Hi Christina,

No problem. I'm glad it works for you, and it has been very useful for me as well.

The coordinates in the FT.mat file are in image space so you can do things like ceil(TRK{1}) and that gives you the voxel indices for each coordinate for the first tract. Right before making the .trk file, these are scaled up by their voxel dimensions so the tracts are in a space with coordinates that match the real-world lengths of the tracts (in mm). If you let vox be a vector of voxel dimensions (eg vox = [3 3 3]), then bsxfun(@times,TRK{1},vox) = trk(1).matrix, so you can use whichever one you want, you just have to know if you want the actual length or the image representation, vox_to_ras (which is similar to the affine transformation in the nifti header) comes from the image space, for example. Sorry for the confusion! I need to put something about all of this clearly in the manual....

Best,

Russell