Hi Adam, you'll need to add AFNI into your path (this is a recent change). You can do that in your .cshrc file with something like:

setenv AFNIDIR /usr/pubsw/packages/AFNI/current/ set path = ($path $AFNIDIR/bin)

doug

Adam Nitenson wrote:

Hi Doug and Freesurfers,

 I encountered an error during preproc-sess (Stable 5) that I have

never seen before:

ERROR: cannot find AFNI command 3dvolreg

The commands I entered were:

setenv USE_STABLE_5_0_0 source /usr/local/freesurfer/nmr-stable50-env setenv SUBJECTS_DIR /cluster/roffman/users/Stable5_PerRun cd $SUBJECTS_DIR preproc-sess -s MTH20100AA -fwhm 5 -per-run

I've run this set of commands many times without this problem, so did something change or am I missing something simple?

Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital nitenson@nmr.mgh.harvard.edu Phone: 617-643-3215 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer