Hello Burke, you might want to check out https://github.com/NeuroanatomyAndConnectivity/surfdist . It works directly on Freesurfer output. The approach is described here: Margulies, D.S., Falkiewicz, M. and Huntenburg, J.M., 2016. A cortical surface-based geodesic distance package for Python. GigaScience, 5(suppl_1), pp.19-20; https://gigascience.biomedcentral.com/articles/10.1186/s13742-016-0147-0
I hope that helps! Cheers, Marcel 2017-03-31 0:19 GMT+02:00 Burke Rosen <bqro...@gmail.com>: > I am interested in finding the distance between two vertices along the > cortical surface. > > So far I have used two methods: > > (1) Compute the shortest path with a variant of Dijkstra's algorithm on the > white surface. > > (2) Compute the great circle distance on the sphere surface. > (as done by Risk et.al. 2016 Neuroimage) > > Method (1) is slow and will tend to overestimate distances as the path only > goes along mesh edges. > > Method (2) is very fast and gives a true geodesic but gives a scaled result > because the radius of sphere surface is arbitrary; also this method is > subject to distortions introduced by the inflation algorithm. > > My current strategy is to perform a linear regression between the triangle > face areas of the sphere and white surfaces. And then apply the coefficients > to the sphere surface diameter before calculating geodesic distances. This > yields a distance matrix with a similar pattern to the Method (1) at about > 62% scale. That scale seems like it might be reasonable. However, the > regression only explains ~58% of the variance. My hunch is that the rest is > due to inflation distortions. > > Is there a better way of scaling the sphere surface? Or a way to inflate in > such a way that inter-vertex distances are preserved? Or, more generally, > what is a good method of computing geodesic distances on freesurfer > surfaces. > > Thank you, > > Burke Rosen > > _______________________________________________ > 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. > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
