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Hello,Two final questions: when I did autorecon1 and autorecon2-volonly, I then ran the following command:mri_segstats –brain-vol-from-seg –seg aseg.presurf.mgz –sum statsHowever, it is just printing the volumes of each segmentation and not adding them up. I want the BrainSegNotVent measurement without having to do the entire recon all. What am I doing wrong?Is there a way to obtain the aseg.stats file or brainvol.stats file without using recon-all?Just trying to save time.Thanks for your help.
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgreve@mgh.harvard.edu>
Sent: Monday, August 24, 2020 9:12 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] BrainSegNotVent {Disarmed}Right, you will actually need to run both autorecon1 and -autorecon2-volonly
-autorecon2-volonly will take a few hours
On 8/23/2020 7:35 PM, Harkey, Thomas Jarrott wrote:
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Ok, I tried that command and it didn’t work because aseg.presurf.mgz doesn’t exist in that directory
I don’t think that file was generated with autorecon1.
So do you think I need to run reconall -all to get the BrainSegNotVent?
If there were a more efficient way to obtain this volume, I would be open to learning it.
--
Thomas Harkey
University of Arkansas for Medical SciencesCollege of Medicine, Class of 2022
501-553-6318
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 runningrecon-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 SciencesCollege of Medicine, Class of 2022
501-553-6318
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