hi Margaret-
you need to specify -notalairach after -stage1 on the command line.
-notalairach turns it off, -stage1 turns it on.
thanks,
brian
On Fri, 3 Jun 2005, Margaret Duff wrote:
Hello, I am running the line recon-all-nmr -notalairach -stage1 -stage2
-subjid SM2C3 from SUBJECTS_DIR /sp
put -notalairach at the end (as described in the help:)
recon-all-nmr -help
SPECIFYING DIRECTIVES
Directives instruct recon-all which part(s) of the reconstruction
stream to run. While it is possible to do everything in one shot
(using the -all flag), there can be some benefits to customizing
Hello, I am running the line recon-all-nmr -notalairach -stage1 -stage2
-subjid SM2C3 from SUBJECTS_DIR /space/troy/users/2/mikesfolder and in
the std-env. The
recon-all-nmr program is still creating a bad talairach transform that
overwrites the good one I just made. So, the recon-all-nmr kee
