On Sun, Feb 26, 2017 at 4:49 PM, Antonin Skoch <ansk@ikem.cz> wrote:

Dear Paul,

I think that the transform window in freeview opens by default to enable manual refinement of registration if needed.

If you are not sure, try also tkregister2. It should work to simply replace tkregisterfv by tkregister2, the command would be

tkregister2 --mov your_moveable --targ your_target --reg your_lta

or, if you registered your PET to freesurfer-processed subject and want also to display surfaces, you should use tkregister2, no tkregisterfv (according to the freeview warning). The command in this case would be

tkregister2 --mov your_moveable --s your_subject_id --reg your_lta --surfs

Antonin

Hello Antonin,

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.

Best,

Paul

Sent from my BlackBerry 10 smartphone.

From: Antonin Skoch

Sent: Sunday, February 26, 2017 3:50 PM

To: freesurfer@nmr.mgh.harvard.edu

Reply To: Freesurfer support list

Subject: Re: [Freesurfer] Fw: PETsurfer mri_coreg problem

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

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