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nipreps / fmriprep

fMRIPrep is a robust and easy-to-use pipeline for preprocessing of diverse fMRI data. The transparent workflow dispenses of manual intervention, thereby ensuring the reproducibility of the results.
https://fmriprep.org
Apache License 2.0
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CIFTI space output RPI orientation #2118

Closed saigerutherford closed 4 years ago

saigerutherford commented 4 years ago

The HCP task analysis scripts require the subcortical volumetric data to have RPI orientation, but the fMRIPrep (version 20.0.4) CIFTI output has LPI orientation for the subcortical volumetric data which creates an error when merging the task contrast maps back into CIFTI space (the script splits the CIFTI file into surface & volume, runs task analysis, then merges back together). If anyone would like to run HCP task analysis on this data they need to flip the subcortical data to be RPI orientation in order for the HCP task scripts to work.

mgxd commented 4 years ago

@saigerutherford the CIFTI subcortical orientation has been changed to be compatible with HCP analysis in the upcoming 20.1.0 LTS release. The latest release candidate 20.1.0rc2 includes this change, if you would like to pilot one of your participants.

mgxd commented 4 years ago

@saigerutherford now that 20.1.0 has been released, could you try running one participant and see if the orientation is fixed?

oesteban commented 4 years ago

@saigerutherford could you reopen this issue if you see we really didn't fix it? Also confirming this worked for you would be great, but I'll close this issue for now.