Christina,

You need an additional flag specifying a stage, like -all, or - autorecon1. I'll update the help text, as this is not obvious, sorry.

Nick

On Thu, 2007-03-01 at 15:51 -0500, ccongle@nmr.mgh.harvard.edu wrote:

Hello,

I'm trying to run the longitudinal processing pipeline, but can't figure out a command that works. Below is what I've tried and what has happened (MC-07M_prereconEDIT is the 'pre' timepoint, and MC-07M_post is the 'post'). Can you help?

In dev env: jizo:ccongle[103] recon-all-long -long -tp1 MC-07M_prereconEDIT -s MC-07M_post recon-all-long: Command not found.

jizo:ccongle[104] recon-all -long -tp1 MC-07M_prereconEDIT -s MC-07M_post INFO: SUBJECTS_DIR is /autofs/space/jizo_001/users/STRUCTURALS/MBSR Actual FREESURFER_HOME /autofs/space/freesurfer/centos4.0_x86_64/dev ERROR: nothing to do

In stable env: jizo:ccongle[85] recon-all -long -tp1 MC-07M_prereconEDIT -s MC-07M_post ERROR: Flag -long unrecognized. -long -tp1 MC-07M_prereconEDIT -s MC-07M_post

jizo:ccongle[87] recon-all-long -tp1 MC-07M_prereconEDIT -s MC-07M_post recon-all-long: Command not found.

Thanks, Christina _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer