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:
#@# 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: #-------------------------------------------- #@# 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 nicks@kani (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