Hello,
I have a dataset that some of the fMRI data were scanned in a phase encoding direction different from the field map.
Specifically, the fMRI data phase encoding direction was j, and the field map in j-. And we used the double echo method for getting the field map.
Is there any way to salvage this subset of data and do distortion correction? Usually, we use FSL but I’m open to other software.
Also, would it cause a problem to do group analysis on the fMRI dataset since some of it was scanned in j-, and some in j?
Please let me know if more info is needed. Thank you.
Hey @fugueeet, generally-speaking it doesn’t matter if your GRE fieldmap is collected with the same PE direction as the BOLD data you’d like to unwarp. Note that in FEAT, under Pre-stats → B0 unwarping, you’ll be asked to provide the ‘unwarp direction’ (i.e., the PE direction) of the scan you’re applying the fieldmap to.
So as long as this is correctly defined, it’s totally fine to use an A >> P fieldmap on a P >> A scan, and I also don’t think there are any problems with combining A >> P and P >> A data in a group-level analysis (as long as they were properly unwarped).
Here’s a general reference for working with fieldmaps that you may find helpful: Acquiring and using field maps – Lewis Center for Neuroimaging
