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
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Greve, Douglas N.,Ph.D. -
Pfannmoeller, Joerg Peter