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: poldrack@ucla.edu
web: www.poldracklab.org

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--- 

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: poldrack@ucla.edu 

web: www.poldracklab.org