Re: [Freesurfer] BrainSegNotVent {Disarmed}

eve" *Reply-To: *Freesurfer support list *Date: *Thursday, September 3, 2020 at 8:17 AM *To: *"freesurfer@nmr.mgh.harvard.edu" *Subject: *Re: [Freesurfer] BrainSegNotVent {Disarmed} Not really, since it requires having the surfaces. You can add them up yourself, or you can binarize aseg.

Re: [Freesurfer] BrainSegNotVent {Disarmed}

. *From:* freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve *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

Re: [Freesurfer] BrainSegNotVent {Disarmed}

: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve 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

Re: [Freesurfer] BrainSegNotVent {Disarmed}

*Subject: *Re: [Freesurfer] BrainSegNotVent {Disarmed} No, you need a segmentation On 8/23/2020 8:18 PM, Harkey, Thomas Jarrott wrote: *External Email - Use Caution * Will this work on the brainmask.auto.mgz if I use the --brain-vol-from-seg command? -- *Thomas Harkey **

Re: [Freesurfer] BrainSegNotVent {Disarmed}

y-To: Freesurfer support list Date: Monday, August 24, 2020 at 9:14 AM To: "freesurfer@nmr.mgh.harvard.edu" Subject: Re: [Freesurfer] BrainSegNotVent {Disarmed} No, you need a segmentation On 8/23/2020 8:18 PM, Harkey, Thomas Jarrott wrote: External Email - Use Cau

Re: [Freesurfer] BrainSegNotVent {Disarmed}

No, you need a segmentation On 8/23/2020 8:18 PM, Harkey, Thomas Jarrott wrote: External Email - Use Caution Will this work on the brainmask.auto.mgz if I use the --brain-vol-from-seg command? -- *Thomas Harkey ** University of Arkansas for Medical Sciences*** *College of Medicine

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 i

Re: [Freesurfer] BrainSegNotVent {Disarmed}

External Email - Use Caution Will this work on the brainmask.auto.mgz if I use the --brain-vol-from-seg command? -- Thomas Harkey University of Arkansas for Medical Sciences College of Medicine, Class of 2022 501-553-6318 tjhar...@uams.edu From: on b

Re: [Freesurfer] BrainSegNotVent {Disarmed}

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 eff