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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,
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
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:
External Email - Use CautionHello,
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
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1SkfYTGplTGZkUmGQ4QczqticfHXX8i9Ntb0tv4nkUblaMm... The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1apP5b73sJ-CiMBu0d89iVD_17tcYL1hOut7ORyZ_qzJxO9... < https://secure-web.cisco.com/1apP5b73sJ-CiMBu0d89iVD_17tcYL1hOut7ORyZ_qzJxO9... .
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
External Email - Use Caution 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.edumailto: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:
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
freesurfer@nmr.mgh.harvard.edu
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Beatriz Cavendish -
Douglas N. Greve -
Huang, Yujing