Hi,
Following some system upgrade to our Linux 2.6 systems, freesurfer has
ceased to work. When running recon-all on bert, we get a message
referring to a broken pipe and a crash in mincinfo. We are running Gentoo:
doolin ~ # uname -a
Linux doolin 2.6.21-gentoo-r4 #1 SMP Thu Aug 9 09:33:11 PDT 2007 i686
AMD Athlon(tm) 64 X2 Dual Core Processor 4400+ AuthenticAMD GNU/Linux
doolin ~ #
Any help and/or advice would be appreciated.
Thank you,
Chuck
mri_add_xform_to_header -c
/vxfsvol/home/staff/chuck/freesurfer-test/bert/mri/transforms/talairach.xfm
/vxfsvol/home/staff/chuck/freesurfer-test/bert/mri/orig.mgz
/vxfsvol/home/staff/chuck/freesurfer-test/bert/mri/orig.mgz
INFO: extension is mgz
#--------------------------------------------
[EMAIL PROTECTED] Nu Intensity Correction Fri Oct 12 10:37:03 PDT 2007
mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2
/vxfsvol/home/staff/chuck/freesurfer-test/bert/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 1.3.2.1 2006/11/24 20:16:38 nicks Exp $
Linux doolin 2.6.21-gentoo-r4 #1 SMP Thu Aug 9 09:33:11 PDT 2007 i686
AMD Athlon(tm) 64 X2 Dual Core Processor 4400+ AuthenticAMD GNU/Linux
Fri Oct 12 10:37:03 PDT 2007
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.28553
/vxfsvol/home/staff/chuck/freesurfer-test/bert/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.28553/nu0.mnc
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.28553/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.28553/nu0.mnc...
--------------------------------------------------------
Iteration 1 Fri Oct 12 10:37:11 PDT 2007
nu_correct -clobber ./tmp.mri_nu_correct.mni.28553/nu0.mnc
./tmp.mri_nu_correct.mni.28553/nu1.mnc
[EMAIL PROTECTED]:/vxfsvol/home/staff/chuck/freesurfer-test/bert/mri/]
[2007-10-12 10:37:11] running:
/usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log
-sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask
-nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp
-tmpdir /usr/tmp/nu_correct_28603/
./tmp.mri_nu_correct.mni.28553/nu0.mnc
./tmp.mri_nu_correct.mni.28553/nu1.imp
nu_estimate_np_and_em: broken pipe
nu_estimate_np_and_em: crashed while running mincinfo (termination
status=13)
nu_correct: crashed while running nu_estimate_np_and_em (termination
status=65280)
ERROR: nu_correct
Linux doolin 2.6.21-gentoo-r4 #1 SMP Thu Aug 9 09:33:11 PDT 2007 i686
AMD Athlon(tm) 64 X2 Dual Core Processor 4400+ AuthenticAMD GNU/Linux
recon-all exited with ERRORS at Fri Oct 12 10:37:11 PDT 2007
[EMAIL PROTECTED] /usr/local/freesurfer $
--
Chuck Theobald
System Administrator
The Robert and Beverly Lewis Center for Neuroimaging
University of Oregon
P: 541-346-0343
F: 541-346-0345
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