Hi Bruce,
I've checked the system and found the MNI package is installed. (Someone installed it a while ago) When I did "locate nu_correct" for the error message, there was nothing on "nu_correct". There was a huge directory that includes MNI stuff. So, it is installed but there is NO such thing as "nu_correct".
What would you recommend me to do next? (1) Install it again, or (2) I don't have to do it, since the error message is only due to mistakes in one of the environment variables for MNI package. If so, is there any source for correcting environment variables for the MNI package?
Nam.
Bruce Fischl fischl@nmr.mgh.harvard.edu 10/19/04 3:16 PM >>>
it looks like you don't have the MNI software installed (nu_correct comes from there)
Bruce
On Tue, 19 Oct 2004, Joongnam Yang wrote:
Hi,
I used the following command
recon-all -stage1 -subjid blobby
and I got the following error message (Please let me know what is wrong with Freesurfer).
-------------- copy of the exact error messages ------------------- ######################################## program versions used $Id: recon-all-nmr,v 1.37 2004/01/06 22:21:48 tosa Exp $ $Id: mri_motion_correct2,v 1.7 2004/01/16 20:25:10 tosa Exp $ mri_convert --version $ $Header: /software/source//minc/cvsroot/minc/progs/rawtominc/rawtominc.c,v 6.8 2002/08/05 00:53:50 neelin Exp $ minctracc.c $Header: /software/source/registration/mni_autoreg/minctracc/Main/minctracc.c,v 96.3 2000/03/15 08:42:41 stever Exp $ $Header: /software/source//minc/cvsroot/minc/progs/mincresample/mincresample.c,v
6.11
2002/11/06 13:32:23 jason Exp $ $Header: /software/source//minc/cvsroot/minc/progs/mincaverage/mincaverage.c,v 6.4 2001/04/24 13:38:42 neelin Exp $ $Id: talairach2,v 1.5 2003/08/28 21:45:48 tosa Exp $ mri_convert --version $ # $Id: mritotal.in,v 1.10 2000/06/14 12:55:01 louis Exp $ strings: nu_correct:: No such file or directory strings: Command: No such file or directory strings: not: No such file or directory strings: found.: No such file or directory $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ ####################################### INFO: SUBJECTS_DIR is /home/nam ERROR: nu_correct does not exist --------- end of the copy of the error messages -------------------------- _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Nam,
I'm not sure what to tell you. nu_correct is their script for running John Sled's N3 intensity nonuniformity correction. We have it in our mni_tools directory locally, you must be able to get it from them.
cheers, Bruce
On Tue, 19 Oct 2004, Joongnam Yang wrote:
Hi Bruce,
I've checked the system and found the MNI package is installed. (Someone installed it a while ago) When I did "locate nu_correct" for the error message, there was nothing on "nu_correct". There was a huge directory that includes MNI stuff. So, it is installed but there is NO such thing as "nu_correct".
What would you recommend me to do next? (1) Install it again, or (2) I don't have to do it, since the error message is only due to mistakes in one of the environment variables for MNI package. If so, is there any source for correcting environment variables for the MNI package?
Nam.
Bruce Fischl fischl@nmr.mgh.harvard.edu 10/19/04 3:16 PM >>>
it looks like you don't have the MNI software installed (nu_correct comes from there)
Bruce
On Tue, 19 Oct 2004, Joongnam Yang wrote:
Hi,
I used the following command
recon-all -stage1 -subjid blobby
and I got the following error message (Please let me know what is wrong with Freesurfer).
