FIX: Correctly detect completed ReconAll steps #1824
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CircleCI should be fixed after merging #1825, sorry about that. |
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No worries. This one needs to be tested by hand, anyway. |
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Mislabeled locations caused some parts of ReconAll to be re-done unnecessarily
- Recon-all considers "nothing to do" an error - Add ``force_run`` instance variable to permit user override
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Okay. I've tested this on FSv5.3 and FSv6.0. Rebased to test on new circle config. |
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Mislabeled locations caused some parts of ReconAll to be re-done unnecessarily in v6, specifically
parcstats*andbalabels.Affects both FreeSurfer 5.3 and 6. I missed this before because these are fairly short recon steps, and I was mostly focused on
mri/andsurf/. Some steps were un-/misdocumented, as well, so this PR adds them to match actual behavior.If recon-all decides there's nothing to do, it returns with an exit code of 1, so in this case I've switched to an informative echo. Added a
force_runinstance variable for use with non-standard flags (e.g.-hippo-subfieldsor-clean-*).Tested on a completely reconstructed subject in 5.3. Will test on 6.0 momentarily.
Follow-up to #1790.