fMRIPrep Output Fieldmap Units

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1

Hello,
I’m running both fMRI and ASL analyses on our data, and I was hoping to use the fmriprep-processed fieldmap, e.g. “sub-PD4001_ses-1_fmapid-auto00000_desc-preproc_fieldmap” as the phase image and a brain-masked version of the epi image “sub-PD4001_ses-1_fmapid-auto00000_desc-epi_fieldmap” as magnitude image for input into oxford_asl, instead of rerunning topup and using the fout / iout files as I was previously doing (as is suggested here) in the interest of avoiding redundant data / processing.

However, I cannot find any documentation stating what units this output fieldmap is in. Are these fieldmaps already in rad/s, or are they in Hz like topup’s output typically is? I’m using fMRIprep 20.2.5 if that’s relevant.

Thank you!!

2

The outputs in recent fMRIPrep are in Hz.

I do not believe that we output preprocessed fieldmaps in 20.2.5, so I’m not really sure what you’re looking at.

3

Hi Chris,
Sorry, you’re right, I was looking at the wrong piece of my notes before - it’s version 22.0.2, not 20.2.5, my bad. For 22.0.2, fieldmaps are in Hz?

Thanks!
Natalie

4

Yes.

Adding some additional text because discourse doesn’t like “Yes”.

1 Like
5

Great, thanks so much!