Re: [Freesurfer] distance between two points along cortical surface

On 4/11/11 09:36 , Fariba Sharifian wrote:

Hi, How should I have the distance between two points in mm? If I use the ?h.sphere, as all the spherical surfaces are normalized to have 100 radius. so the geodesic distances should not be the real distance in mm?

Fariba

Another way is to use 'mris_pmake'. In fact, this came up on the 1st April and was answered on the list. I'll repeat it here:

This question comes up sometimes -- and the short answer is 'yes', there is a tool that can allow you to do this. Although it will be available in the next version of FS (5.1), it is still a bit rough around the edges. It is called 'mris_pmake' and to use it to determine the distance between two points, do:

mris_pmake --subject <subject> --hemi -<hemi> --surface0 <surface> --curv0 sulc --curv1 sulc --mpmOverlay euclidean --mpmProg pathFind --mpmArgs startVertex:<startArg>,endVertex:<endArg>

So, if you have a subject called 'ID1' and want to determine the shortest distance along the surface between vertex 11111 and vertex 33333 on the left hemisphere smoothwm, do:

mris_pmake --subject ID1 --hemi lh --surface0 smoothwm --curv0 sulc --curv1 sulc --mpmOverlay euclidean --mpmProg pathFind --mpmArgs startVertex:11111,endVertex:33333

Note, that this is *not* the geodesic, but is very close. The path is constrained to run along the surface mesh, so will in general be slightly longer than the geodesic.