How to Run Fieldmap-Less Distortion Correction (SyN-SDC) in fMRIPrep v25.0.0 when fieldmaps exist?

Software Support
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1

Hi all

We’re only able to get fieldmap-less distortion correction (SyN-SDC) when we remove the fmap folder containing AP and PA fieldmaps and run the fMRIPrep (v25.0.0) command with --use-syn-sdc. If the fieldmaps are present, fMRIPrep defaults to the PEPOLAR correction and does not produce results from the SyN-based method.

Is there a way to force the SyN-SDC to run even when fieldmaps are present? (We want fMRIPrep to run both distortion correction methods for the same subject.)

Here’s what we’ve tried:

  1. –use-syn-sdc flag (without fmap folder): SyN-SDC correction performed
  2. –force-syn-sdc flag (with fmap folder): Only PEPOLAR correction performed
  3. –use-syn-sdc flag (with fmap folder): Only PEPOLAR correction performed
  4. –ignore fieldmaps and --force-syn-sdc flags (with fmap folder): No correction performed
  5. –ignore fieldmaps and --use-syn-sdc flags (with fmap folder): No correction performed

We would appreciate any insights or workarounds!

Many thanks
Anja

2

Hi @Anja and welcome to neurostars!

You will not be able to do this with a single command.

Have you tried --ignore fieldmaps --use-syn-sdc --force-syn? And if that doesn’t work, additionally supplying a BIDS filter file that ignores fmaps?

Best,
Steven