How is the volume of each cortical structure (and hemisphere) calculated? It seems I remember from somewhere that it is the thickness x average surface area of the tesselated triangles? Is this right? What I'm most interested in is how the cortical gray matter volume from mris_anatomical_stats is calculated. Is it the average thickness of the whole hemisphere x surface area, or is by adding up the volumes of all the parcellated structures from the atlas? I remember reading about it earlier, but couldn't find any info in the list archive or on the wiki. Thanks.
-Derin
Hi Derin,
for each face, it's the product of the average thickness at that face (over the 3 vertices attached to it), times the average white and pial surface areas of that face.
cheers, Bruce
On Wed, 5 Sep 2007, Derin Cobia wrote:
How is the volume of each cortical structure (and hemisphere) calculated? It seems I remember from somewhere that it is the thickness x average surface area of the tesselated triangles? Is this right? What I'm most interested in is how the cortical gray matter volume from mris_anatomical_stats is calculated. Is it the average thickness of the whole hemisphere x surface area, or is by adding up the volumes of all the parcellated structures from the atlas? I remember reading about it earlier, but couldn't find any info in the list archive or on the wiki. Thanks.
-Derin _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi,
I was using Matlab R14 in Linux to read a surface and compute a thickness histogram.
I noticed that the read_surf function fails in every lh.thickness or rh.thickness file. Even in bert dataset.
Here the error: [vertex,f] = read_surf ('/usr/local/freesurfer/subjects/p111/surf/lh.thickness'); ??? Subscripted assignment dimension mismatch.
Error in ==> read_surf at 41 faces(i,n) = fread3(fid) ;
I'm using Freesurfer 3.0.5
Thanks,
Pedro Paulo Oliveira Jr.
P.S. - I know that this issue has been previously discussed here but I have patients with a cortex thickness larger than 5mm and the truncation makes the statistical calculation fault in some aspects of my work. It would be possible to have a "raw thickness" calculation?
Tks again
PPJ
Hi Pedro
you can use mris_thickness -max <max thick> to generate a thickness with a different max. Note that the ?h.thickness files are in "curv" format, they are not surfaces (they have no topological information in them), so they should be read with the read_curv.m file.
cheers, Bruce
On Sat, 8 Sep 2007 ppj@netfilter.com.br wrote:
Hi,
I was using Matlab R14 in Linux to read a surface and compute a thickness histogram.
I noticed that the read_surf function fails in every lh.thickness or rh.thickness file. Even in bert dataset.
Here the error: [vertex,f] = read_surf ('/usr/local/freesurfer/subjects/p111/surf/lh.thickness'); ??? Subscripted assignment dimension mismatch.
Error in ==> read_surf at 41 faces(i,n) = fread3(fid) ;
I'm using Freesurfer 3.0.5
Thanks,
Pedro Paulo Oliveira Jr.
P.S. - I know that this issue has been previously discussed here but I have patients with a cortex thickness larger than 5mm and the truncation makes the statistical calculation fault in some aspects of my work. It would be possible to have a "raw thickness" calculation?
Tks again
PPJ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Derin Cobia -
ppj＠netfilter.com.br