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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:
External Email - Use CautionHi 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://secure-web.cisco.com/1VurGVMn29VBCV4gEY-1urMHf0Tc2Q5K6l_Q9RtFkHSD4bo... 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-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
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/1pXTMCre1AsCZTEIbgrEJaknmPI8CmxkcdA4Wms31XfrQ9E... 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:
- 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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