I am a little confused. Does this mean that I do not have talairach.xfm in transforms because of the problem below?

Let's say I follow the first way, after this I should run talairach subject?

thanks,

wan

On Jan 27, 2005, at 1:29 PM, Yasunari Tosa wrote:

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

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-- Yasunari Tosa, Ph.D. Email: tosa@nmr.mgh.harvard.edu NMR Ctr, Mass. General Hospital TEL: 617-726-4050 Building 149, 13th Street Charlestown, MA 02129 USA