Do you mean you want to separate the volume fractions between two 
adjacent segmentations rather than just all of cortex?

On 9/10/19 10:04 AM, Pfannmoeller, Joerg Peter wrote:
> Hello,
> I would like to generate a custom segmentation of the cortex. That 
> segmentation should be restricted to a certain labeled region (e.g. a 
> Brodmann Area). If possible I would also like to restrict the region 
> to the lower half or upper half of the cortex. Let's call these new 
> segmentations sub-segmentations. I would like to use 
> mri_compute_volume_fractions with this segmentation to compute the 
> volume fractions of the voxels in a scan that overlap with these new 
> sub-segmentations of the cortex. Are there tools for this purpose in 
> FreeSurfer?
> Best Joerg
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