External Email - Use Caution 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: https://secure-web.cisco.com/1GYp9YVgT3IIE67jb48sFXaEizpNOJyZRUgKL5vDUwx_U39xxjrLMFBNhTxtj7sMD3dgS4Fi-KQqcsDOLk6tnscZfUR_d5_jnsH4q5mi8mxDjYdGmFfVO1DWbCEAFdW3FZXJddre4EsMQe72s-ietR9ptbeXYa5yp5WL-1KVIwGGK_F8BHpxojM6BS4lqEhT8Mg2Z_-YJa27XiX1WhmK9jYL1vaM4PQ4Fe8kcDmkB24698-WNPLqid3met5WuTLAWwkKUA6ELeeuG394Gl8yHGA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Fmri_segstats Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@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 External Email - Use Caution 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://secure-web.cisco.com/1o-JKFzt6ZOjW1TJu1947tOOT6wRYrM8aQyd70edsXmZHxFfSxuL3l1zg5IzyvSdP1JQp_mPCmI8cEpNXq6NaN7IX5-daXLwUILAwXzYdFrX5Ys5YU4uwVHT59dfb-1LvILukycXfPsJ6VUIe0DIW5lrGV9YtqYZC3ng3aZTzx8pYLbTbxYXYTUnvDFmNBtughuA0vLeKTtnoDjzRyW_ZFJ6k8sYvaxpiGdMtftC4YEeY_1ev0l6yMpLrOaK6UGNYAE0JWlzu-oKaDsgxCYp-PQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FVolumeRoiCorticalThickness<https://secure-web.cisco.com/1Z5OP8XDp2iTZo4YMybrzCFH9SwKBzyQx9vsSEFhl_f6qfhbWsl0xhAi5bYwjQG5MHh7ZBs9ADbhhnZ29DoSVWVVo5AquAm8aIde3IMQMJt9EBOhJ7ZoVI_JUHIYeCdpKAP5_-cZrBLflOE536wS6M31OKaD4bqQsKfG_furvWZ4uDamocw-yUSMKK2QadGa8bUJRw5TZn9pFhy_5xypbEQZ2g25BUdE17bxwUOwwlW1dD_5ekqmwY3sClBqLaWqGJVepW7LfU0bIa2D_8DfcDkx7Bkbp-YS_5h1d5YXXY_pOh7wAebQPQQmZxXhkixsQKQBwYfdv0BEthv-Pp5S9oQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FVolumeRoiCorticalThickness> 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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