Heudiconv fieldmap unpacking

1

Heudiconv has unpacked my fieldmap into three files… essentially:

run-01-phasediff1.nii.gz
run-01-phasediff2.nii.gz
run-02-phasediff.nii.gz
(all with complete BIDS format names, simplified to make it easier to read)

The run-01 json files have different echo times and run-02 matches the longer of the two echo times. Are the run-01 files supposed to be the “magnitude” files?

Any help is appreciated!!

2

Hi @Justin_Smith1 - likely your run-01 files are in fact the magnitude images.

But you can check this out to be certain by loading up each image in a viewer, and comparing with some examples found here
https://lcni.uoregon.edu/kb-articles/kb-0003

HTH

3

Edit: nvm… I had an error from not capitalizing the T in EchoTime2… Re-running again, will update if it worked

4

Was asked to update on this to help people with the same dilemma… Hope this helps!!