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:
External Email - Use Caution
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*
*tjhar...@uams.edu <mailto:tjhar...@uams.edu>*
*From: *<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of "Douglas
N. Greve" <dgr...@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:
* External Email - Use Caution *
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-boun...@nmr.mgh.harvard.edu
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu>
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of
Douglas N. Greve <dgr...@mgh.harvard.edu>
<mailto:dgr...@mgh.harvard.edu>
*Sent:* Monday, August 24, 2020 9:12 AM
*To:* freesurfer@nmr.mgh.harvard.edu
<mailto: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*
*tjhar...@uams.edu <mailto:tjhar...@uams.edu>*
*From: *<freesurfer-boun...@nmr.mgh.harvard.edu>
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of
"Douglas N. Greve" <dgr...@mgh.harvard.edu>
<mailto:dgr...@mgh.harvard.edu>
*Reply-To: *Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu>
<mailto: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.edu>
<mailto: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:
* 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*
*tjhar...@uams.edu <mailto:tjhar...@uams.edu>*
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