Hi Beatriz,
mri_segstats has masking options -
https://surfer.nmr.mgh.harvard.edu/fswiki/mri_segstats
Hope this helps.
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Beatriz Cavendish
Sent: Thursday, December 22, 2022 1:35 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] [WARNING: ATTACHMENT UNSCANNED]Volumetric extraction
from volumetric mask in MNI space
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Sorry, I think I expressed myself incorrectly. I segmented 50 heads and wanted
to quantify the volume for each of the 50 heads using this mask. Is there a
step before mri_segstats to record the mask in each head space and quantify for
each individual?
Em qui., 22 de dez. de 2022 às 01:13, Douglas N. Greve
<dgr...@mgh.harvard.edu<mailto:dgr...@mgh.harvard.edu>> escreveu:
Try
mri_segstats --seg Cluster1_R.nii.gz --id 1 --sum sum.R.dat
That will give you the number of voxels that have a value=1 times the size of
the voxel (so the volume). It will not be in MNI space unless the nifti files
you sent are in MNI space.
On 12/21/2022 5:42 PM, Beatriz Cavendish wrote:
External Email - Use Caution
Hello,
I would like to know the step by step to obtain volume (mm3) from a volumetric
mask in the MNI space (follow the attached nifti file). I checked the forum but
the tutorials are for surface extraction and cortical thickness.
Yours sincerely,
--
Beatriz Araújo Cavendish, MSc
PhD student | Psychologist
University of São Paulo
São Paulo/SP - Brazil
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--
Beatriz Araújo Cavendish, MSc
PhD student | Psychologist
University of São Paulo
São Paulo/SP - Brazil
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