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Revert "initial attempt at moving all resources files to OSF"
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -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' |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,84 @@ | ||
| #!/usr/bin/env python3 | ||
| import argparse | ||
| import errno | ||
| import os | ||
|
|
||
| import requests | ||
| import yaml | ||
| from appdirs import AppDirs | ||
|
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|
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| 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 | ||
|
|
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|
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| def parse_args(model_dict): | ||
| parser = argparse.ArgumentParser( | ||
| prog="hippunfold_download_models", | ||
| description="Tool for downloading U-net models for hippunfold", | ||
| ) | ||
|
|
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| parser.add_argument("--models", nargs="+", dest="models", choices=model_dict.keys()) | ||
| args = parser.parse_args() | ||
| return args | ||
|
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|
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| def main(): | ||
|
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||
| # get the model dict first, so we know what to parse | ||
| model_dict = get_model_dict() | ||
| inputs = parse_args(model_dict) | ||
|
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||
| 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 | ||
|
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||
| 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"]) | ||
|
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||
| # 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}") | ||
|
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||
|
|
||
| if __name__ == "__main__": | ||
| main() |
24 changes: 24 additions & 0 deletions
24
hippunfold/resources/atlases-unfolded/bigbrain/bigbrain_snaplabels.txt
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -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" | ||
|
|
9 changes: 9 additions & 0 deletions
9
hippunfold/resources/atlases-unfolded/bigbrain/desc-subfields_atlas-bigbrain_dseg.tsv
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -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 |
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10 changes: 10 additions & 0 deletions
10
hippunfold/resources/atlases-unfolded/bigbrain/sub-bigbrain_labellist.txt
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -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 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -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. | ||
|
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|
10 changes: 10 additions & 0 deletions
10
hippunfold/resources/atlases-unfolded/freesurfer/desc-subfields_atlas-freesurfer_dseg.tsv
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -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 |
10 changes: 10 additions & 0 deletions
10
hippunfold/resources/atlases-unfolded/freesurfer/desc-subfields_freeview_desg.tsv
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -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 | ||
|
|
88 changes: 88 additions & 0 deletions
88
hippunfold/resources/atlases-unfolded/freesurfer/freesurfer_labellist.txt
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -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 |
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