I don't know about the vtk solution, but if you can make a label out of your patch, I do have a new version of mri_label2label which will assign the vertex numbers. Would that work? I've put a version in

ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_label2label

Specify --paint dmax, where dmax is the max dist that a label point can be to be mapped to a white surface vertex.

doug

On Fri, 11 Apr 2008, Michael Harms wrote:

Hello,

We have some white matter surfaces created using non-FS software in which we have subsequently "cut-out" via hand contouring specific gyri and sulci of interest (e.g., cingulate). I would like to be able to use these extracted surfaces to create a label file in FS corresponding to the matching surface region within FS. Is there a way to accomplish this using existing Freesurfer binary or matlab functions?

More specifically, we can define these extracted surfaces in the native scan space, and get them into a vtk format (which should be readable by mris_convert). Do you have any suggestions for the easiest way to then "translate" the region defined by this surface into a corresponding region on the FS white matter surface? Ideally, since our in-house surface defines an enclosed set of vertices, the ensuing label file in FS would represent an enclosed set of vertices as well.

thanks for your suggestions, Mike H.