BrainVISA

Hello,

I'm trying to export a surface from brainvisa to AFNI/SUMA. I've found that I can export the surface in GIFTI and the corresponding surface volume in NIFTI. Both of which are compatible with AFNI/SUMA. However when I go to view them the surface isn't aligned with the volume. Does Brainvisa apply a transform (ACPC?) "live" when viewing the volume/surface in Anatomist that makes them aligned with each other. I've found a couple files *.APC and *.trm that look like that might be the case. Any help is much appreciated.

I've searched through the forum but didn't quite find the answer I was looking for, but if I did miss a pertaining post please point me in the right direction.

Thanks
Jed

Hi,
There is no transform applied automatically, but the mesh coords are specified in a coords system that is non-standard for you: coordinates are in a millimetric system associated with the volume that produced the mesh: that is, origin in the center of the first voxel, this voxel is on the right, front, top corner. The coords system is described here.
Now, you can apply a transform to the mesh to go to another coords system, for instance the destination of a transform stored in the NIFTI file of the volume. To get the transform info originating in this mesh/volume coords system, you can use the AimsFileInfo command ant get the matrix in the "transformations" field (or use a program or a script to do so). Then you can apply the transform using the AimsMeshTransform command.
We plan to rework the GIFTI IO in our libs to allow specifying the mesh coords in another system to ease import/export with other software - well, that's what the Marseille team (Olivier Coulon, Arnaud Le Troter) plans to do, as they are actually the guys developing and supporting the GIFTI plugin.
Denis