Dear FreeSurfer expert
I am trying to create a mask for the right hemisphere frontal lobe cortex in order to calculate the mean cortical thickness for this specific ROI.
I am using the following commands:
To create a mask for the specific region: mri_binarize --i /mri/aparc+aseg --match 2028 --match 2027 --match 2003 --match 2024 --match 2018 --match 2020 --match 2019 --match 2014 --match 2032 --match 2002 --match 2026 --o /mri/rh_frontal_ctx.mgz
But I am not sure what the next step is -
I tried to follow this link: https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness(Cortica... Thickness of a Volume-defined ROI) fslregister --s fsaverage --mov /mri/T1.mgz --reg T1_to_fsaverage.dat but I am not sure if that is the correct way, and also my ROI in the fsaverage subject volume is not perfectly matched to what I expect it to be - how can I fix that? They are very different.
I also tried the mri_tessellate command to create surface by tessellating given input volume: mri_tessellate /data/Temp_efrat/subjects/TB_281_test/mri/rh_frontal_ctx_1.mgz -a 2028 2027 2003 2024 2018 2020 2019 2014 2032 2002 2026 frontal_ctx_test
I get this massage: changing type of input volume to 8 bits/voxel... $Id: mri_tessellate.c,v 1.32 2007/04/26 21:44:21 fischl Exp $ $Id: mrisurf.c,v 1.557.2.19 2009/08/05 22:10:21 nicks Exp $ slice 110: 431 vertices, 495 faces slice 120: 2986 vertices, 3215 faces slice 130: 6636 vertices, 7037 faces slice 140: 12817 vertices, 13506 faces slice 150: 22361 vertices, 23291 faces slice 160: 32454 vertices, 33549 faces slice 170: 44058 vertices, 45346 faces slice 180: 56174 vertices, 57633 faces slice 190: 67020 vertices, 68612 faces slice 200: 75820 vertices, 77402 faces slice 210: 78847 vertices, 80236 faces slice 220: 78900 vertices, 80278 faces slice 230: 78900 vertices, 80278 faces slice 240: 78900 vertices, 80278 faces slice 250: 78900 vertices, 80278 faces using the conformed surface RAS to save vertex points... writing 2028 using vox2ras matrix: -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000;
But I can not find the output file of that command.
And then to calculate the thickness of the frontal cortex by using the mris_anatomical_stats TB_281_test rh -t frontal_ctx_test
I am a little confused, I will be grateful if you can help me with that.
Thanks a lot
Efrat