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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> Sent: Tuesday, July 18, 2023 9:40 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto: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

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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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer@nmr.mgh.harvard.edu> Cc: Gopinath, Karthik <KGOPINATH@mgh.harvard.edumailto:KGOPINATH@mgh.harvard.edu>; Iglesias Gonzalez, Juan E. <JIGLESIASGONZALEZ@mgh.harvard.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> Sent: Tuesday, July 18, 2023 9:40 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto: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

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