Niels,
If you are using a 'dev' release from the past six months, after installation, you will need to run this command once:
fixup_mni_paths
This will enter the MINC_BIN_DIR directory and fixup files that contain hard-coded paths to perl to the correct path to perl on your system. This just needs to be run once. After it is run, typing:
nu_correct
should return a version number (1.10) and usage message.
Nick
On Thu, 2006-01-26 at 18:52 +0100, N.M. van Strien wrote:
Hi,
I am having a problem with running the recon-all script. As soon as I get to intensity normalization, the script stops and gives an error for nu_correct (see output below). The MNI tools seem to be set up correctly however. The environment is set up as such that:
MINC_BIN_DIR /usr/local/freesurfer/lib/mni/bin
and this is where nu_correct does live. Any idea how to overcome this problem? I am running Fedora Core 3 and both the RH9 dev release as well as the CentOS4_x64 dev release show this problem.
Thank you for your help,
Niels van Strien
Nu Intensity Correction Thu Jan 26 16:42:22 CET 2006 mri_convert orig.mgz nu0.mnc mri_convert orig.mgz nu0.mnc reading from orig.mgz... TR=1000.00, 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 nu_correct: Command not found. ERROR: nu_correct Linux VUMC 2.6.12-1.1381_FC3smp #1 SMP Fri Oct 21 04:22:48 EDT 2005 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with errors at Thu Jan 26 16:42:30 CET 2006
Niels M. van Strien (MSc)
Dept. of Anatomy Vrije Universiteit University Medical Center Room MF-G130
Van der Boechorststraat 7 1081 BT Amsterdam The Netherlands
tel: +31 20 44 48047 fax: + 31 84 222 7040
e-mail: n.vanstrien@vumc.nl
http://anatomie.med.vu.nl/afdeling/persons/vanstrien.html
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