You can't easily transform a single vertex. One way to do it is to create an overlay with your vertex = 1 and all others = 0, then convert that to fsaverage and see where it lands. The mapping itself is a little tricky and can result in some unexpected behavior. The first step is to go through each target vertex and map the vertex from the source that is the closest. If your vertex is the closest vertex to multiple target vertices, then you will have several 1s in the output. There is also the chance that your vertex was not the closest to any target vertex. To handle this situation, there is a second loop that goes through all the source vertices that were never selected in the first loop and finds the closest target vertex. This means that there could be two or more source vertices that map to a given target vertex. In this case, the target vertex is given the value of the average of all the source vertices. So, when you look at the output map, there could be a single target vertex with a value of 1.0 or multiple target vertices with a value of 1.0, or a single target with a value that is less than 1.0.
On 01/25/2017 06:26 PM, Dorian P. wrote: > Thank you Bruce. > > I am not that familiar with this process. How can I look the > transformation of a specific vertex index? Is this done still with > mri_surf2surf? > > Dorian > > On Wed, Jan 25, 2017 at 4:50 PM, Bruce Fischl > <fis...@nmr.mgh.harvard.edu <mailto:fis...@nmr.mgh.harvard.edu>> wrote: > > Hi Dorian > > the transform should be by looking up the spherical coordinates on the > sphere.reg for that vertex index and using that to find the > corresponding > fsaverage sphere.reg vertex. > > cheers > Bruce > On Wed, 25 Jan 2017, Dorian P. wrote: > > > Hi, I am trying to find the corresponding coordinate of a vertex > in lh.pial > > in fsaverage space. I manage to transform lh.pial in fsaverage > space but > > this does not give corresponding points or a way to do point by > point > > transformation. > > I want to do the same with some vertices from > lh.pial-outer-smoother. Trying > > to transform this with mri_surf2surf gives an error because > obviously there > > is no registration of that mesh. Any idea if this can be > achieved at all? > > > > Last question: am I correct assuming that the surface to surface > > registration (sphere.reg) does a better job at matching gyri and > sulci on > > fsaverage than the simple conversion in MNI305 (aka fsaverage): > > MNI305RAS = TalXFM*Norig*inv(Torig)*[tkrR tkrA tkrS 1]' > > > > Thank you. > > Dorian > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <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 > <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 -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
