completely different color overlays on the mesh after projecting the retinotopic maps on the surface

[ahmadi123]

Hello, I am working with an Ubuntu 12.4 system. Building, visualization and drawing an ROI on a mesh can be successfully done by executing 'mrMeshSrv_Ubuntu1204.glxa64'. However, When I project the eccentricity and polar angle maps of pRF mapping on the mesh, the colour overlay doesn't match at all. For instance, the occipital pole gets entirely orange for eccentricity and blue for polar angle map while the colour maps look all right on the Gray view. To make sure that nothing went wrong during pRF calculations, I recreated the mesh of the same subject in my old windows computer. The projected colour maps completely matched those in the Gray view. Updating the mesh in linux leads to 2 additional steps as following which doesn't happen in windows:

1. Computing between layer connections
2. Creating connection tables I could not figure out that which part of the 'meshColorOverlay' code generates these two steps. Can the problem happen due to the graphical drivers that I am using or it is likely related to the code? Here is some information about the graphics: OpenGL vendor string: NVIDIA Corporation OpenGL renderer string: GeForce GTX 960/PCIe/SSE2 OpenGL version string: 4.5.0 NVIDIA 361.45.18 Any help would be very much appreciated. Regards, Ahmadi

[JWinawer]

There is a dropdown menu item under Gray/Mesh Display Options/Recompute vertex / gray map.

Try that.

If it works, you can also run this from the command line rather than GUI. And I think you can set your preferences to always do the recompute:

setpref('VISTA', 'autoComputeG2VMap', true);

-Jon

On Fri, Jun 16, 2017 at 12:02 PM, Ahmadi Khazar notifications@github.com wrote:

Hello, I am working with an Ubuntu 12.4 system. Building, visualization and drawing an ROI on a mesh can be successfully done by executing 'mrMeshSrv_Ubuntu1204.glxa64'. However, When I project the eccentricity and polar angle maps of pRF mapping on the mesh, the colour overlay doesn't match at all. For instance, the occipital pole gets entirely orange for eccentricity and blue for polar angle map while the colour maps look all right on the Gray view. To make sure that nothing went wrong during pRF calculations, I recreated the mesh of the same subject in my old windows computer. The projected colour maps completely matched those in the Gray view. Updating the mesh in linux leads to 2 additional steps as following which doesn't happen in windows:

1. Computing between layer connections
2. Creating connection tables I could not figure out that which part of the 'meshColorOverlay' code generates these two steps. Can the problem happen due to the graphical drivers that I am using or it is likely related to the code? Here is some information about the graphics: OpenGL vendor string: NVIDIA Corporation OpenGL renderer string: GeForce GTX 960/PCIe/SSE2 OpenGL version string: 4.5.0 NVIDIA 361.45.18 Any help would be very much appreciated. Regards, Ahmadi

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-- Jonathan Winawer Assistant Professor of Psychology and Neural Science

New York University 6 Washington Place New York, NY, 10003 (212) 998-7922 (phone) (212) 995-4018 (fax) jonathan.winawer@nyu.edu http://psych.nyu.edu/winawer/

[ahmadi123]

Hi, Thanks a lot for your reply. I had actually tried 'recompute vertex' before, it doesn't solve the problem! I realized that if I comment line 70 of the 'meshColorOverlay.m' where it calls 'mrmMapVerticesToGray', then the color problem gets solved but another issue arises: I can draw a ROI on the mesh and transfer it to gray view but after updating the mesh, the initially drawn ROI disappears. Without commenting the above mentioned line, there is no problem with the ROI but the color map is wrong. Please have a look at the attached file. I very much appreciate your opinion on this. Best,

[JWinawer]

One possibility is that your mesh preferences are set to show the maximum value at each vertex. This setting seems to have a bug, which I will look into.

Meantime, can you try,

setpref('mesh', 'overlayLayerMapMode', 'mean');

Jon

On Fri, Jun 23, 2017 at 3:22 AM, Ahmadi Khazar notifications@github.com wrote:

Hi, Thanks a lot for your reply. I had actually tried 'recompute vertex' before, it doesn't solve the problem! I realized that if I comment line 70 of the 'meshColorOverlay.m' where it calls 'mrmMapVerticesToGray', then the color problem gets solved but another issue arises: I can draw a ROI on the mesh and transfer it to gray view but after updating the mesh, the initially drawn ROI disappears. Without commenting the above mentioned line, there is no problem with the ROI but the color map is wrong. Please have a look at the attached file. I very much appreciate your opinion on this. Best, Ahmadi/home/user/Bilder/MeshColorOverlay.png

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/vistalab/vistasoft/issues/238#issuecomment-310592203, or mute the thread https://github.com/notifications/unsubscribe-auth/ACBX3h6_jJAvmsGFibHsz-zQEg0wOi7Kks5sG2eogaJpZM4N8pFf .

-- Jonathan Winawer Assistant Professor of Psychology and Neural Science

New York University 6 Washington Place New York, NY, 10003 (212) 998-7922 (phone) (212) 995-4018 (fax) jonathan.winawer@nyu.edu http://psych.nyu.edu/winawer/

[ahmadi123]

Dear Jon, Many thanks for your reply. I was getting disappointed as all my efforts were useless. In deed, it was the right solution. Thank you so much again for your help!