Will this work on the brainmask.auto.mgz if I use the --brain-vol-from-seg command?

 

 

 

 

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

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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