Hi, Doug,
You mentioned on the list that you are preparing a tool that uses clustering to reduce the multiple comparison penalty. Do you have time to post some more details, or perhaps just pass along some of your references? This area is very interesting to me.
+glenn
It's basically something I've modelled after randomise (FSL's permutation program) and AlphaSim (AFNI's monte carlo simulator).
I've built a simulator into the glm analysis program. It will allow you to perform either monte carlo or permutation simulations. On each iteration it will perform clustering to determine the size of the largest cluster, in order to determine the distribution of the max cluster size. You can then pass this distribution to mri_surfcluster and it will determine the pvalue for each of the clusters. I may try to add a random field theory pvalue as well, but we'll have to see. FDR is already built into tksurfer.
note: We can't use randomsise or AlphaSim because they do not operate on our surface geometry.
doug
Glenn Lawyer wrote:
Hi, Doug,
You mentioned on the list that you are preparing a tool that uses clustering to reduce the multiple comparison penalty. Do you have time to post some more details, or perhaps just pass along some of your references? This area is very interesting to me.
+glenn
--
I want to go farther, farther!
A. E. L.Glenn Lawyer < +352 061 967 244 < Instituttgruppe for psykiatri < Postboks 1130 Blindern < 0318 Oslo <
< http://folk.uio.no/davidgl >H <><><><><><><><><><><><><><><><><:)
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi,
Anywhere in the "surf" directory I can find the normal direction of each node on the GM/WM surface? Or anyway I can calculate the normal direction from the surface files? How about the direction between the correspoding two points on the GM/WM surface and pial surface? Thanks.
XJ Kang
sure. You can convert the surface into ascii with mris_convert or load it directly into matlab with read_surf. The normal is then the cross product of two of the legs of each triangle. Sorry, I don't remember the ordering but it should be obvious if you have it wrong. The indices of the vertices in the surfaces are invariant, so the same index can be used to find the corresponding surface on the ?h.white and ?h.pial surfaces.
Bruce
On Wed, 18 Jan 2006, XJ Kang wrote:
Hi,
Anywhere in the "surf" directory I can find the normal direction of each node on the GM/WM surface? Or anyway I can calculate the normal direction from the surface files? How about the direction between the correspoding two points on the GM/WM surface and pial surface? Thanks.
XJ Kang _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I've also just modified mri_surf2surf to extract the surface normals at each vertex. You can get the new version from:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_surf2surf
There's an example in the --help on how to run it.
doug
Bruce Fischl wrote:
sure. You can convert the surface into ascii with mris_convert or load it directly into matlab with read_surf. The normal is then the cross product of two of the legs of each triangle. Sorry, I don't remember the ordering but it should be obvious if you have it wrong. The indices of the vertices in the surfaces are invariant, so the same index can be used to find the corresponding surface on the ?h.white and ?h.pial surfaces.
Bruce
On Wed, 18 Jan 2006, XJ Kang wrote:
Hi,
Anywhere in the "surf" directory I can find the normal direction of each node on the GM/WM surface? Or anyway I can calculate the normal direction from the surface files? How about the direction between the correspoding two points on the GM/WM surface and pial surface? Thanks.
XJ Kang _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
p.s. thanks to Xiao Han for writing up a wiki page on this:
https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferWiki/SurfaceNormal
On Wed, 18 Jan 2006, XJ Kang wrote:
Hi,
Anywhere in the "surf" directory I can find the normal direction of each node on the GM/WM surface? Or anyway I can calculate the normal direction from the surface files? How about the direction between the correspoding two points on the GM/WM surface and pial surface? Thanks.
XJ Kang _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Doug Greve -
Glenn Lawyer -
XJ Kang