[MINC-users] problem with MNI tools in Freesurfer

[Michele Perry]

Hi,
I have been using Freesurfer for about 5 months now.  It was working
normally for most of that time.  About 2 weeks ago, I started having
problems with one of the processing steps.  I posted questions to the
Freesurfer mailing list and they said I should contact MNI because the
problems I was having involved MNI tools.

When I run recon-all -stage1 -subjid <subjectID>, it exits after the
following:

---------------------------------------------
Nu Intensity Correction Fri Mar 18 17:19:49 PST 2005
mri_convert orig nu0.mnc
mri_convert orig nu0.mnc
reading from orig...
TR=2730.00, TE=3.31, TI=1000.00, flip angle=7.00
i_ras = (-1, 0, 0)
j_ras = (0, -0, -1)
k_ras = (0, 1, -0)
writing to nu0.mnc...
nu_correct -clobber nu0.mnc nu1.mnc
[mperry@ip06:<SUBJECTS_DIR>/<subjectID>/mri/] [2005-03-18 17:19:59] running:
  /usr/pubsw/packages/mni/1.2/bin/nu_estimate_np_and_em -parzen -log
-sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask
-nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp
-tmpdir /usr/tmp/nu_correct_31180/ nu0.mnc nu1.imp

Can't locate MNI/Startup.pm in @INC (@INC contains:
/usr/lib/perl5/5.8.0/i386-linux-thread-multi /usr/lib/perl5/5.8.0
/usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi
/usr/lib/perl5/site_perl/5.8.0 /usr/lib/perl5/site_perl
/usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi
/usr/lib/perl5/vendor_perl/5.8.0 /usr/lib/perl5/vendor_perl
/usr/lib/perl5/5.8.0/i386-linux-thread-multi /usr/lib/perl5/5.8.0 .) at
/usr/pubsw/packages/mni/1.2/bin/sharpen_volume line 33.
BEGIN failed--compilation aborted at
/usr/pubsw/packages/mni/1.2/bin/sharpen_volume line 33.
nu_estimate_np_and_em: crashed while running sharpen_volume (termination
status=512)
nu_correct: crashed while running nu_estimate_np_and_em (termination
status=512)
ERROR: nu_correct
------------------------------------------
Filesystem           1K-blocks      Used Available Use% Mounted on

                     693727244 310617732 347870136  48%
------------------------------------------
recon-all exited with errors at Fri Mar 18 17:19:59 PST 2005




vi /usr/pubsw/packages/mni/1.2/bin/sharpen_volume line 33 is:
use MNI::Startup qw(nocputimes);
That's the first line after all the initial comments.


Any advice?
Thank you for your help,
Michele Perry