8 Sep
2020
8 Sep
'20
6:46 p.m.
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 mailto: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:
* 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-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces@nmr.mgh.harvard.edu> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgreve@mgh.harvard.edu> <mailto:dgreve@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* *TJHarkey@uams.edu <mailto:TJHarkey@uams.edu>* *From: *<freesurfer-bounces@nmr.mgh.harvard.edu> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Douglas N. Greve" <dgreve@mgh.harvard.edu> <mailto:dgreve@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* *TJHarkey@uams.edu <mailto:TJHarkey@uams.edu>* ------------------------------------------------------------------------ Confidentiality Notice: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. 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