Add warning for fslr32k histology data resolution mismatch#373
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zihuaihuai merged 2 commits intomasterfrom Nov 25, 2025
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Add warning for fslr32k histology data resolution mismatch#373zihuaihuai merged 2 commits intomasterfrom
zihuaihuai merged 2 commits intomasterfrom
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Known issue: The fslr32k histology profile data on the server contains fs_LR_64k resolution (64984 vertices) instead of fs_LR_32k (32492 vertices). - Add warning in read_histology_profile() when template is fslr32k - Add warning in download_histology_profiles() when downloading fslr32k data - Reference issue #369 in warnings for users to track the status - Remove skip for fslr32k test in test_histology.py (netneurotools issue fixed) This is a server-side data hosting issue. The correct fix requires uploading the proper 32k resolution data file to the server. Fixes #369
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Pull request overview
This PR addresses a known data resolution mismatch issue (#369) where the fslr32k histology profile data on the server contains fs_LR_64k resolution (64984 vertices) instead of the expected fs_LR_32k resolution (32492 vertices). The changes add user-facing warnings to inform users about this server-side data hosting issue.
- Add warning messages in both
read_histology_profile()anddownload_histology_profiles()when using fslr32k template - Remove pytest skip for fslr32k test that was related to a now-fixed netneurotools Unicode bug
- Reference issue #369 in warnings to help users track the status of this known issue
Reviewed changes
Copilot reviewed 2 out of 2 changed files in this pull request and generated 2 comments.
| File | Description |
|---|---|
| brainstat/context/histology.py | Adds warning messages (lines 160-168, 208-213) to alert users about the fslr32k data resolution mismatch when reading or downloading histology profiles |
| brainstat/tests/test_histology.py | Removes the pytest skip for fslr32k template testing (lines 21-23 removed) now that the netneurotools Unicode bug has been fixed |
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- Add retry mechanism with 3 attempts and exponential backoff - Handle RemoteDisconnected, URLError, and TimeoutError exceptions - Add timeout=30 to urlopen to prevent hanging - Improves CI test reliability when downloading from box.bic.mni.mcgill.ca This fixes intermittent CI failures like: 'http.client.RemoteDisconnected: Remote end closed connection without response'
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Known issue: The fslr32k histology profile data on the server contains fs_LR_64k resolution (64984 vertices) instead of fs_LR_32k (32492 vertices).
This is a server-side data hosting issue. The correct fix requires uploading the proper 32k resolution data file to the server.
Fixes #369