Dear FreeSurfers,
In the course of checking my skull-strips I discovered that one of my subjects does not have a T1.mgz because they did not pass the automatic Talairach failure detection. I checked the transformation with tkregister2 and -fstal, and it actually looks quite good; the brain is tilted, but the Talairach brain follows the tilt nicely. Nonetheless, to move things forward I made a few small edits and saved the registration. I then re-ran autorecon1 using the -notalairach option (at the end of the command line) in order to make use of my edits. However, I got the exact same error back-Talairach transformation ***FAILED***--and consequently there's no T1.mgz.
I thought that by specifying -notalairach at the end of the command line while running autorecon1, I would be bypassing the Talairach detector and thus would be able to avoid this problem, but I'm obviously wrong. How do I make use of my edited Talairach and get autorecon1 to continue?
Thanks in advance,
Dan Dillon, Ph.D.
Post-doctoral Fellow
Affective Neuroscience Lab
Dept. of Psychology, Harvard University
Phone: (617) 495-1889
E-mail: dillon@wjh.harvard.edu
Dan,
Include the flag:
-notal-check
and this will skip the talairach failure detection stage.
Nick
On Thu, 2007-11-29 at 16:57 -0500, Dan Dillon wrote:
Dear FreeSurfers,
In the course of checking my skull-strips I discovered that one of my subjects does not have a T1.mgz because they did not pass the automatic Talairach failure detection. I checked the transformation with tkregister2 and –fstal, and it actually looks quite good; the brain is tilted, but the Talairach brain follows the tilt nicely. Nonetheless, to move things forward I made a few small edits and saved the registration. I then re-ran autorecon1 using the –notalairach option (at the end of the command line) in order to make use of my edits. However, I got the exact same error back—Talairach transformation ***FAILED***--and consequently there’s no T1.mgz.
I thought that by specifying –notalairach at the end of the command line while running autorecon1, I would be bypassing the Talairach detector and thus would be able to avoid this problem, but I’m obviously wrong. How do I make use of my edited Talairach and get autorecon1 to continue?
Thanks in advance,
Dan Dillon, Ph.D.
Post-doctoral Fellow
Affective Neuroscience Lab
Dept. of Psychology, Harvard University
Phone: (617) 495-1889
E-mail: dillon@wjh.harvard.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Wonderful, thanks.
DD
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Nick Schmansky Sent: Thursday, November 29, 2007 5:19 PM To: Dan Dillon Cc: Freesurfer Mailing List Subject: Re: [Freesurfer] Another talairach question . . .
Dan,
Include the flag:
-notal-check
and this will skip the talairach failure detection stage.
Nick
On Thu, 2007-11-29 at 16:57 -0500, Dan Dillon wrote:
Dear FreeSurfers,
In the course of checking my skull-strips I discovered that one of my subjects does not have a T1.mgz because they did not pass the automatic Talairach failure detection. I checked the transformation with tkregister2 and -fstal, and it actually looks quite good; the brain is tilted, but the Talairach brain follows the tilt nicely. Nonetheless, to move things forward I made a few small edits and saved the registration. I then re-ran autorecon1 using the -notalairach option (at the end of the command line) in order to make use of my edits. However, I got the exact same error back-Talairach transformation ***FAILED***--and consequently there's no T1.mgz.
I thought that by specifying -notalairach at the end of the command line while running autorecon1, I would be bypassing the Talairach detector and thus would be able to avoid this problem, but I'm obviously wrong. How do I make use of my edited Talairach and get autorecon1 to continue?
Thanks in advance,
Dan Dillon, Ph.D.
Post-doctoral Fellow
Affective Neuroscience Lab
Dept. of Psychology, Harvard University
Phone: (617) 495-1889
E-mail: dillon@wjh.harvard.edu
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
freesurfer@nmr.mgh.harvard.edu
-
Dan Dillon -
Nick Schmansky