a change in 5.1 over 5.0 is that in 5.1 the talairach stage takes orig.mgz as input, whereas in 5.0 and prior, it used nu.mgz as input. (this was done so that the nu correction stage could make use of the talairach.xfm).
you can either: - add the flag -use-mritotal to the end of recon-all to have it use an alternate tal registration program that sometimes works better on some images. or - use tkregister2 --s subjid --fstal to check the registration. either manually adjust it, or if it looks good, add -notalcheck to the end of recon-all to have it skip the tal checking step. n. On Tue, 2011-06-14 at 13:30 -0400, Bruce Fischl wrote: > is this the talairach.xfm? > On Tue, 14 Jun 2011, Yiyu Chou wrote: > > > Dear Freesurfer users, > > > > I got different transformation matrices (shown below) when running ver 5.0 > > and ver 5.1 on the same subject > > - ver 5.0 was doing great but ver 5.1 failed: > > I would appreciate it if you can give me some advice. > > Yi-Yu Chou > > ------------------------------------------------------------------------------------------------------------------------- > > ver 5.0 > > 1.09499812 -0.07903829 -0.05864276 3.68856287 > > -0.00531462 1.04585004 0.30695227 -12.39152050 > > 0.05851136 -0.39031574 1.20183659 13.30094814 > > ver 5.1 > > 1.128152 -0.008014 -0.149835 2.440697 > > 1.389055 4.761067 -3.739542 -67.997681 > > -0.828629 -2.725178 3.870089 46.025513 > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://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.
