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 greve@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
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What is paraview? I would contact the developers.
On 8/30/16 10:24 AM, Islem Rekik wrote:
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 <greve@nmr.mgh.harvard.edu mailto:greve@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 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>_______________________________________________ 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.-- Dr. Islem Rekik; MSc, PhD IDEA Lab, UNC-Chapel Hill Biomedical Research Imaging Center Chapel Hill, NC 27599
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