Hi there,

 

I have several participants that, when ran through Freesurfer 7.3, end of losing portions of brain matter during skull-stripping. Interestingly, when I run them through mri_synthstrip alone, this issue does not happen. If mri_synthstrip is the default for 7.3, how can this be happening? Is there perhaps a step before in the standard recon-all pipeline that is causing the issue? I’ve attached two images: one skull stripped with synthstrip and the other the brainmask.mgz file generated through recon-all.

 

 

 

Thanks so much,

Carly

 

 

FREESURFER_HOME   /Users/mackilloplab/Applications/freesurfer7.3

FSFAST_HOME       /Users/mackilloplab/Applications/freesurfer7.3/fsfast

FSF_OUTPUT_FORMAT nii.gz

SUBJECTS_DIR      /Applications/freesurferOLDdownload/subjects_OLDFSDOWNLOAD/NEUROALC_SS

MNI_DIR           /Users/mackilloplab/Applications/freesurfer7.3/mni