Warping the vertices should not need to change the faces, so that shouldn't be a problem. That scrambling makes me wonder if something is getting the endianness wrong, are the values extremely large?
If you can put your warpfield into a 3-brick nifti volume, with format of relative x, y, and z offset (relative shifts), you should be able to get wb_command to apply the warp with -surface-apply-warpfield (as the command help says, make sure it is the inverse of the warpfield used to resample a volume), assuming it uses the nifti sform/qform for alignment to the surface. Tim On Thu, Aug 22, 2013 at 4:33 PM, Colin Reveley <[email protected]> wrote: > I should say: it loads in workbench. it just doest work. > > images (gifti in matlab, same in workbench) attached. also the header I'm > trying to load. You'll see the header has quite a lot of detritus. > > best > > Colin > > > On 22 August 2013 22:24, Colin Reveley <[email protected]> wrote: > >> hi. >> >> we have a system (a bespoke system) for non-linear registration of >> volumes. >> >> we wondered if we could take the output transform and use that data to >> shift the vertices of a surf.gii so that it's transformed. >> >> much like wb_command and fnirt. >> >> we tried it. in matlab (using gifti lib) it works. >> >> unfortunately the resulting surface renders in matlab, but when saved not >> in caret or workbench. >> >> there are a million reasons why that could be. And I'm happy to mess with >> the headers till it works. >> >> but before i do I wondered if there might be an in-principle problem: >> >> we move the vertices. but the face definitions remain the same, as in >> >> gii = >> >> vertices: [211995x3 single] >> mat: [4x4 double] >> faces: [423986x3 int32] >> >> is that the basic problem, or is it just a question of messing with the >> xml till caret or workbench accepts it? >> >> I accept it's complicated. But our code does appear to work in terms of >> moving vertices and aligning to a nifti within matlab, so unless the face >> definitions are the fundamental issue for loading in caret5/7 (mainly >> caret5 for the moment) I can just twiddle with headers till it loads >> hopefully. >> >> but if it's the faces I have a bigger problem. >> >> best wishes >> >> Colin >> > > > _______________________________________________ > caret-users mailing list > [email protected] > http://brainvis.wustl.edu/mailman/listinfo/caret-users > >
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