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DCAN-Labs / dcan-macaque-pipeline

The actual pipeline code, based on hcp, for non-human-primates - sp macaques.
BSD 3-Clause "New" or "Revised" License
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No ptseries in output of DCANBOLDProcessing #5

Open amitch3 opened 4 years ago

amitch3 commented 4 years ago

DCANBOLDProc is not creating ptseries (any of them - the only output file is the dtseries) output files for analysis. this prevents the use of file_mapper.sh.

b3n3dikt commented 4 years ago

Figured I would add my two cents. This issue has to do with the current pipeline not pointing to the correct parcellations folder. Currently, it is pointing to a human parcellations folder and not a monkey folder. e.g. this folder /opt/dcan-tools/dcan_bold_proc/templates/parcellations needs to point at actual macaque parcellations dlabel files. I have been working around this by mountain my own parcellations folder to have the pipeline use this instead e.g. -v /mnt/rose/shared/projects/FAIR_users/bene/parcellations:/opt/dcan-tools/dcan_bold_proc/templates/parcellations hope that helps.

ericearl commented 4 years ago

@b3n3dikt That is a perfect workaround for now, thank you! @amitch3 You're right, this is a bug and will be addressed.