Hello Doug,

I have two different separations that I would like to achieve. Both are about a finer subdivision of the cortex:

1) I would like to separate the volume fractions between two directly neighboring cortical regions (close in 2-D surface space).
2) I would like to separate the volume fractions between two neighboring gyri (close together in 3-D space but far away from each other in 2-D space).

My naive idea is to generate new sub-segmentations of the cortex. Since they are for highly specialized applications I will most probably need to generate them by myself. Is that possible or is there another way to achieve this in FreeSurfer that I am not aware of?

Best Joerg
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu>
Sent: Tuesday, September 10, 2019 11:48 AM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Custom Segmentation of the Cortex usable with mri_compute_volume_fractions
 
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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