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[RF] Remove the recon workflows from QSIPrep #802
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When I disabled test_main, I got the weirdest error:
|
This is from a bad call to the logger in interfaces/dsi_studio.py. There were a couple other instances in there that I fixed, but it switched from a print (that allowed multiple arguments) to a logger.info, where it is expecting the second and later arguments to be used in formatting the first |
It's still really weird that the way I run the tests affects it. I'll have to dig into that in a follow-up PR. |
I was wondering about that too. qsiprep will print the error but exit with a 0 status |
Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## master #802 +/- ##
==========================================
- Coverage 29.86% 28.59% -1.27%
==========================================
Files 97 69 -28
Lines 14627 10218 -4409
Branches 1892 1331 -561
==========================================
- Hits 4368 2922 -1446
+ Misses 10126 7195 -2931
+ Partials 133 101 -32 ☔ View full report in Codecov by Sentry. |
Closes #697.
It's difficult to maintain the recon workflows and preprocessing workflows in one package. We're creating a separate package that takes QSIPrep (or UKBB) preprocessed data and runs the recon workflows on it. The new QSIRecon repo can be found here.
For users this means that the following options will no longer be available from qsiprep:
--recon-only
--recon-spec
--recon-input
--recon-input-pipeline
--freesurfer-input
--skip-odf-reports
--interactive-reports-only
And because preprocessing doesn't directly use freesurfer, we don't need
--fs-license-file
Also, QSIPrep will no longer append
qsiprep
to the output directory.