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> on behalf of "Douglas
N. Greve" <dgr...@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:
* 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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