BrainStat
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The urls of bigbrain histology data for fslr32k is actually 64k, not 32k
- What is the current behavior?
When running the following code:
histology_profiles = read_histology_profile(template="fslr32k")
, the error will occur:
"File /opt/miniconda3/envs/imagingwork/lib/python3.8/site-packages/brainstat/context/histology.py:159, in read_histology_profile(data_dir, template, overwrite)
[154](https://file+.vscode-resource.vscode-cdn.net/opt/miniconda3/envs/imagingwork/lib/python3.8/site-packages/brainstat/context/histology.py:154) download_histology_profiles(
[155](https://file+.vscode-resource.vscode-cdn.net/opt/miniconda3/envs/imagingwork/lib/python3.8/site-packages/brainstat/context/histology.py:155) data_dir=data_dir, template=template, overwrite=overwrite
[156](https://file+.vscode-resource.vscode-cdn.net/opt/miniconda3/envs/imagingwork/lib/python3.8/site-packages/brainstat/context/histology.py:156) )
[158](https://file+.vscode-resource.vscode-cdn.net/opt/miniconda3/envs/imagingwork/lib/python3.8/site-packages/brainstat/context/histology.py:158) with h5py.File(histology_file, "r") as h5_file:
--> [159](https://file+.vscode-resource.vscode-cdn.net/opt/miniconda3/envs/imagingwork/lib/python3.8/site-packages/brainstat/context/histology.py:159) profiles = h5_file.get(template)[...]
[160](https://file+.vscode-resource.vscode-cdn.net/opt/miniconda3/envs/imagingwork/lib/python3.8/site-packages/brainstat/context/histology.py:160) if civet_template:
[161](https://file+.vscode-resource.vscode-cdn.net/opt/miniconda3/envs/imagingwork/lib/python3.8/site-packages/brainstat/context/histology.py:161) fsaverage_surface = fetch_template_surface("fsaverage")
TypeError: 'NoneType' object is not subscriptable"
I debugged it and found that the bigbrain_profiles download from the urls for template "fslr32k" in brainstat/data/data_urls.json
is actually for the template "fs_LR_64k", not "fslr32k".
},
"bigbrain_profiles": {
"fsaverage": {
"url": "https://box.bic.mni.mcgill.ca/s/znBp7Emls0mMW1a/download"
},
"fsaverage5": {
"url": "https://box.bic.mni.mcgill.ca/s/N8zstvuRb4sNcSe/download"
},
"fslr32k": {
"url": "https://box.bic.mni.mcgill.ca/s/6zKHcg9xXu5inPR/download"
}
},
Maybe this can be fixed by modifing the fslr32k to fslr64k and downsampling the mesh.