On 9/20/2024 9:54 AM, Sneha Pandya wrote:
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Thank you Doug,
Just to clarify, do we superimpose on aparc+aseg or gtmseg? I believe
subfileds and gtmseg would have same resolution.
I don't think they are the same reg as gtmseg should be 0.5mm, but you
can run
mri_vol2vol --regheader --mov subfields.mgz --targ gtmseg.mgz --interp
nearest --o subfields-in-gtmseg.mgz
If not combining subfields can we superimpose just one segmentation
(in particularly we are interested in inferior colliculi, which
freesurfer segments -> 7100 , Brainstem-inferior-colliculus as in
FreeSurferColorLUT.txt) to gtmseg with suggested approach? If so can
we just resample this segmentation to gtmseg resolution and the
combine it?
Yes, that is the gist. You will probably want to make sure that there is
no hippocampus voxels in the output; there could be because of edge
effects. I don't think we seg colliculus unless it is one of the newer
segs (just because it is in the LUT does not mean we segment it).
On a separate note, when we run mri_gtmpvc with save-input flag,
input.nii.gz is not pvc’ed at all right, like not even gtm which is
default even when other PVC and tfe is turned off?
Correct. I think it may just be rescaled. You can use mueller-gartner
(--mgx) to voxel-wise pvc of GM
Regards,
Sneha
*From:*freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Douglas N. Greve
*Sent:* Friday, September 20, 2024 9:36 AM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* [EXTERNAL] Re: [Freesurfer] petsurfer using brainstem subfields
It is tricky but possible, but not might be worth it. You need to have
a whole brain segmentation, so you could superimpose the subfields
onto the aparc+aseg. You will need to create a color table for it (see
gtmseg. ctab after running gtmseg).
It is tricky but possible, but not might be worth it. You need to have
a whole brain segmentation, so you could superimpose the subfields
onto the aparc+aseg. You will need to create a color table for it (see
gtmseg.ctab after running gtmseg). You can then specify the new seg
with --seg to mri_gtmpvc. How well it works is another question. The
smaller the ROI, the harder it is to do the PVC. It will give you an
answer, probably without complaining, but it might not be an accurate one.
On 9/18/2024 10:40 PM, Sneha Pandya wrote:
* External Email - Use Caution *
Dear team,
I wanted to follow up on the following question. Thank you.
Regards,
Sneha
*From:*Sneha Pandya
*Sent:* Tuesday, August 27, 2024 12:22 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* petsurfer using brainstem subfields
Dear team,
We need to use PVC brainstem subfield which we intend to use as
high binding region for MRTM based kinetic analysis. Can we run
mri_gtmpvc using brainstemSsLabels.v12.mgz as input segmentation?
Or is to possible to combine gtmseg and brainstem subfields and
use this combined segmentation for mri_gtmpvc (will be using GTM
or RBV for PVC).
Thank you,
Sneha
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