It won't give you talairach coords in the label file, it will give you MNI305 coords. Use the View->Information in tkmedit to get MNI305 coords.
doug Jed Singer wrote: > That almost works; tkmedit is giving talairach coordinates of, for a few > examples: > > 14.7 23.9 -22.3 > 24.8 21.9 -18.8 > 35.6 20.8 -20.9 > 54.2 14.1 -17.1 > 61.1 10.9 -9.6 > 62.3 6.0 -1.8 > > Running mri_label2label with fsaverage as the target subject yields a label > in which those same points have the coordinates: > > 14.877 25.802 -25.101 > 25.004 23.475 -20.993 > 35.985 22.497 -23.559 > 54.764 15.410 -19.482 > 61.693 11.670 -10.781 > 62.952 6.235 -1.732 > > For comparison purposes, the RAS coordinates in the original label are: > > 12.000 43.000 5.000 > 21.000 41.000 9.000 > 31.000 41.000 7.000 > 48.000 35.000 11.000 > 54.000 31.000 19.000 > 55.000 25.000 27.000 > > And talairach.xfm is: > 1.1105 0.0582 0.0623 -0.1394 > -0.0761 1.0376 0.1083 -21.5909 > -0.0404 -0.0732 1.0813 -26.6708 > > Multiplying those RAS coordinates by the given talairach transformation gives > coordinates of: > > 16.0028 22.6522 -24.8958 > 26.1303 20.3252 -20.7878 > 37.1110 19.3473 -23.3543 > 55.8898 12.2610 -19.2767 > 62.8184 8.5205 -10.5760 > 64.0778 3.0855 -1.5270 > > > The three sets of values are close, but not the same. The discrepancy is > really making me uncomfortable; any ideas what's going on? > > Thanks so much, > Jed > > On Jul 22, 2011, at 5:39 PM, Douglas N Greve wrote: > > >> You're so close! Use fsaverage as the target subject. The output >> coordinates will be in MNI305 space. >> doug >> >> >> >> Jed Singer wrote: >> >>> I'm at my wits' end with what seems like it should be an easy question. I >>> have a lot of volume labels that have been saved for a lot of brains. I >>> want the Talairach coordinates corresponding to those points. It seems like >>> mri_label2label should be able to do this, by putting in 'talairach' as the >>> target subject, but this returns an error that the subject 'talairach' >>> isn't found: >>> >>> mri_label2label --srcsubject m00045 --srclabel label/all.label --trgsubject >>> talairach --trglabel all_talairach.label --regmethod volume >>> >>> It seems like I should be able to do it manually by loading the >>> talairach.xfm generated by recon-all and multiplying that matrix by the RAS >>> points in the labels; this yields results that are pretty close to those >>> given in tkmedit, but not that close. Usually within a few, sometimes off >>> by more. >>> >>> Probably my inability to do this reflects some misunderstanding or lack of >>> information, but I've been poring over documentation, forum, and wiki for >>> hours now and feel like I've hit a wall. Any suggestions? >>> >>> Thanks so much, >>> Jed >>> _______________________________________________ >>> > > > > -- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ 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.
