Using fmriprep with brain-extracted raw data

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Hi All,

I’m trying to process several open datasets with fmriprep but for some of them, the T1 images are shared with the brain already extracted which leads to poor fmriprep results.

I’m wondering if anyone had an idea of how this could be circumvented to allow me to still use fmriprep with those data?

Thank you for your help!

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Hi I saw this in the fmriprep documentation but never tried it myself:

Occasionally, openly shared datasets may contain preprocessed anatomical images as if they are unprocessed. In the case of brain-extracted (skull-stripped) T1w images, attempting to perform brain extraction again will often have poor results and may cause fMRIPrep to crash. fMRIPrep can attempt to detect these cases using a heuristic to check if the T1w image is already masked. This must be explicitly requested with ---skull-strip-t1w auto . If this heuristic fails, and you know your images are skull-stripped, you can skip brain extraction with --skull-strip-t1w skip . Likewise, if you know your images are not skull-stripped and the heuristic incorrectly determines that they are, you can force skull stripping with --skull-strip-t1w force , which is the current default behavior.

https://fmriprep.org/en/stable/workflows.html

1 Like
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Wow, I don’t know how I completely missed this. Thanks so much will give it a try!