Fmriprep – Failed normalisation with lesion mask

[heffjos]

@sandrushba

One more question though: After the preprocessing without freesurfer, the brain mask does not include the lesioned area anymore (see image below). Is that normal?

Yes this is normal. fmriprep uses ANTs to register the T1w to a template and fmriprep uses an exclusion mask to mask the T1w image in ANTs rather than the brain mask. The exclusion mask has the same dimensions as the T1w and has value 1 at every voxel except at the lesion. For the lesion voxels, their value is set to 0.

@sandrushba

And do you know if there is a a way in fmriprep to output a normalized version of the lesion mask as well or do you usually also use other tools for this?

Other tools are need for this, probably only ANTs. The transformation from T1w to template space is in the .h5 file in the anat directory (example: sub-001s01_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5). This topic might have more useful and detailed information how to use the .h5 files: Extracting individual transforms from composite .h5 files (fmriprep) I used the first example in the first post to transform a lesion mask from T1w to template space, and the results looked fine.