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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 stats
However, 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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve
<dgr...@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 Sciences
College of Medicine, Class of 2022
501-553-6318
tjhar...@uams.edu<mailto:tjhar...@uams.edu>
From:
<freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
on behalf of "Douglas N. Greve"
<dgr...@mgh.harvard.edu><mailto:dgr...@mgh.harvard.edu>
Reply-To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu>
Date: Sunday, August 23, 2020 at 2:03 PM
To: "freesurfer@nmr.mgh.harvard.edu"<mailto:freesurfer@nmr.mgh.harvard.edu>
<freesurfer@nmr.mgh.harvard.edu><mailto: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:
External Email - Use Caution
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
tjhar...@uams.edu<mailto:tjhar...@uams.edu>
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