Fmriprep: resampling of denoised BOLDs & SUSAN smoothing options

Hi everyone,

When running ICA-AROMA within fmriprep 1.2.4, BOLDs are automatically resampled. However, I would like to keep resampling to a minimum (and be able to use the brain masks provided by fmriprep). So I thought of manually smoothing my preprocessed BOLDs (MNI) using SUSAN and then removing fmriprep-derived components using fsl_regfilt.

Can anyone direct me to fmriprep’s implementation of SUSAN? Looking at these defaults (https://rdrr.io/cran/fslr/man/susan.html), I am not sure whether fmriprep used the very same ones (except for sigma, obviously)…

Also: Does anyone know why/at which step BOLDs are being resampled in ICA-AROMA?

Many thanks for your help!

Best,
Elmsch

fMRIPrep uses the nipype wrapper for SUSAN.

The full workflow is here:

BOLD series are resampled to MNI152NLin6Asym before being passed to that workflow. If you’re interested, I can pull out the relevant bits.

Many thanks for your help, @effigies!

So fmriprep does not explicitly pass any brightness threshold to the nipype wrapper but must be using some kind of default, right?

Just a quick follow-up question: After resampling of my BOLDs to MNI space, they have a shape of 78 x 93 x 78 x time (MNI152NLin2009cAsym_desc-preproc_bold). When inspecting my BOLDs after running ICA-AROMA, they have a shape of 91 x 109 x 91 x time (MNI152NLin2009cAsym_desc-smoothAROMAnonaggr_bold). So there must happen some additional resampling within the AROMA workflow in fmriprep. Do you know where and why this happens?

Best,
Elmsch

It calculates the median value within a mask and thresholds at 0.75x the median value.

Unless things have changed I’m not aware of, AROMA outputs are only provided in MNI152NLin6Asym. Each template is likely to have slightly different dimensions.

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