That scan looks low res and T2 weighted, so you would not run recon-all on it. But even if it were the right contrast/resolution, I think it is too extensive. I don't know if there is going to be something that we have that is going to do that for you.

On 9/8/2020 1:44 PM, Harkey, Thomas Jarrott wrote:

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Douglas,

We are conducting a study with stroke patients using DWI MRI. Image attached. Is Freesurfer capable of taking an MRI with an infarct (as you can see in the picture) and providing a volume for that hyperintense area?

Is there a command we can run do specify for that?

Would recon all do it?

Thanks

 

-- 

Thomas Harkey
University of Arkansas for Medical Sciences

College of Medicine, Class of 2022
501-553-6318

TJHarkey@uams.edu

 

 

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Thursday, September 3, 2020 at 8:17 AM
To: "freesurfer@nmr.mgh.harvard.edu" <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.presurf.mgz to just the regions you want (mri_binarize --match id1 id2 ...), then run mri_segstats on that

On 9/2/2020 2:04 PM, Harkey, Thomas Jarrott wrote:

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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:

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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

TJHarkey@uams.edu

 

 

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Douglas N. Greve" <dgreve@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:

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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.edu

 

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