The quick and dirty way ================= You have to find where mni libraries is located. Then look for GetOpt directory. I assume that this is $DIR. Then
$ setenv PERL5LIB $DIR
You see Perl is giving you a nice debugging information in how it is trying to find the module. Try a few variation on the location on PERL5LIB. Eventually, you get it.
The best way ========== If you are courageous, add the following to all the MNI perl binaries:
# use FindBin module available from Perl 5.02. use FindBin; # tell this module to use the lib location to find the module, # using the relative path with respect to this Perl bin location use lib "$FindBin::Bin/../lib/perl5/site_perl/5.8.0";
You have to modify ../lib/perl5/site_perl/5.8.0 to suite your installation.
We will be fixing this problem in the coming release, using the relative path for the module. I don't know when at this time.
Tosa
Wan Park wrote:
Hi,
To create the surface, I have to define the corpus callosum and the pons as well. I have been suggested to get a talairach transform first, so I did: (22970 is the subject folder)
$ talairach 22970
but I have received this message:
wpark% talairach 22970 registering 22970 mri_convert orig orig/orig.mnc reading from orig... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to orig/orig.mnc... Can't locate Getopt/Tabular.pm in @INC (@INC contains: /usr/local/mni/lib/mni_autoreg /System/Library/Perl/5.8.1/darwin-thread-multi-2level /System/Library/Perl/5.8.1 /Library/Perl/5.8.1/darwin-thread-multi-2level /Library/Perl/5.8.1 /Library/Perl /Network/Library/Perl/5.8.1/darwin-thread-multi-2level /Network/Library/Perl/5.8.1 /Network/Library/Perl .) at /usr/pubsw/packages/mni/bin/mritotal line 56. BEGIN failed--compilation aborted at /usr/pubsw/packages/mni/bin/mritotal line 56. Error: could not open file "/usr/local/freesurfer_package/freesurfer/subjects/22970/mri/transforms/talairach.xfm".
System message: No such file or directory mri_add_xform_to_header: could not read xform file '/usr/local/freesurfer_package/freesurfer/subjects/22970/mri/transforms/talairach.xfm'
No such file or directory [ogden:freesurfer_package/freesurfer/subjects] wpark%
I checked and I have no talairach.xfm under transforms. what should i do?
The COR-.info file in mri/wm does not have a line beginning with xform, so I added:
xform /usr/local/freesurfer_package/freesurfer/subjects/22970/mri/transforms/talaraich.xfm
and ran the talairach 22970 again, but I received the same message.
Thanks!!
Wan
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer