I want to use the HCP Pipeline BIDS app to preprocess T1w, T2w, and BOLD data collected at the CMRR. The BOLD data were acquired to apply the "PEpolar" method, whereby one short (TR=1.5s, 10 reps) set of EPI data were collected with AP phase-encoding, and one long (TR=1.5s, 400 reps) set of EPI data were collected with PA phase-encoding. Per BIDS specifications and others' suggestions (e.g., https://neurostars.org/t/fmriprep-docker-fieldmap-correction/623 ), I have stored the short acquisition AP data in the "fmap" directory and the long acquisition PA data in the "func" directory; the JSON sidecar for the "fmap" file points to the appropriate BOLD series via the "IntendedFor" key (see directory contents below).
I know that the HCP Pipeline BIDS app expects a fieldmap in order for the functional data to be preprocessed. However, based on documentation, I suspect the BIDS app in its current version does not support when the "fmap" is a paired reverse-phase encode image? I.e., the BIDS app does not sense that FSL's TOPUP should be used (rather than FUGUE or whatever program is currently used for this distortion correction). Has anyone else encountered this dilemma? Are there plans to add this functionality to the BIDS app? Any information would be greatly appreciated. Thank you in advance. Best, Scott *##bids subject session directory contents:* *./func/sub-7536262_ses-00_task-rest_run-01_bold.nii.gz* *./func/sub-7536262_ses-00_task-rest_run-01_bold.json* *./func/sub-7536262_ses-00_task-rest_run-01_events.tsv* *-* *./fmap/sub-7536262_ses-00_acq-rest_dir-AP_run-01_epi.nii.gz* *./fmap/sub-7536262_ses-00_acq-rest_dir-AP_run-01_epi.json* *-* *cat ./fmap/sub-7536262_ses-00_acq-rest_dir-AP_run-01_epi.json* * "PhaseEncodingDirection": "j-", * * "IntendedFor": "func/sub-7536262_ses-00_task-rest_run-01_bold.nii.gz", * * "TotalReadoutTime": 0.0527996, * -- Scott J. Burwell, PhD Postdoctoral Research Fellow Department of Psychiatry University of Minnesota, Minneapolis, MN burw...@umn.edu _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
