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DCAN-Labs / dcan_bold_processing

functional connectivity preprocessing for resting state fMRI outputs of the dcan-fmri-pipelines
BSD 3-Clause "New" or "Revised" License
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-cifti-parcellate error when empty grayordinates exist (due to change in wb_command >= v1.4.0) #14

Closed madisoth closed 3 years ago

madisoth commented 3 years ago

As of wb_command v1.4.0, the default behavior of -cifti-parcellate is to throw an error if data is missing for any grayordinate in a parcel. On a subject I was testing this caused the parcellation step to fail, although the pipeline (abcd-hcp-pipeline) was able to continue running to the end.

There is the -legacy-mode flag to make -cifti-parcellate function as it did in wb_command < v1.4.0; I'm going to test if that fixes the issue:

If -legacy-mode is specified, parcels will be defined as the overlap between
a label and the data, with no errors for missing data vertices or voxels,
and empty parcels discarded.

https://www.humanconnectome.org/software/workbench-command/-cifti-parcellate

madisoth commented 3 years ago

resolved in PR #15, merge pending

arueter1 commented 3 years ago

Since this will be resolved by the pull request I am closing this issue.