Real/imaginary images to BIDS compliant magnitude/phase difference maps for fMRIPREP

1

Hi there

I have the following images in nifti format from an old dataset. I just about have enough details on the dataset to manually create jsons including the essential fields for fMRIPREP (I think).

fieldmap-magnitude-2.nii.gz
fieldmap-imaginary-1.nii.gz
fieldmap-real-1.nii.gz
fieldmap-real-2.nii.gz
fieldmap-imaginary-2.nii.gz
fieldmap-magnitude-1.nii.gz

However, I wondered how I can get the phase difference maps from here? Or am i missing something? I am not overly familiar with using field maps.

thanks in advance!

2

Hello,
You might want to include the JSON files that will reveal the scanner manufacturer. I assume this is a FSL FUGUE compatible gradient echo Fieldmap (rather than a TOPUP spin echo sequence). You can determine details with visual inspection. You will want to follow these instructions. Note that some scanners can be set to save the estimated Fieldmap (in Hz), while other manufacturers require you to calculate this.