Russ, Thank you for pointing this out. Our script does indeed need an update to account for a pre-defined PERL5LIB (ie appending to it). This will appear in the upcoming release.
Nick On Wed, 2005-07-27 at 09:58 -0700, Russ Poldrack wrote: > 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 > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
