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Maybe for post-processing in case you have multi frames, you can merge all of
them (multi-echo MPRages) and then take the RMS to get one 3D volume.
Ahmed
Ahmed A. Bahrani, Ph.D.,
Sanders-Brown Center on Aging
University of Kentucky
Hi Ammar
In the mri dir there are segmented volumed called aseg.mgz and aparc+aseg.mgz
where every voxel has an index into the FreeSurferColorLUT.txt lookup file
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Ammar Shujaa
Sent: Tuesday, August 3, 2021 4:19 AM
To:
do you mean you want a binary mask? If so you can run something like
mri_binarize --i aseg.mgz --match 17 --o left.hippocampus.mgz
where 17 is the index for left hippo as found in
$FREESURFER_HOME/FreeSurferColorLUT.txt
On 8/3/2021 4:18 AM, Ammar Shujaa wrote:
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yes, that looks good. I don't have a ton of experience with these
nonlinear interactions between continuous variables, but it might be a
good idea to multiply the demeaned variables.
On 8/2/2021 6:08 PM, Avi Gharehgazlou wrote:
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Thank you so much for
But do you know why it has multiple frames? We collect multi-echo T1
MPRAGEs that will have multiple frames. We then reduce it to one frame
by computing the RMS across frames (actually the scanner can output a
separate RMS series). Check to see whether you got an RMS series in
their. If not,
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Hello FreeSurfur Developers,
A have completed the segmentation of T1 MRI image using recon all.
I want to know how to get the segmentation of specific structures using mri and
surf folders. For example, Thalamus, prefrontal lobe, grey matter and then
