Can fmriprep be run without Susceptibility Distortion Correction?

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As I mentioned in a previous post, we’re trying to run our custom lab pipeline and fmriprep against each other to see if they provide similar outputs. However, since a standalone tool is not available for performing SDC, we would like to remove SDC from the fmriprep workflow as well for comparison.

Is there a way we can word the fmriprep command to bypass SDC?

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Yes, there is. Please check this section of the documentation https://fmriprep.readthedocs.io/en/latest/usage.html

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Hi @oesteban,

Thanks for the clarification. However, I still don’t entirely follow.

I went through the documentation and the two relevant options I found were --use-syn-sde which is an option to run SDC in the absence of fieldmaps and --ignore fieldmaps to disable corresponding parts of the workflow.

This seems to suggest that SDC is only performed either in the presence of externally provided fieldmaps, or if the command is worded such that SDC should be performed in the absence of fieldmaps, using an experimental technique.

In my run of fmriprep, I neither provided fieldmaps, nor used the --use-syn-sde flag to the command. The Visual Quality assessment report stated nonetheless that SDC had been performed - ‘The BOLD time-series (including slice-timing correction when applied) were resampled onto their original, native space by applying a single, composite transform to correct for head-motion and susceptibility distortions.’

Please let me know why this is the case.

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Hi @Shreya_13, you are right, the boilerplate is wrong, it shouldn’t state that.

I’ve started this https://github.com/poldracklab/fmriprep/issues/1818 to follow up.

Thanks for reporting. Just to clarify, your data didn’t go through SDC, it is just the citation boilerplate that is wrong.