I don't think there is a better way than visual inspection. You could look at the final cost value, but that is relative, ie, you could get a bunch of subjects who you know have a good registration and create a table of the final costs, then when you get a new subject, compute the z-score of the cost based on known good values.
On 02/27/2017 11:33 AM, miracle ozzoude wrote: > Hello Doug, > Thanks for replying. It might help evaluate the accuracy of the > co-registration. Usually, We use visual inspection (placing the > crosshair on 1 image (either MRI or PET) and comparing the position of > the crosshair in 1 image to another image). However, this is > subjective and based on experience. I want to use a objective method > to inspect the accuracy of the co-registration. Please, do you have > any suggestions on how I can accomplish it? > Best, > Paul > > On Mon, Feb 27, 2017 at 11:05 AM, Douglas Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > But what would you compare if you had these coordinates? What > would the coordinates tell you? > > > On 2/27/17 11:01 AM, miracle ozzoude wrote: >> 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 <mailto: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 >>> <mailto: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 >>> <mailto: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://freesurfer.net/fswiki/CoordinateSystems> >>> http://www.grahamwideman.com/gw/brain/fs/coords/fscoords.htm >>> <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 >>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> <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 >>> <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 list >>> Freesurfer@nmr.mgh.harvard.edu >>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> _______________________________________________ Freesurfer >> mailing list Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> <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 >> <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 list >> Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > _______________________________________________ Freesurfer mailing > list Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <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 > <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 list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
