Add missing filename patterns #131
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I took a crack at adding the missing patterns. @araikes any chance you could test this branch out? As long as you have |
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I'll grab it and check for some of the lower hanging fruits first. |
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## main #131 +/- ##
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Coverage 33.53% 33.53%
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Files 57 57
Lines 7114 7114
Branches 964 964
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Hits 2386 2386
Misses 4626 4626
Partials 102 102 ☔ View full report in Codecov by Sentry. |
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Did not work. Tested Example but all outputs fail: |
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Thanks! I think that one's a problem with how DerivativesDataSink was called instead of the patterns. I just pushed a fix. |
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No joy. Also, qsirecon isn't detecting errors "correctly" as no outputs get written due to the failures for |
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I changed the extension from |
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Dumb question... Is that the right bind point? If I shell into image without binding that branch , that path ( |
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You're right, sorry about that. The correct path is |
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Ok... That runs for
Testing |
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Aside from the issue in #130, |
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@araikes I just tried to fix the problems in reorient_fslstd. |
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@tsalo works as expected. Just gonna a quick test on the hsvs outputs. |
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Updates write Questions:
Appears to address #112, barring the questions here. |
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I think the atlas/desc discrepancy is just a bug. Any cases where we have I didn't realize the hsvs files were probsegs instead of dsegs, but I can change that. |
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Ok. Last two things and then I think everything related to expected file writing is addressed (AFAIK):
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Technically the "atlas" entity in those files needs to be changed to "seg", but I have that change in #123. With BIDS-Atlas, any standard-space atlases or segmentations get called |
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Ok. That works for me. Also, I'm testing @mattcieslak's comment in #128 that this will address the matrix plot issue in the reports. |
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Connectivity plots work, addressing #128. |
Open
mattcieslak
approved these changes
Oct 28, 2024
| @@ -154,6 +155,7 @@ def init_qsirecon_to_fsl_wf( | |||
| DerivativesDataSink( | |||
| dismiss_entities=("desc",), | |||
| suffix="mask", | |||
| extension=".nii.gz", | |||
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Does this need compress=True? Or does the extension take care of that?
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Either works. compress=True is probably more flexible if we ever support non-NIfTI outputs here.
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Closes #122 and closes #128.
Changes proposed in this pull request