downloaded to {local_path}")
+
+
+if __name__ == "__main__":
+    main()

hippunfold/resources/atlases-unfolded/bigbrain/bigbrain_snaplabels.txt

@@ -0,0 +1,24 @@
+################################################
+# ITK-SnAP Label Description File
+# File format: 
+# IDX   -R-  -G-  -B-  -A--  VIS MSH  LABEL
+# Fields: 
+#    IDX:   Zero-based index 
+#    -R-:   Red color component (0..255)
+#    -G-:   Green color component (0..255)
+#    -B-:   Blue color component (0..255)
+#    -A-:   Label transparency (0.00 .. 1.00)
+#    VIS:   Label visibility (0 or 1)
+#    IDX:   Label mesh visibility (0 or 1)
+#  LABEL:   Label description 
+################################################
+    0     0    0    0        0  0  0    "Clear Label"
+    1   255    0    0        1  1  1    "Subiculum"
+    2     0  255    0        1  1  1    "CA1"
+    3     0    0  255        1  1  1    "CA2"
+    4   255  255    0        1  1  1    "CA3"
+    5     0  255  255        1  1  1    "CA4"
+    6   255    0  255        1  1  1    "DG"
+    7   255  239  213        1  1  1    "SRLM"
+    8   240   86  224        1  1  1    "Cyst"
+

hippunfold/resources/atlases-unfolded/bigbrain/desc-subfields_atlas-bigbrain_dseg.tsv

@@ -0,0 +1,9 @@
+index	name	abbreviation
+1	subiculum	Sub
+2	CA1	CA1
+3	CA2	CA2
+4	CA3	CA3
+5	CA4	CA4
+6	dentate_gyrus	DG
+7	SRLM	SRLM
+8	cysts	Cyst

hippunfold/resources/atlases-unfolded/bigbrain/sub-bigbrain_hemi-L_label-hipp_desc-manualsubfields_dseg.nii.gz

@@ -0,0 +1,10 @@
+Subiculum
+1 0 0 255 255
+CA1
+2 133 222 255 255
+CA2
+3 0 255 170 255
+CA3
+4 255 162 0 255
+CA4
+5 255 0 0 255

hippunfold/resources/atlases-unfolded/bigbrain/sub-bigbrain_hemi-R_label-hipp_desc-manualsubfields_dseg.nii.gz

@@ -0,0 +1,6 @@
+Freesurfer subfield atlas
+
+Generated using workflow from https://github.com/khanlab/hippunfold-create-atlas#freesurfer
+This creates probalistic and maxprob (used here) labels by running hippunfold & freesurfer subfield segmentation on ds002168 (openneuro, 48 subjects) and mapping the freesurfer labels to the unfolded space.
+
+ 

hippunfold/resources/atlases-unfolded/bigbrain/sub-bigbrain_labellist.txt

@@ -0,0 +1,10 @@
+index	name	abbreviation
+203	parasubiculum	ParaSub
+204	presubiculum	PreSub
+205	subiculum	Sub
+206	CA1	CA1
+208	CA3	CA3
+209	CA4_and_dentate gyrus	CA4_DG
+226	tail	Tail
+227	SRLM	SRLM
+228	cysts	Cyst

hippunfold/resources/atlases-unfolded/freesurfer/README.md

@@ -0,0 +1,10 @@
+#No.	Label Name	R	G	B	A
+1	subiculum	255	0	0	0
+2	CA1	0	255	0	0
+3	CA2	0	0	255	0
+4	CA3	255	255	0	0
+5	CA4	0	255	255	0
+6	dentate_gyrus	255	0	255	0
+7	SRLM	255	239	213	0
+8	cysts	0	0	205	0
+

hippunfold/resources/atlases-unfolded/freesurfer/desc-subfields_atlas-freesurfer_dseg.tsv

@@ -0,0 +1,88 @@
+alveus
+201 255 204 153 255
+perforant_pathway
+202 255 128 128 255
+parasubiculum
+203 175 175 75  255
+presubiculum
+204 64  0   64  255
+subiculum
+205 0   0   255 255
+CA1
+206 255 0   0   255
+CA2
+207 128 128 255 255
+CA3
+208 0   128 0   255
+CA4
+209 196 160 128 255
+GC-DG
+210 32  200 255 255
+HATA
+211 128 255 128 255
+fimbria
+212 204 153 204 255
+lateral_ventricle
+213 121 17  136 255
+molecular_layer_HP
+214 128 0   0   255
+hippocampal_fissure
+215 128 32  255 255
+entorhinal_cortex
+216 255 204 102 255
+molecular_layer_subiculum
+217 128 128 128 255
+Amygdala
+218 104 255 255 255
+Cerebral_White_Matter
+219 0   226 0   255
+Cerebral_Cortex
+220 205 63  78  255
+Inf_Lat_Vent
+221 197 58  250 255
+Perirhinal
+222 33  150 250 255
+Cerebral_White_Matter_Edge
+223 226 0   0   255
+Background
+224 100 100 100 255
+Ectorhinal
+225 197 150 250 255
+HP_tail
+226 170 170 255 255
+Polymorphic-Layer
+227 128 255 128 255
+Intracellular-Space
+228 204 153 204 255
+HP_body
+231 0 255 0 255
+HP_head
+232 255 0 0 255
+presubiculum-head
+233 32  0   32  255
+presubiculum-body
+234 64  0   64  255
+subiculum-head
+235 0   0   175 255
+subiculum-body
+236 0   0   255 255
+CA1-head
+237 175 75   75   255
+CA1-body
+238 255 0   0   255
+CA3-head
+239 0   80 0   255
+CA3-body
+240 0   128 0   255
+CA4-head
+241 120 90 50 255
+CA4-body
+242 196 160 128 255
+GC-ML-DG-head
+243 75   125 175 255
+GC-ML-DG-body
+244 32  200 255 255
+molecular_layer_HP-head
+245 100 25   25   255
+molecular_layer_HP-body
+246 128 0   0   255