External Email - Use Caution        

Hi Andrew,

We do not currently support wm-hypointensities with recon-all-clinical runs. The synthseg based segmentation saved as aseg.mgz will not contain this label and thus your asset.stats has no information on this.

Karthik

On Jul 20, 2023, at 9:39 AM, Huang, Yujing <YHUANG43@mgh.harvard.edu> wrote:

        External Email - Use Caution        


You can try ‘—empty’ to see if it reports differently.
 
Yujing
 
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Huang, Yujing
Sent: Thursday, July 20, 2023 9:38 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Cc: Gopinath, Karthik <KGOPINATH@mgh.harvard.edu>; Iglesias Gonzalez, Juan E. <JIGLESIASGONZALEZ@mgh.harvard.edu>
Subject: Re: [Freesurfer] WM Hypointensities
 

        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
 

        External Email - Use Caution        

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
 

        External Email - Use Caution        

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

 
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer