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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-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:
External Email - Use Caution 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 TJHarkey@uams.edumailto:TJHarkey@uams.edu
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Douglas N. Greve" dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto: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.edumailto: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.edumailto:TJHarkey@uams.edu
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