Hi all, I have a similar problem using Paraview: When I visualize the surface lh.pial and the anatomical image brainmask.mgz using FreeView they nicely overlap; however, after I convert lh.pial to lh.pial.vtk and brainmask*.mgz* to brainmask*.mha* and visualize them using Paraview, they are in different spaces.
Do I need to apply a transformation matrix to lh.pial using the command line mri_surf2surf so the VTK surface will overlap with the image when using Paraview? I find this quite confusing. Thanks! Kindly, Islem On Tue, Aug 30, 2016 at 9:21 AM, Douglas Greve <gr...@nmr.mgh.harvard.edu> wrote: > tksurfer always uses the ?h.orig coordinates. Also keep in mind that the > vertex index is 0-based whereas matlab is 1-based. When you click on a > point, you should see something like the following print out > selected vertex 123491 out of 163842 > current -39.11 15.65 11.26 > orig -55.67 -10.37 19.95 > pial 0.00 0.00 0.00 > white -55.76 -10.29 19.93 > > > > > On 8/30/16 5:12 AM, Dongnandi wrote: > > Dear Experts, > > I tried to extract vertex coordinates information from > ‘fsaverage/surf/lh.pial’ file using matlab function ‘read_surf’, but I > found that the coordinates returned by the function are different from what > I saw in tksurfer, here are the screenshots: > > The vertex index starts from 0 in tksurfer, so I select the second > elements in matlab. Why is the result different from what has been shown in > tksurfer(also different in freeview)? Which one should I report? > > Is there any way to transform the surface coordinates to the MNI152 space? > > > > Thank you very much! > > Dong > > > > > _______________________________________________ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > 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. > > -- Dr. Islem Rekik; MSc, PhD IDEA Lab, UNC-Chapel Hill Biomedical Research Imaging Center Chapel Hill, NC 27599
_______________________________________________ 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.
