Hi All:
I am trying to measure the cortical thickness of specific ROI. I got a ROI, and are able to save it to a label file. Should I use mris_thickness to measure the thickness? If so, how do I get the thickness file, using mri_label2vol? Thanks in advance!
Tao
you can use mris_anatomical_stats -l <label file>
On Fri, 22 Jun 2007, T. Song wrote:
Hi All:
I am trying to measure the cortical thickness of specific ROI. I got a ROI, and are able to save it to a label file. Should I use mris_thickness to measure the thickness? If so, how do I get the thickness file, using mri_label2vol? Thanks in advance!
Tao _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Bruce:
I have a question regarding the command xfm_read. Should I use the 'talairach.xfm' under subject/mri/transforms/ as the input file? It seems that there is transformation matrix in it. Now, in tksurfer, if I click a point in the surface, I will get a "vertex RAS" xyz, and a "vertex Talairach" xyz. I assume that if I apply the transformation matrix (from xfm_read) to "vertex RAS" xyz in MATLAB, I shall get the same "vertex Talairach" xyz as in tksurfer. Am I right? Thanks!
Tao
Hi Tao,
Doug would know the answer to this. In principle yes, but it depends on the origin of the various coordinate systems. I think it's documented in excruciating detail on our wiki.
Bruce
On Wed, 1 Aug 2007, T. Song wrote:
Hi Bruce:
I have a question regarding the command xfm_read. Should I use the 'talairach.xfm' under subject/mri/transforms/ as the input file? It seems that there is transformation matrix in it. Now, in tksurfer, if I click a point in the surface, I will get a "vertex RAS" xyz, and a "vertex Talairach" xyz. I assume that if I apply the transformation matrix (from xfm_read) to "vertex RAS" xyz in MATLAB, I shall get the same "vertex Talairach" xyz as in tksurfer. Am I right? Thanks!
Tao
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
T. Song