HI,
I am wondering if there is a way to calculate inter vertex distance on fsaverage surface with freesurfer. thanks for your help.
YUMI
do you mean on along the surface or in the volume? On Mon, 27 Dec 2010, YUMI MAEDA wrote:
HI,
I am wondering if there is a way to calculate inter vertex distance on fsaverage surface with freesurfer. thanks for your help.
YUMI
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
If you run 'mris_curvature_stats' on the surface (see 'mris_curvature_stats -u' for usage help), one of the summary rows in the report is the average inter vertex distance.
You could probably just do:
$>mris_curvature_stats -F smoothwm <subjID> lh curv
given appropriate SUBJECTS_DIR env variable which will give the average vertex separation distance on the lh.smoothwm surface (plus some stats on the lh.curv curvature file).
On 12/27/2010 10:22 PM, YUMI MAEDA wrote:
HI,
I am wondering if there is a way to calculate inter vertex distance on fsaverage surface with freesurfer. thanks for your help.
YUMI
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
thanks Rudolph
and what if you wanted the topological (shortest distance along the surface) between two specific vertices? so, say i have two known locations and i want to know how separated they are over the surface - is there a command where i can input the two vertices and the output is separation distance?
thanks
vitaly
On Tue, Dec 28, 2010 at 12:05 PM, Rudolph Pienaar rudolph@nmr.mgh.harvard.edu wrote:
If you run 'mris_curvature_stats' on the surface (see 'mris_curvature_stats -u' for usage help), one of the summary rows in the report is the average inter vertex distance.
You could probably just do:
$>mris_curvature_stats -F smoothwm <subjID> lh curv
given appropriate SUBJECTS_DIR env variable which will give the average vertex separation distance on the lh.smoothwm surface (plus some stats on the lh.curv curvature file).
On 12/27/2010 10:22 PM, YUMI MAEDA wrote:
HI,
I am wondering if there is a way to calculate inter vertex distance on fsaverage surface with freesurfer. thanks for your help.
YUMI
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Rudolph Pienaar, M.Eng, D.Eng / email: rudolph@nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging 149 (2301) 13th Street, Charlestown, MA 02129 USA
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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On 12/28/2010 12:20 PM, Vitaly Napadow wrote:
is there a command where i can input the two vertices and the output is separation distance?
Yes -- sort of. There is an app called 'mris_pmake' that calculates paths on FreeSurfer meshes based on Dijkstra's algorithm. Mesh edges can be arbitrarily weighed. It can be used in a mode where it is fed two vertex indices, and it calculates the shortest path across the mesh between then two (the edge cost function is set such that each edge weight is equal to the edge length). This is not the same as the geodesic distance, since 'mris_pmake' is constrained to run along the actual mesh, but can be a reasonable approximation. I can give you more info if you'd like. It was written for a different, batch-orientated purpose, but can be used in this way. It's been in dev/alpha status for more than a year or so, so it does need some handholding to run.
-=R
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Rudolph Pienaar -
Vitaly Napadow -
YUMI MAEDA