-------------- copy of the exact error messages ------------------- ######################################## program versions used $Id: recon-all-nmr,v 1.37 2004/01/06 22:21:48 tosa Exp $ $Id: mri_motion_correct2,v 1.7 2004/01/16 20:25:10 tosa Exp $ mri_convert --version $ $Header: /software/source//minc/cvsroot/minc/progs/rawtominc/rawtominc.c,v 6.8 2002/08/05 00:53:50 neelin Exp $ minctracc.c $Header: /software/source/registration/mni_autoreg/minctracc/Main/minctracc.c,v 96.3 2000/03/15 08:42:41 stever Exp $ $Header: /software/source//minc/cvsroot/minc/progs/mincresample/mincresample.c,v
6.11
2002/11/06 13:32:23 jason Exp $ $Header: /software/source//minc/cvsroot/minc/progs/mincaverage/mincaverage.c,v 6.4 2001/04/24 13:38:42 neelin Exp $ $Id: talairach2,v 1.5 2003/08/28 21:45:48 tosa Exp $ mri_convert --version $ # $Id: mritotal.in,v 1.10 2000/06/14 12:55:01 louis Exp $ strings: nu_correct:: No such file or directory strings: Command: No such file or directory strings: not: No such file or directory strings: found.: No such file or directory $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ ####################################### INFO: SUBJECTS_DIR is /home/nam ERROR: nu_correct does not exist --------- end of the copy of the error messages -------------------------- _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi,
nu_correct is N3 package from MNI.
We use two tools from MNI: mni_autoreg and N3. Unfortunately in order to use them, you must have the following list of MNI tools installed.
1. netcdf 2. mni_perllib 3. GetOpt-Tabular Perlmodule 4. Text::Format Perl module (get this from CPAN) 5. minc 6. EBTKS lib 7. N3
in the order of installation.
Tosa
Joongnam Yang wrote:
Hi Bruce,
I've checked the system and found the MNI package is installed. (Someone installed it a while ago) When I did "locate nu_correct" for the error message, there was nothing on "nu_correct". There was a huge directory that includes MNI stuff. So, it is installed but there is NO such thing as "nu_correct".
What would you recommend me to do next? (1) Install it again, or (2) I don't have to do it, since the error message is only due to mistakes in one of the environment variables for MNI package. If so, is there any source for correcting environment variables for the MNI package?
Nam.
Bruce Fischl fischl@nmr.mgh.harvard.edu 10/19/04 3:16 PM >>>
it looks like you don't have the MNI software installed (nu_correct comes from there)
Bruce
On Tue, 19 Oct 2004, Joongnam Yang wrote:
Hi,
I used the following command
recon-all -stage1 -subjid blobby
and I got the following error message (Please let me know what is wrong with Freesurfer).
-------------- copy of the exact error messages ------------------- ######################################## program versions used $Id: recon-all-nmr,v 1.37 2004/01/06 22:21:48 tosa Exp $ $Id: mri_motion_correct2,v 1.7 2004/01/16 20:25:10 tosa Exp $ mri_convert --version $ $Header: /software/source//minc/cvsroot/minc/progs/rawtominc/rawtominc.c,v 6.8 2002/08/05 00:53:50 neelin Exp $ minctracc.c $Header: /software/source/registration/mni_autoreg/minctracc/Main/minctracc.c,v 96.3 2000/03/15 08:42:41 stever Exp $ $Header: /software/source//minc/cvsroot/minc/progs/mincresample/mincresample.c,v
6.11
2002/11/06 13:32:23 jason Exp $ $Header: /software/source//minc/cvsroot/minc/progs/mincaverage/mincaverage.c,v 6.4 2001/04/24 13:38:42 neelin Exp $ $Id: talairach2,v 1.5 2003/08/28 21:45:48 tosa Exp $ mri_convert --version $ # $Id: mritotal.in,v 1.10 2000/06/14 12:55:01 louis Exp $ strings: nu_correct:: No such file or directory strings: Command: No such file or directory strings: not: No such file or directory strings: found.: No such file or directory $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ ####################################### INFO: SUBJECTS_DIR is /home/nam ERROR: nu_correct does not exist --------- end of the copy of the error messages -------------------------- _______________________________________________ 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
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Joongnam Yang -
Yasunari Tosa