Yes, just copy aseg.mgz and edit the copy. Then run mri_segstats. Look in recon-all.log for the mri_segstats command that is used to create the aseg.stats file. Adapt that command. The output will have an entry for the lesion (make sure to use code 99 for the label id).
On 7/24/2020 1:43 PM, Manuel, Morganne wrote:
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Hey Freesurfer,
I am new to Freesurfer. I wanting to use Freesurfer for measuring grey and white matter volumes in Multiple sclerosis. However I am wondering if there is a way to manually make a lesion mask for each individual and then use the mask to subtract the lesion volume from the white matter volume. We run recon we break it apart. So is there a certain recon set I can use to add the lesion mask to tell Freesurfer to subtract this volume from the white matter?
Many thanks,
Morganne
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