Stefan, Centos4 on VMWare on WindowsXP? Sounds interesting, and hope it can be made to work.
What if you type: nu_correct Does it return something like this? nu_correct, version 1.10 Usage: nu_correct [-help] [options] in.mnc out.mnc If not, then please send me the error message. 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 > Hi freesurfers, > > the script crashed when running "recon-all -s bert -all" to test a newly > installed CentOS 4 version (v3.0.3) on a Windows XP system with VMware and > Fedora Core 4. The path for both nu_correct (and nu_estimate_np_and_em: > see second error message) seem to be correct > (/mnt/d/Freesurfer/freesurfer/mni/bin/nu_correct). > > Any suggestions greatly appriciated > > Thanks, > > Stefan > > > The error is as follows: > > [EMAIL PROTECTED] Nu Intensity Correction Thu Jul 20 07:47:00 BST 2006 > > mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2 > > /mnt/d/Freesurfer/freesurfer/subjects/bert/mri > /mnt/d/Freesurfer/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 > Thu Jul 20 07:47:00 BST 2006 > Setuid/gid script is writable by world. > tmpdir is ./tmp.mri_nu_correct.mni.10059 > /mnt/d/Freesurfer/freesurfer/subjects/bert/mri > mri_convert orig.mgz ./tmp.mri_nu_correct.mni.10059/nu0.mnc > mri_convert orig.mgz ./tmp.mri_nu_correct.mni.10059/nu0.mnc > reading from orig.mgz... > 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) > writing to ./tmp.mri_nu_correct.mni.10059/nu0.mnc... > > -------------------------------------------------------- > Iteration 1 Thu Jul 20 07:47:09 BST 2006 > nu_correct -clobber ./tmp.mri_nu_correct.mni.10059/nu0.mnc > /tmp.mri_nu_correct.mni.10059/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 Thu Jul 20 07:47:09 BST 2006 > > > ***********the error is slightly different with one of myt own subjctes: > #-------------------------------------------- > [EMAIL PROTECTED] Nu Intensity Correction Thu Jul 20 07:32:48 BST 2006 > > mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2 > > /mnt/d/Freesurfer/freesurfer/subjects/sMS04134/mri > /mnt/d/Freesurfer/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 > Thu Jul 20 07:32:48 BST 2006 > Program nu_correct, built from: > Package MNI N3, version 1.10, compiled by [EMAIL PROTECTED] > (i686-pc-linux-gnu) > on 2005-11-15 at 21:02:27 > tmpdir is ./tmp.mri_nu_correct.mni.9466 > /mnt/d/Freesurfer/freesurfer/subjects/sMS04134/mri > mri_convert orig.mgz ./tmp.mri_nu_correct.mni.9466/nu0.mnc > mri_convert orig.mgz ./tmp.mri_nu_correct.mni.9466/nu0.mnc > Can't find the talairach xform > '/mnt/d/Freesurfer/freesurfer/subjects/sMS04134/mri/transforms/talairach.xfm' > Transform is not loaded into mri > reading from orig.mgz... > Talairach transform > /mnt/d/Freesurfer/freesurfer/subjects/sMS04134/mri/transforms/talairach.xfm > does not exist ... > Cannot load tal xfm file > /mnt/d/Freesurfer/freesurfer/subjects/sMS04134/mri/transforms/talairach.xfm > 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) > writing to ./tmp.mri_nu_correct.mni.9466/nu0.mnc... > > -------------------------------------------------------- > Iteration 1 Thu Jul 20 07:32:57 BST 2006 > nu_correct -clobber ./tmp.mri_nu_correct.mni.9466/nu0.mnc > /tmp.mri_nu_correct.mni.9466/nu1.mnc > Setuid/gid script is writable by world. > nu_correct: crashed while running nu_estimate_np_and_em (termination > status=6400) > 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 > > _______________________________________________ > 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
