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

TJHarkey@uams.edu

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