The error I am getting is after running freesurfer on mprage T1 images. I am doing volumetrics study where I am using freesurfer to determine the measurements of cortical an dsubcortical regions. The subcortical masks as well as the white matter/gray matter outlines seems to be OK after the freesurfer run. I am using whole brain volume as a co-variate for statistical analysis, but due to errors in freesurfer skull stripping the brain masks are either including non-brain tissue or excluding some brain tissues. This will affect the whole brain volume calculation.
May you suggest how this skullstrip error may be avoided.
Is there a way to 3dskullstrip the data and then use the skullstripped mprage data to run freesurfer for obtaining cortical and subcortical segmentation?
Thank you!
Rashmi
