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 > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
