fMRIPrep not outputting preprocessed skull-stripped T1w images

Hi everyone,
I am using fMRIPrep 20.2.3 for a task-based fMRI analysis. For some reason, there are no skull-stripped T1w images output in MNI space in the derivatives folder.

I get these two files - one with the mask and one with the preprocessed, skull-in data; here are the suffixes:

  • space-MNI152NLin2009cAsym_res-2_desc-brain_mask.nii.gz
  • space-MNI152NLin2009cAsym_res-2_desc-preproc_T1w.nii.gz

How do I obtain the skull-stripped, preprocessed T1w image?


Hi @avannucci,

You can use these two fmriprep derivative files to generate a skull-stripped T1w image. An example, using FSL, is:

fslmaths space-MNI152NLin2009cAsym_res-2_desc-preproc_T1w.nii.g -mas space-MNI152NLin2009cAsym_res-2_desc-brain_mask.nii.gz space-MNI152NLin2009cAsym_desc-masked_T1w.nii.gz

1 Like

Thank you - this worked!