Re: "pepolar" unwarping method with fmriprep - single reverse-encoded EPI for all BOLD runs?

[zreagh]

Hi all,

I imagine this will be a pretty quick one, but I have a dataset where I have acquired several EPI BOLD runs with P>>A phase encoding, and a single brief EPI with reversed A>>P phase encoding. The intention is of course to use the “pepolar” TOPUP method for unwarping.

As I intend for this acquisition to be used to unwarp all of my P>>A acquisitions, is it possible for me to list multiple BOLD runs in the “IntendedFor” section of the JSON file, or do I need to do something like create multiple copies of the reverse-encoded NIFTI and JSON files with different “IntendedFor” values for each BOLD run I wish to unwarp?

(Sorry if this is obvious, I haven’t been able to find an answer in the bids_spec document.)

Thanks!
-Zach

[effigies]

is it possible for me to list multiple BOLD runs in the “IntendedFor” section of the JSON file

Yes. From the spec (Section 8.3.5):

The IntendedFor field may contain one or more filenames with paths relative to the subject subfolder. The path needs to use forward slashes instead of backward slashes. Here’s an example with multiple target scans:

{
   "IntendedFor": ["ses-pre/func/sub-01_task-motor_run-1_bold.nii.gz",
                   "ses-post/func/sub-01_task-motor_run-1_bold.nii.gz"]
}

[zreagh]

Thanks, and sorry for overlooking that!