Can I skip skull stripping in Freesurfer?

Hi everyone,

I have low quality T1w images. Freesurfer can not extract brain as well. ANT can do that in a good way. So I want to use ANTs output as Freesurfer input. Is there a way to skip skull stripping in Freesurfer? Can I use skull-stripped brain as input?

I appreciate it if you could help me to clarify this issue.

Hi, this is exactly the strategy used by FMRIPREP: see details here:

the T1w reference is skull-stripped using a Nipype implementation of the tool (ANTs), which is an atlas-based brain extraction workflow

Surface reconstruction is performed in three phases. The first phase initializes the subject with T1w and T2w (if available) structural images and performs basic reconstruction (autorecon1) with the exception of skull-stripping. Skull-stripping is skipped since the brain mask calculated previously is injected into the appropriate location for FreeSurfer. For example, a subject with only one session with T1w and T2w images would be processed by the following command:

$ recon-all -sd <output dir>/freesurfer -subjid sub-<subject_label> \ -i <bids-root>/sub-<subject_label>/anat/sub-<subject_label>_T1w.nii.gz \ -T2 <bids-root>/sub-<subject_label>/anat/sub-<subject_label>_T2w.nii.gz \ -autorecon1 \ -noskullstrip
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