Partial field of view and wholebrain fieldmap corrections using FSL Feat

Hello NeuroStars,

I have an experiment where we have acquired fMRI data using a 0.8mm partial field of view sequence. We have additionally acquired a whole-brain 1.2mm BOLD image to help with registration to a 1mm T1w mprage image.

I am running the preprocessing using FEAT and my question is about the fieldmap corrections. I have a mag and phase diff image that is acquired at the beginning of the scanning session. These are converted to a rads image using the fsl_create_fieldmaps command using the appropriate values. The mag and rads image are then used as inputs to Feats fieldmap correction. To perform registration, I select the whole-brain scan as the ‘initial highres’ image.

It appears that the Feat-based fieldmap correction is being applied to both my partial field of view image and my whole-brain image, is this correct? If so, I don’t think this would be done correctly as both images have different dwell times (indeed the unwarping outputs do not look correct, happy to share if necessary). Has anyone delt with a similar issues before? Do I need to manually perform the fieldmap corrections on both BOLD images independently?

Many thanks for your help!



Just thought I’d update for anyone having similar issues. I got around this by performing fsl_prepare_fieldmap and FUGUE on the 1.2mm and 0.8mm BOLD images outside of FEAT. To do this I had to register the rads image to both. This worked fine using FLIRT to the 1.2mm image, however FLIRT struggled with the rads to the partial field of view 0.8mm image. To resolve this, I first registered the 1.2mm BOLD image to 0.8mm BOLD image using FLIRT, which worked, and then applied this transformation to the 1.2mm rads image, bringing it into the 0.8mm space. Following this I ran FUGUE.