Thank you for your response. If I wanted to calculate the surface area of this cortical ROI, would i pass lh.area.pial into <in>? Do i still use --accumulate flag?

Thank you,

Carlos

On Thu, Jun 15, 2023 at 5:17 PM Huang, Yujing <YHUANG43@mgh.harvard.edu> wrote:

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Hi Carlos,

Your commands look correct to calculate mean cortical thickness.

To calculate the total volume, pass lh.volume to –in <>, and specify –accumulate on the command line: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/mri_segstats

Best,

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Carlos Alcocer
Sent: Thursday, June 15, 2023 11:36 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Calculate cortical thickness of a volumetric ROI

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Hello,

I am trying to calculate the cortical thickness of a volumetric ROI that I created that I have in subject space for every subject in my dataset. I was using MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness as a guide.

Since, I already have the volumes in subject space. I did a modified pipeline and only did the following for each subject:
1. mri_vol2surf --mov /path/to/ROI5.nii --regheader --projfrac-max 0 1 0.1 --interp nearest --hemi lh --out lh.ROI5.mgh
2. mri_segstats --seg $SUBJECTS_DIR/subjid/surf/lh.ROI5.mgh --in lh.thickness --sum segstats-ROI5.txt

Does this make sense? Also, separately, is the volume that is also computed in this method accurate? I noticed that the volume is always equal to the number of voxels, which I assume a voxel is equal to 1mm^3? However, when looking at aseg.stats these volumes have different values from their number of voxels.

Thank you,

Carlos

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