Dear Nick and colleagues,
after solving the first problem with nu_correct (fix_mni_paths ... the way you suggested, thanks) we face the fact that the mni paths have to be fixed again after every 2nd, 3rd subject if we try to preprocess a number of subjects data. We run freesurfer with a CentOS 4 version (v3.0.3) on a Windows XP system with VMware and Fedora Core 4.
Any suggestions are greatly appreciated... Many thanks
Stefan & Bogdan
Your last suggestion regarding those issues was:
nu_correct is a script which assumes that perl is installed in /usr/bin/perl. If it is not instaled there (and it is by default on centos), then the script fixup_mni_paths will correct the mni scripts to point to your perl path.
Also confirm that the environment variables MNI_DATAPATH and MNI_PERL5LIB point into the $FREESURFER_HOME/mni path.
You should try running the MNI tools, like nu_correct, and others (see $FREESURFER_HOME/mni/bin) to confirm they work, since there may be some funny interaction with VMWare (but I obviously don't know this just yet).
Nick
The error is as follows:
#@# Nu Intensity Correction Sat Aug 12 09:24:33 BST 2006
mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2
/mnt/d/freesurfer/subjects/sub18/mri /mnt/d/freesurfer//bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.3 2005/12/08 01:27:21 greve Exp $ Linux localhost.localdomain 2.6.15-1.1830_FC4 #1 Thu Feb 2 17:23:41 EST 2006 i686 athlon i386 GNU/Linux Sat Aug 12 09:24:33 BST 2006 Setuid/gid script is writable by world. tmpdir is ./tmp.mri_nu_correct.mni.27966 /mnt/d/freesurfer/subjects/sub18/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.27966/nu0.mnc mri_convert orig.mgz ./tmp.mri_nu_correct.mni.27966/nu0.mnc Can't find the talairach xform '/mnt/d/freesurfer/subjects/sub18/mri/transforms/talairach.xfm' Transform is not loaded into mri reading from orig.mgz... Talairach transform /mnt/d/freesurfer/subjects/sub18/mri/transforms/talairach.xfm does not exist ... Cannot load tal xfm file /mnt/d/freesurfer/subjects/sub18/mri/transforms/talairach.xfm TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, -1.46282e-09) j_ras = (7.41336e-09, 0, -1) k_ras = (0, 1, 0) writing to ./tmp.mri_nu_correct.mni.27966/nu0.mnc...
-------------------------------------------------------- Iteration 1 Sat Aug 12 09:24:42 BST 2006 nu_correct - clobber ./tmp.mri_nu_correct.mni.27966/nu0.mnc ./tmp.mri_nu_correct.mni.27 966/nu1.mnc Setuid/gid script is writable by world. ERROR: nu_correct Linux localhost.localdomain 2.6.15-1.1830_FC4 #1 Thu Feb 2 17:23:41 EST 2006 i686 athlon i386 GNU/Linux
recon-all exited with ERRORS at Sat Aug 12 09:24:42 BST 2006