Fmriprep pepolar with paired bold runs

4

Hi @bryjack0890,

Yes, you can’t use two BOLD series of opposite encoding directions together directly to perform pepolar SDC. Instead, you need to provide _epi.nii.gz files that indicate how you want to use each image with respect to the other. Your suggestions seem like they’re going in the right direction, but just to be clear, I would suggest the following:

Assuming you have two images

  • sub-OA01/func/sub-OA01_task-control_acq-MB_dir-PA_run-01_bold.nii.gz
  • sub-OA01/func/sub-OA01_task-control_acq-MB_dir-AP_run-01_bold.nii.gz

You could copy them, respectively, to:

  • sub-OA01/fmap/sub-OA01_task-control_acq-MB_dir-PA_run-01_epi.nii.gz
  • sub-OA01/fmap/sub-OA01_task-control_acq-MB_dir-AP_run-01_epi.nii.gz

If you want to truncate these to 1 or several volumes, you should. I don’t have particular notions of the best number. fMRIPrep will combine however many volumes you have into a single volume, so if you want to perform your own motion-correction and averaging, you can do that.

These should also have .json sidecar files. Please see Section 8.3.5.4 of the BIDS specification for the necessary metadata. The IntendedFor field should point to the opposite-encoded BOLD image.

Hope this helps.

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