Hi, I recently collected some fMRI data using the spiral in and out sequence, and want to use fMRIprep for preprocessing, I wonder if anyone has run spiral functional data (not fieldmap data) by fMRIprep and could potentially share the experience or if anyone foresees a problem with fMRIprep processing spiral fMRI data?
My current concern is spiral sequence doesn’t have the conventional phase encoding direction (AP/PA/RL/LR), not sure if fMRIprep can allow that the .json doesn’t have such information.
You should be able to use fMRIPrep, but we don’t have any susceptibility distortion correction methods that work with spiral sequences. If you are okay without that (I assume it’s an issue for spiral, but I haven’t looked into it at all), then you should have no problems. If not, we’d be happy to work with you or anybody else to add support for those methods.
Hi Chris, Thanks a lot for your instant reply. To provide more information, we didn’t collect fieldmap for this spiral in and out sequence given it has shown reduced signal dropout due to susceptibility-induced field gradients, so it’s fine I can’t do SDC correction.
I have two more questions,
Can I assume the default SDC and experimental SDC will be off if I don’t provide fieldmap?
Regarding the .json file for spiral fMRI data, is that okay if I remove the phase encoding direction and polarity parameters or maybe I put fake values there?
Yes, SDC will only be run if fieldmaps are found or --use-syn-sdc is passed. (--use-syn-sdc requires PhaseEncodingDirection, so it would fail in any case. If it runs, SDC hasn’t been applied.
Removing should be fine. The only field fMRIPrep requires for BOLD data is RepetitionTime (and that’s dictated by BIDS). If you find that it fails because of other missing metadata let us know and we can fix it.