Hi, I have just recently gotten an error when running recon-all-nmr. I
am on the computer troy and my command line is recon-all-nmr -stage1
-subjid SM2S2 and my SUBJECTS_DIR is /space/troy/1/users/FREESURFER.
I tried resetting my LANG to C and en_US and neither made a difference.
It seems like it can't find a start up file, which I found in
/usr/lib/perl5/5.8.5/MNI, but this doesn't seem to be one of the paths its
looking in. Is there anything I can do to prevent this error? I have
attached the error file from the terminal window below. Thanks,
Margaret
(nmr-std-env) recon-all-nmr -stage1 -subjid SM2S2
########################################
program versions used
$Id: recon-all-nmr,v 1.53 2004/12/08 20:45:06 greve Exp $
$Id: mri_motion_correct2,v 1.9 2004/12/14 03:37:42 greve Exp $
mri_convert --version
stable2
minctracc.c
$Id: talairach2,v 1.7 2004/08/31 18:07:37 tosa Exp $
mri_convert --version
stable2
# $Id: mritotal.in,v 1.12 2004/02/12 05:55:18 rotor Exp $
# $Id: nu_estimate.in,v 1.1 2003/04/16 14:29:34 bert Exp $
stable2
stable2
stable2
stable2
stable2
stable2
stable2
stable2
stable2
stable2
stable2
stable2
stable2
stable2
stable2
stable2
#######################################
INFO: SUBJECTS_DIR is /autofs/space/troy_001/users/FREESURFER
WARNING: current FREESURFER_HOME does not match that of previous
processing.
Current: /usr/local/freesurfer/beta
Previous: /usr/local/freesurfer/dev
---------------------------------------------
MotionCor Fri Jun 17 16:16:50 EDT 2005
/autofs/space/troy_001/users/FREESURFER/SM2S2/mri/orig
mri_motion_correct2 -o . -i 001 -i 002
tmpdir is ./tmp-mri_motion_correct2-27002
--------------------------------------------------------------
mri_motion_correct2 logfile is ./mri_motion_correct2.log
--------------------------------------------------------------
-----------------------------------------
Converting 001
Fri Jun 17 16:16:54 EDT 2005
mri_convert 001
/autofs/space/troy_001/users/FREESURFER/SM2S2/mri/orig/tmp-mri_motion_correct2-27002/cor-1.mnc
^[[B^[[A^[[B^[[B^[[B^[[Breading from 001...
TR=2730000.00, 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
/autofs/space/troy_001/users/FREESURFER/SM2S2/mri/orig/tmp-mri_motion_correct2-27002/cor-1.mnc...
-----------------------------------------
Converting 002
Fri Jun 17 16:17:06 EDT 2005
mri_convert 002
/autofs/space/troy_001/users/FREESURFER/SM2S2/mri/orig/tmp-mri_motion_correct2-27002/cor-2.mnc
reading from 002...
TR=2730000.00, 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
/autofs/space/troy_001/users/FREESURFER/SM2S2/mri/orig/tmp-mri_motion_correct2-27002/cor-2.mnc...
-----------------------------------------
Motion Correcting
/autofs/space/troy_001/users/FREESURFER/SM2S2/mri/orig/tmp-mri_motion_correct2-27002/cor-2.mnc
Fri Jun 17 16:17:17 EDT 2005
COG of v1: 4.496311 15.253652 -23.867643
COG of v2: 4.493972 15.296473 -24.011532
[trans] = -0.002339 0.042821 -0.143888
Initial objective function val = 0.01666989
Final objective function value = 0.01148322
successful write
-----------------------------------------
Resampling
/autofs/space/troy_001/users/FREESURFER/SM2S2/mri/orig/tmp-mri_motion_correct2-27002/cor-2.mnc
Fri Jun 17 16:18:21 EDT 2005
Transforming
slices:................................................................................................................................................................................................................................................................Done
-----------------------------------------
Averaging
Fri Jun 17 16:18:27 EDT 2005
Processing:................................................................................................................................................................................................................................................................Done
-----------------------------------------
Converting Average to output
Fri Jun 17 16:18:32 EDT 2005
mri_convert
/autofs/space/troy_001/users/FREESURFER/SM2S2/mri/orig/tmp-mri_motion_correct2-27002/avgvol.mnc
. -tr 2.73e+06 -te 0 -TI 0 -flip_angle 0
reading from
/autofs/space/troy_001/users/FREESURFER/SM2S2/mri/orig/tmp-mri_motion_correct2-27002/avgvol.mnc...
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)
Original Data has (1, 1, 1) mm size and (256, 256, 256) voxels.
Data is conformed to 1 mm size and 256 voxels for all directions
writing to ....
Started at: Fri Jun 17 16:16:54 EDT 2005
Ended at: Fri Jun 17 16:18:41 EDT 2005
mri_motion_correct2: done
---------------------------------------------
Nu Intensity Correction Fri Jun 17 16:18:41 EDT 2005
mri_convert orig nu0.mnc
mri_convert orig nu0.mnc
reading from orig...
TR=2730000.00, 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 nu0.mnc...
nu_correct -clobber nu0.mnc nu1.mnc
Can't locate MNI/Startup.pm in @INC (@INC contains:
/usr/lib/perl5/5.8.5/i386-linux-thread-multi /usr/lib/perl5/5.8.5
/usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi
/usr/lib/perl5/site_perl/5.8.4/i386-linux-thread-multi
/usr/lib/perl5/site_perl/5.8.3/i386-linux-thread-multi
/usr/lib/perl5/site_perl/5.8.2/i386-linux-thread-multi
/usr/lib/perl5/site_perl/5.8.1/i386-linux-thread-multi
/usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi
/usr/lib/perl5/site_perl/5.8.5 /usr/lib/perl5/site_perl/5.8.4
/usr/lib/perl5/site_perl/5.8.3 /usr/lib/perl5/site_perl/5.8.2
/usr/lib/perl5/site_perl/5.8.1 /usr/lib/perl5/site_perl/5.8.0
/usr/lib/perl5/site_perl
/usr/lib/perl5/vendor_perl/5.8.5/i386-linux-thread-multi
/usr/lib/perl5/vendor_perl/5.8.4/i386-linux-thread-multi
/usr/lib/perl5/vendor_perl/5.8.3/i386-linux-thread-multi
/usr/lib/perl5/vendor_perl/5.8.2/i386-linux-thread-multi
/usr/lib/perl5/vendor_perl/5.8.1/i386-linux-thread-multi
/usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi
/usr/lib/perl5/vendor_perl/5.8.5 /usr/lib/perl5/vendor_perl/5.8.4
/usr/lib/perl5/vendor_perl/5.8.3 /usr/lib/perl5/vendor_perl/5.8.2
/usr/lib/perl5/vendor_perl/5.8.1 /usr/lib/perl5/vendor_perl/5.8.0
/usr/lib/perl5/vendor_perl .) at
/usr/pubsw/packages/mni/current/bin/nu_correct line 37.
BEGIN failed--compilation aborted at
/usr/pubsw/packages/mni/current/bin/nu_correct line 37.
ERROR: nu_correct
------------------------------------------
Filesystem 1K-blocks Used Available Use% Mounted on
troy:/local_mount/space/troy/1
201855952 169100440 32755512 84%
/autofs/space/troy_001
------------------------------------------
recon-all exited with errors at Fri Jun 17 16:18:53 EDT 2005
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