Dear Freesurfer experts, I want to do tracking (using FSL probtrackx) from the "white matter" Freesurfer surface, in particular the "cortex" label on the white surface of both hemispheres. Probtrackx nicely works with Freesurfer surfaces now (after conversion to GIFTI) and the label(s) can be applied with FSL's label2surf.
However, the original Freesurfer surface has a lot of vertices, approx. 250,000 for both hemispheres (somewhat less if only cortical vertices are used). This leads to very long processing times and probably non-meaningful results since tracking is done in native DTI space and several vertices will be effectively in the same voxel. In some earlier posts it was suggested to downsample the surface, which I do with mris_decimate. Does the job nicely, however, since the vertices numbers change, the cortical label is no longer valid and label2surf (rightfully) refuses to apply this to the downsampled surface (segmentation fault). The same is true for Freeview. Without cortex label tracking will also start (and terminate) from the medial wall, affecting the cortex-cortex connectivity that I am interested in. Is there a possibility to also "downsample" the cortex label? Or have a vertex-wise transformation from the high-res to low-res surface to transform the cortex label e.g. in matlab? Any ideas / pointers are much appreciated, Niels Focke _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
