Hi Beatriz,

mri_segstats has masking options - https://surfer.nmr.mgh.harvard.edu/fswiki/mri_segstats

Hope this helps.

Best,

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@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 <dgreve@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:

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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