Hello Doug, Thanks for replying. I meant like coordinate points on both images to compare (i.e., any metric different from visual inspection). Best, Paul.
On Mon, Feb 27, 2017 at 10:50 AM, Douglas Greve <gr...@nmr.mgh.harvard.edu> wrote: > I'm not sure what you mean. If the registration looks good, what do you > need to extract? > > On 2/27/17 9:03 AM, miracle ozzoude wrote: > > 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. >> >> > > > _______________________________________________ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > 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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