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
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
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: poldrack@ucla.edu web: www.poldracklab.org
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: poldrack@ucla.edu 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: poldrack@ucla.edu
web: www.poldracklab.org
freesurfer@nmr.mgh.harvard.edu
-
Nick Schmansky -
Russ Poldrack