External Email - Use Caution        

Hi Andrew,

 

I see you specified ‘—nonempty’.  ‘wm-hypointensity’ is probably excluded because the voxel count is zero. I’m only looking at this from programmer point of view. I don’t know how wm-hypointensity is assigned in recon-all-clinical.

 

Best,

 

Yujing

 

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Andrew Dedinas Geoly
Sent: Wednesday, July 19, 2023 1:59 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] WM Hypointensities

 

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I ran the following as an example:

 

mri_segstats --seg /Users/andrewgeoly/Desktop/Stanford_BSL/TBI/Structural_Analysis/BIDS_data/ses-V2_reconall_clin/sub-54095s001/mri/aseg.mgz --ctab /Applications/freesurfer/7.4.0/FreeSurferColorLUT.txt --nonempty --excludeid 0 --sum /Users/andrewgeoly/Desktop/Stanford_BSL/TBI/Structural_Analysis/BIDS_data/ses-V2_reconall_clin/sub-54095s001/stats/aseg.stats 

 

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Huang, Yujing <YHUANG43@mgh.harvard.edu>
Sent: Tuesday, July 18, 2023 9:40 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] WM Hypointensities

 

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Hi Andrew,

 

I can’t answer if wm-hypointensity is supported in recon-all-clinical. I’m assuming that you obtained aseg.stats by running mri_segstats. How does your command look like?

 

Best,

 

Yujing

 

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Andrew Dedinas Geoly
Sent: Tuesday, July 18, 2023 11:44 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] WM Hypointensities

 

        External Email - Use Caution        

Hi Freesurfer experts!

 

I am hoping to extract the wm-hypointensity data from some recon-all-clinical runs. I was able to extract aseg.stats information correctly but noticed there was no information regarding the wm-hypointensities.

 

Is this supported by recon-all-clinical?

 

Best,

Andrew

 

 

---  

 

Andrew D. Geoly, MS 

 

Research Data Analyst 1

 

Brain Stimulation Lab 

 

Department of Psychiatry and Behavioral Sciences 

 

Stanford University School of Medicine