Using GR scans with opposite PE to create fieldmaps

[jsein]

@Giada

@Giada

2. Is there a way to derive the phasediff and magnitude.nii files from the rfMRI?

I am wondering whether these files can be extracted somehow from the rfMRI NIFTI/DICOM or if they should be provided from the scanner. I understand that this should not be possible if the only acquisition parameter that differs in the two scans (fMRI and rfMRI) is the PE. There would be a phase difference if the two scans were acquired at different echo times, right?

No, these files (phasediff and magnitude) come from the measurent made by a different sequence, a gradient-echo sequence, with two echo times, not a gradient-echo EPI image as it is the case for bold.

In the case where you have only GRE-EPI images with reversed PE, you can still try the PEPOLAR method , the correction should work.
Otherwise you can still do SDC with Syn-BOLD DisCo, for wich you don’t need any fieldmap:

Using synthetic field map from synbold-disco with fmriprep

I’m working with an older clinical fMRI resting-state dataset that does not contain field maps. I would like to correct for distortions but do not like the syn-sdc option in fmriprep (produced wonky images) and have thus opted to use synbold-disco GitHub - MASILab/SynBOLD-DisCo: Synthetic BOLD images for distortion correction of fMRI without additional calibration scans to create synthetic field maps .I want to further preprocess the data using fmriprep and am unsure how best to do that. The to…