Re: [Freesurfer] Perl problems with mac install

[Russ Poldrack]

hi - yes, nu_correct complained that it couldn't find various Perl files.  I did source the FreeSurferEnv.csh file before running - it seems that the PERL5LIB environment variable is not getting properly set by the script, as this is what I see even after sourcing the script: [russ-poldracks-power-mac-g5:freesurfer/subjects/bert] poldrack% env|grep PERL PERL5LIB=/sw/lib/perl5:/sw/lib/perl5/darwin It looks to me like FreeSurferEnv.csh only sets the PERL5LIB variable if it doesn't already exist:     if (! $?PERL5LIB) then         if ( -e $MINC_LIB_DIR/../System/Library/Perl/5.8.6 ) then             # Max OS X Tiger default:             setenv PERL5LIB       "$MINC_LIB_DIR/../System/Library/Perl/5.8.6"         else if ( -e $MINC_LIB_DIR/../System/Library/Perl/5.8.1 ) then             # Max OS X Panther default:             setenv PERL5LIB       "$MINC_LIB_DIR/../System/Library/Perl/5.8.1"         else if ( -e $MINC_LIB_DIR/perl5/5.8.5) then             # Linux default:             setenv PERL5LIB       "$MINC_LIB_DIR/perl5/5.8.5"         else if ( -e $MINC_LIB_DIR/perl5/site_perl/5.8.3) then             # Linux default:             setenv PERL5LIB       "$MINC_LIB_DIR/perl5/site_perl/5.8.3"         endif     endif perhaps it should be changed in order to append the new path if the variable already exists. I think that this is probably a better solution in the long run than copying things into the system Perl directories. cheers russ On Jul 26, 2005, at 5:53 PM, Nick Schmansky wrote: Russ, Hi, I'm wondering if you could provide more details on the failure that you encountered.  Did an MNI utility, such as nu_correct, fail to run and complain about not finding MNI/Startup ?  This is a typical failure if perl cannot find the MNI perl files. Do you get the failure even after executing the statement: source /Users/Shared/freesurfer/SetUpFreeSurfer.csh This script will setup PERL5LIB to point to the MNI tools, which should enable them to work. We are in the midst of preparing a new official release of Freesurfer to be released in about two weeks, and so your input is appreciated.  The Mac Tiger version available now was prepared for a recent Freesurfer course, and could use some improvements in terms of making it a bullet-proof install on the Mac.  I will consider moving the MNI toolkit to /System/Library/Perl/5.8.6 so as it does not require having to source the SetUpFreeSurfer.csh file to setup a special PERL5LIB path.  Also, the current install path (/Users/Shared/freesurfer) is likely to change to something more reasonable. Do you have any other suggestions or comments? Thanks, Nick hi folks - I wanted to let you know that the tiger snapshot installer for mac doesn't properly install the perl libraries needed for some of the MNI tools.  I was able to get things to work by copying the relevant files into /System/Library/Perl/5.8.6, but I assume that you want the installer to do this automagically. cheers russ --- Russell A. Poldrack, Ph.d. Assistant Professor UCLA Department of Psychology Franz  Hall, Box 951563 Los Angeles, CA 90095-1563 phone: 310-794-1224 fax: 310-206-5895 email: [EMAIL PROTECTED] web: www.poldracklab.org _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ---  Russell A. Poldrack, Ph.d.  Assistant Professor  UCLA Department of Psychology  Franz  Hall, Box 951563  Los Angeles, CA 90095-1563  phone: 310-794-1224  fax: 310-206-5895  email: [EMAIL PROTECTED]  web: www.poldracklab.org

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