ENH: Add M-CRIB-S surface processing #283
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- Add new flag `--surface-recon-method` to support various surface processing pipelines: - FreeSurfer's `recon-all` and `infant_recon_all`, as well as a new `mcribs` option. - Deprecate redundant `--force-reconall` flag.
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Codecov ReportPatch coverage:
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## master #283 +/- ##
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- Coverage 32.07% 31.99% -0.08%
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Files 53 53
Lines 4727 4772 +45
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- Misses 3211 3245 +34
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- Remove defaults from inputs. It now is required to explicitly pass in processing steps. - Add helper methods to verify outputs of crucial checkpoints (after neonatal cortex reconstruction, FS file generation) - Save the brain mask under the proper intermediate filename.
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This PR adds a new workflow (
init_mcribs_surface_recon_wf) that can be used as an alternative torecon-all/infant_recon_allto produce anatomical surfaces.To use this workflow, the new flag
--surface-recon-methodneeds to be used with the optionmcribs.With the addition of this new flag, the now redundant
--force-reconallflag is deprecated.Additionally, the infantFS surface workflow was renamed to better reflect which method is being used.
To Do
brain.mgzin FreeSurfer directory (needed forrecon_report)