Hi - If one has a surface that is aligned to a volume in CARET, is it possible (or rather, is there a general procedure) to export the volume and the surface into freesurfer?
The volume in CARET won't be conformed. It's header will define the origin such that CARET interprets a specific voxel/coordinate as the anterior commisure. The surface will be aligned to the volume in the sense that it's co-ordinates are with respect to that anterior commisure definition. What I need to do is run mri_convert -c to conform the volume, and then convert the surface to freesurfer format in such a way that it's now aligned to the conformed volume in freesurfer. Then I'd do some stuff (refine the surface) in freesurfer, and export the surface back to CARET. That's the general issue. Details include: the surface will need to be transformed so that it appears to freesurfer to be 1mm data, and the volume will have it's header changed so that it claims 1mm voxels (the data is higher resolution than 1mm). The problem can be considered as finding the inverse of Van Essen's Freesurfer to F99 pipeline. Or, "Surefit to Freesurfer" is a better way to look at it. The surfaces are *white and *pial though. It's some scaling, translating, conforming and format conversions. Other stuff is not a worry. connectome workbench, FS, CARET, FSL, MATLAB whatever are all relevant/involved tools hope can help Colin Reveley
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