ok, it is working now. thanks! margaret
On Fri, 17 Jun 2005, Nick Schmansky wrote:
Try it now.
I have recently rebuilt the MINC toolkit, but it seems I overlooked its dependencies, and just now reverted the path back to where it was (and will leave it that way).
Sorry for the hassle.
On Fri, 2005-06-17 at 16:32 -0400, Margaret Duff wrote:
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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