Jeurgen,
nu_correct uses perl, so make sure that perl is found at:
/usr/bin/perl
If it is not found there, but elsewhere, then edit the first line of the nu_correct script to point it at the proper location. Or, to do this automatically, run:
fixup_mni_paths
(found in $FREESURFER_HOME/bin).
Nick
On Tue, 2008-02-05 at 08:23 +0100, Juergen Haenggi wrote:
Dear FS experts
I tried to run FS4.0.2 on Linux and the following error occurred:
INFO: extension is mgz #-------------------------------------------- #@# Nu Intensity Correction Tue Feb 5 07:59:56 CET 2008
mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2
/usr/local/freesurfer/subjects/Turner_Control_01/mri /usr/local/freesurfer/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.7 2007/01/06 00:01:14 nicks Exp $ Linux 130.60.235.1 2.6.9-67.0.4.ELsmp #1 SMP Fri Jan 18 05:00:58 EST 2008 i686 i686 i386 GNU/Linux Tue Feb 5 07:59:56 CET 2008 nu_correct: Command not found. tmpdir is ./tmp.mri_nu_correct.mni.5963 /usr/local/freesurfer/subjects/Turner_Control_01/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.5963/nu0.mnc mri_convert orig.mgz ./tmp.mri_nu_correct.mni.5963/nu0.mnc $Id: mri_convert.c,v 1.146.2.1 2007/11/30 23:18:44 greve Exp $ reading from orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 6.12323e-17, 3.7494e-33) j_ras = (-3.7494e-33, 1.94311e-24, -1) k_ras = (6.12323e-17, 1, 1.94311e-24) writing to ./tmp.mri_nu_correct.mni.5963/nu0.mnc...
Iteration 1 Tue Feb 5 08:00:04 CET 2008 nu_correct -clobber ./tmp.mri_nu_correct.mni.5963/nu0.mnc ./tmp.mri_nu_correct.mni.5963/nu1.mnc nu_correct: Command not found. ERROR: nu_correct Linux 130.60.235.1 2.6.9-67.0.4.ELsmp #1 SMP Fri Jan 18 05:00:58 EST 2008 i686 i686 i386 GNU/Linux
recon-all exited with ERRORS at Tue Feb 5 08:00:04 CET 2008
[Neuropsycho@130 subjects]$
Any idea what is wrong here?
Thanks in advance Best regards Juergen
Juergen Haenggi Ph.D. (Dr. des.) Division of Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi@psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website)
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