Hello Antonin and Doug, I viewed it in tkregister2 and I think the co-registration worked. Is there a way to extract info from both PET and anatomical to confirm the co-registration? Best, Paul
On Sun, Feb 26, 2017 at 4:49 PM, Antonin Skoch <a...@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 > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > >
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