Ok thank you!

If we conducted a study measuring brain to intracranial volume ratio, do you think that BrainVolNotVent and Etiv-only ratio would provide accurate measures? Is there another more robust way to make this calculation using FreeSurfer? 

We are studying brain atrophy in MCA stroke patients. I have seen studies indicating there is some bias regarding etiv but that the correlation with manual segmentations is roughly R =.8. 

Is the BrainVolNotVent to Etiv-only ratio a valid estimation of atrophy or are there statistical normalizations or corrections that complicate that procedure? 

 

 

 

Thank you so much for your time.

 

 

No, you need a segmentation

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Will this work on the brainmask.auto.mgz if I use the --brain-vol-from-seg command?

 

 

-- 

Thomas Harkey
University of Arkansas for Medical Sciences

College of Medicine, Class of 2022
501-553-6318

TJHarkey@uams.edu

 

 

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Sunday, August 23, 2020 at 2:03 PM
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] BrainSegNotVent

 

Actually, that file won't be there either because it does not get created until all processing is done (not just autorecon1). You can run mri_segststats like
mri_segstats --seg subject/mri/aseg.presurf.mgz --ctab-default --sum subject/stats/aseg.presurf.stats
Then add up all the segmentations you want to get BrainSegNotVent

On 8/23/2020 11:42 AM, Douglas N. Greve wrote:

Are you using v7? If so, look in subject/stats/brainvol.stats

On 8/22/2020 5:39 PM, Harkey, Thomas Jarrott wrote:

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Hello,
I am a student learning free surfer. I was able to obtain intracranial volume by running 

recon-all   –i  file.dcm   –subject  bert –autorecon1

and then

mri_segstats --subject bert --etiv-only

 

How can I obtain the BrainSegNotVent volume? I have tried 

mri_segstats --subject bert --brain-vol-from-seg 

 

however, “ERROR: must specify a segmentation volume”

 

Can this be calculated using the data from autorecon1, or do I need to run -all? Which segmentation do I need to specify? 

 

My contact information is below,

Thank you!

-- 

Thomas Harkey
University of Arkansas for Medical Sciences

College of Medicine, Class of 2022
501-553-6318

TJHarkey@uams.edu

 

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