Add ability to read/write freesurfer surface files in scanner ras#1420
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jduemose wants to merge 2 commits intonipy:masterfrom
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Add ability to read/write freesurfer surface files in scanner ras#1420jduemose wants to merge 2 commits intonipy:masterfrom
jduemose wants to merge 2 commits intonipy:masterfrom
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Sorry, you caught me just as I was heading off on vacation, and following up with nibabel has been low on my queue since getting back. Merging |
Codecov Report❌ Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## master #1420 +/- ##
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- Coverage 95.44% 95.37% -0.07%
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Files 209 209
Lines 29782 29788 +6
Branches 4472 4472
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- Hits 28424 28410 -14
- Misses 925 943 +18
- Partials 433 435 +2 ☔ View full report in Codecov by Sentry. 🚀 New features to boost your workflow:
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Sep 22, 2025
| assert any('extension code' in str(ww.message) for ww in w) | ||
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| # Test reading/writing a surface file in scanner RAS | ||
| cmd = f"mris_convert --to-scanner {pjoin(data_path, 'surf', 'lh.inflated')} {surf_path}" |
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We don't install FreeSurfer to run tests. Could you contribute the converted file to https://codeberg.org/nipy-data/nitest-freesurfer?
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Previously, only freesurfer surface files with coordinates in unknown or surface ras/tkregister space could be read. Following #1419, this PR adds the ability to read surface files whose coordinates are stored in scanner ras as well.
Let me know if calling a freesurfer function via
subprocessas part of the test is a problem - but I wasn't sure how to test this feature otherwise.