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 the stream. These benefits include stopping to perform manual editing as well as parallelization. Directives are either clustered or step-wise. Clustered directives are sets of steps that can be performed by specifying a single flag. A step-wise directive refers to a single step. Directives accumulate. For example, specifying -stage1 and -stage3 will perform all the steps in both stage 1 and 2. A step can be removed from a cluster by adding -no<step> after the cluster flag. For example, specifying -all followed by -notalairach will perform all the reconstruction steps except talairaching. However, note that if -notalairach *preceeded* -all, talairaching would still be performed.
Margaret Duff wrote:
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 keeps exiting with errors because of the bad talairach. Is -notalairach still the correct option for not creating a transform during this step? Thanks, Margaret _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer