Hi Nooshin

if you want to specify a label such as cortex.label then use the -l <label name> flag. I don't think the -t needs subjid/surf, but I would have thought it would either give you an error message or work properly. Did you get any errors? It sounds like you got it to work in any case. Bruce On Thu, 5 Apr 2012, Nooshin Zadeh wrote:

Whu when I use "mris_anatomical_stats subjid lh", I get different result?  Here average CT is 2.163+-0.898, while with 2 previous commands they were zeros. number of vertices                      = 110852 total surface area                      = 71971 mm^2 total gray matter volume                = 174387 mm^3 average cortical thickness              = 2.136 mm +- 0.898 mm average integrated rectified mean curvature     = 0.168 average integrated rectified Gaussian curvature = 0.133 folding index                           = 5368 intrinsic curvature index               = 529.3

On Thu, Apr 5, 2012 at 1:25 PM, Nooshin Zadeh nooshin.zade@gmail.com wrote: Dear Freesurfer group I want to get cortical thickness, and I am confused between using these two command lines:

mris_anatomical_stats -t subjid/surf/lh.thickness -b subjid lh

that gives following information     number of vertices     total surface area (mm^2)     total gray matter volume (mm^3)     average cortical thickness +- standard deviation (mm)     integrated rectified mean curvature     integrated rectified Gaussian curvature     folding index     intrinsic curvature index     structure name

110852  71971      0  0.000 0.000     0.168     0.133     5368   529.3  /Users/christine/Result_FS_Corrected/N219c/surf/lh.white

and  mris_anatomical_stats -t subjid/label/lh.cortex.label -b subjid lh

that gives following information     number of vertices     total surface area (mm^2)     total gray matter volume (mm^3)     average cortical thickness +- standard deviation (mm)     integrated rectified mean curvature     integrated rectified Gaussian curvature     folding index     intrinsic curvature index     structure name

110852  71971      0  0.000 0.000     0.168     0.133     5368   529.3  /Users/christine/Result_FS_Corrected/N219c/surf/lh.white.

Can you please guide me which one is the right one for measuring cortical thickness? Why for both of them (mean+-STD) is zero? Thanks in advance.

Best Regards

Nooshin N. Zadeh Graduate Assistant

Departments of Electrical Engineering and Neurology University of Miami

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Best Regards

Nooshin N. Zadeh Graduate Assistant

Departments of Electrical Engineering and Neurology University of Miami