Thank you, Nick This is much appreciated !! It works now and the talairach.xfm is: 1.08349275588989 -0.0557942688465118 -0.0535474419593811 3.1632091999054 0.0642405077815056 1.0216326713562 0.235359072685242 -13.4880638122559 0.0452854037284851 -0.281521290540695 1.20965027809143 16.3635120391846
Yi-Yu
________________________________________ From: Nick Schmansky [nicks@nmr.mgh.harvard.edu] Sent: Tuesday, June 14, 2011 11:14 AM To: Bruce Fischl Cc: Yiyu Chou; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Talairach Transformation failed on Freesurfer 5.1
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
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