Thank you for your quick reply. Does this mean I should close the transform window when it opens? The alignment looks good to me, I was worried because the transform window opened and the info on the terminal window. I haven't used tkregister2 before. Do I replace tkregisterfv with tkregister2 like this " tkregister2 --mov template.nii.gz --reg template.reg.lta --surfs"? ‎Thanks.

Dear Paul,

LTA means transformation matrix stored in .lta format.

This matrix can encode transformation between various coordinate spaces.

What coordinate systems transform this .lta from and to is specified by string in the .lta file. Typically this type could be vox2RAS, RAS2vox, vox2vox or RAS2RAS. Most typically the type is vox2vox.

The explanation of coordinate systems is specified for example here:
http://freesurfer.net/fswiki/CoordinateSystems
http://www.grahamwideman.com/gw/brain/fs/coords/fscoords.htm

The output of freeview is only info, not error, indicating that your .lta is not of type vox2vox. I personally still use tkregister2 for checking of registration, since the freeview does not contain full functionality for checking transformations (see the warning). Therefore I have no experience with tkregisterfv and consider tkregister2 still as a "gold standard". However, if you use tkregisterfv for checkning transformation between volumes and the output is only "info", I would guess that everything is OK and you do not need to be bothered.

Btw, does the alignment of the images seem reasonable? How does it look in tkregister2?

Regards,

Antonin