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 > niten...@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 > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
