Hello;

first, regarding the information here:

http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferTrackVisTransforms

This looks to me very much like snippets of code to help people write their own code to read and transform files, byte by byte, with the help of the trackvis .trk header/file spec.

That's great. Thanks. But has anyone written a script or some C or something to actually do that. If not, and if I do that in the form probably of C source, does anyone want the code?

second:

I'm using freeesurfer for ex-vivo macaque data. It's been a struggle but I've got there.

There is something I would like to do: as well as keeping what I have, I would like to tilt the volume's nose up a few degrees (I'd probably use the afni "nudge" plugin for that, or something) and then apply the same transform to my white and pial surfaces.

The idea there being to use the surfaces as diagrams in the same cut plane as diagrams in an atlas (the pandya white matter atlas, the paxinos atlas), mark areas and then transform those areas off else where (into diffusion data as masks in fact).

I hope that's clear. I just want to apply an arbitrary (actually, a rigid body) linear transform to the surfaces and volumes so that when viewed coronally in sequence in freeview they are in the same plane as diagrams in an atlas, and I can compare the two by eye. the pial and white surfaces together look line like diagrams, and this is very helpful actually. especially if they are in the same cut plane as the atlas diagrams.

thanks,

Colin