use -l lh.cortex.label or rh.cortex.label to exclude the non-zero regions
On Mon, 1 Jun 2009, Feng-Xian wrote:
Hi, From your response, I thick that if I want to get the global thickness statistics (mean +/- SD) without any regions where the thickness is 0, I would consider these regions where the thickness is 0. But, I donÿÿt know what can I do? Would you teach me?
First, I get the global thickness statistics with all regions by the following command: mris_anatomical_stats -t subjid/surf/lh.thickness -b subjid lh And, I get the following information: table columns are: 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 155006 103166 299737 2.608 1.022 0.121 0.041 2632 269.2 /usr/local/freesurfer/subjects/analysis/noise_analysis/noise/noise0.5_0 /surf/lh.white
Then, I get the global thickness statistics with some regions where the thickness is 0 by the following command: mris_anatomical_stats -t subjid/label/lh.cortex.label -b subjid lh And, I get the following information: table columns are: 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
155006 103166 0 0.000 0.000 0.121 0.041 2632 269.2 /usr/local/freesurfer/subjects/analysis/noise_analysis/noise/noise0.5_ 0/surf/lh.white
Thank you in advance!
Feng-Xian
On Mon, 1 Jun 2009 10:47:19 -0400 (EDT), Bruce Fischl wrote
that's right, but it will average over the whole surface including e.g. the callosum where the thickness is 0. If you specify the ?h.cortex.label file it will exclude these regions Bruce On Mon, 1 Jun 2009, Feng-Xian wrote:
Hi, From your suggestion, I get the global thickness statistics (mean +/-
SD)
by the following command: mris_anatomical_stats -t subjid/surf/lh.thickness -b subjid lh
Then, I get the following information: table columns are: 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 155006 103166 299737 2.608 1.022 0.121 0.041 2632
269.2 /usr/local/freesurfer/subjects/analysis/noise_analysis/noise/noise0.5_0
/surf/lh.white
So, I think 2.608 & 1.022 is the global thickness statistics (mean +/-
SD)
for this subject. Do I have something wrong?
Thank you in advance!
Feng-Xian
On Mon, 1 Jun 2009 07:29:46 -0400 (EDT), Bruce Fischl wrote
Hi Feng-Xian,
the ?h.thickness files in each subject's surf dir contain the vertex- wise thickness, and mris_anatomical_stats will compute the average. Make sure to give it -l ?h.cortex.label so it only computes them over the cortial region of the surface
cheers, Bruce
On Mon, 1 Jun 2009, Feng-Xian wrote:
Hi, I want to calculate the global thickness statistics (mean +/- SD) for
all
my subjects. And, I could calculate the global thickness statistics by
some
information about cortical thickness values of each pixel. But I canÿÿt
find
any files regarding cortical thickness values of each pixel. Could you suggest me how to calculate the global thickness
statistics
or
tell me where to get the file regarding cortical thickness values of
each
pixel?
Thank you in advance!
Feng-Xian
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Bruce Fischl