Petr,
Which freesurfer distribution do you have? type
cat $FREESURFER_HOME/build-stamp.txt
Nick
autorecon1 with the 4.0.4 version I have the following ERROR (at the end of this excerpt):
mri_convert ./tmp.mri_nu_correct.mni.11745/nu2.mnc nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.11745/nu2.mnc nu.mgz --like orig.mgz WARNING: --like does not work on multi-frame data $Id: mri_convert.c,v 1.146.2.2 2008/03/02 02:53:20 nicks Exp $ reading from ./tmp.mri_nu_correct.mni.11745/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 8.05145e-09, -3.11374e-08) j_ras = (-7.66902e-08, -2.80897e-09, -1) k_ras = (3.66e-08, 1, -5.54119e-10) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz...
Tue Jun 10 11:51:25 CEST 2008 mri_nu_correct.mni done #-------------------------------------------- #@# Talairach Tue Jun 10 11:51:25 CEST 2008 /home/batch/subjects/1030/mri
talairach_avi --i nu.mgz --xfm transforms/talairach.auto.xfm
/home/batch/subjects/1030/mri /home/freesurfer/freesurfer_4.0.4/bin/talairach_avi --i nu.mgz --xfm transforms/talairach.auto.xfm $Id: talairach_avi,v 1.4 2007/05/29 23:24:27 nicks Exp $ Linux millais.comp.neuro 2.6.23.8-63.fc8 #1 SMP Wed Nov 21 18:51:08 EST 2007 i686 i686 i386 GNU/Linux Tue Jun 10 11:51:25 CEST 2008
mri_convert nu.mgz talsrcimg.img $Id: mri_convert.c,v 1.146.2.2 2008/03/02 02:53:20 nicks Exp $ reading from nu.mgz... TR=2730.00, TE=3.93, TI=1000.00, flip angle=7.00 i_ras = (-1, 8.05145e-09, -3.11374e-08) j_ras = (-7.66902e-08, -2.80897e-09, -1) k_ras = (3.66e-08, 1, -5.54119e-10) writing to talsrcimg.img... Analyze Output Matrix -1.000 -0.000 0.000 125.111; 0.000 -0.000 1.000 -71.398; -0.000 -1.000 -0.000 116.126; 0.000 0.000 0.000 1.000;
INFO: set hdr.hist.orient to -1
mpr2mni305 talsrcimg Tue Jun 10 11:51:28 CEST 2008 /home/freesurfer/freesurfer_4.0.4/bin/mpr2mni305 talsrcimg $Id: mpr2mni305,v 1.3 2007/08/04 02:23:35 nicks Exp $ target=711-2C_as_mni_average_305
analyzeto4dfp talsrcimg -O0 -y
$Id: ifh2hdr.c,v 1.3 2007/05/05 10:45:03 nicks Exp $ Tue Jun 10 11:51:30 2008 Writing: talsrcimg.4dfp.hdr $Id: analyzeto4dfp.c,v 1.2 2007/05/05 00:00:06 nicks Exp $ Reading: talsrcimg.hdr header size 348 bytes hdr.dime.datatype offset=70 value=2 hdr.dime.bitpix offset=72 value=8 hdr.hist.orient offset=252 value=-1 dimensionality 4 dimensions 256 256 256 1 Reading: talsrcimg.img Writing: talsrcimg.4dfp.img Writing: talsrcimg.4dfp.ifh ifh2hdr talsrcimg -r0to255 ori=2
gauss_4dfp talsrcimg 1.1
gauss_4dfp: error while loading shared libraries: libg2c.so.0: cannot open shared object file: No such file or directory ERROR: 'gauss_4dfp talsrcimg 1.1' failed! status=127 ERROR: mpr2mni305 execution aborted ERROR: mpr2mni305 failed, see transforms/talairach_avi.log Linux millais.comp.neuro 2.6.23.8-63.fc8 #1 SMP Wed Nov 21 18:51:08 EST 2007 i686 i686 i386 GNU/Linux
recon-all exited with ERRORS at Tue Jun 10 11:51:30 CEST 2008
Seems that it´s a problem with the shared libraries. Think I remember that we had to deal with this kind of problem previously, but now exactly how... We have been running several other versions recently without changing things too much (I think).
Anything apart from this that I have to be aware of?
Thanks in advance!
Petr S. Bjerkan Dept. of psychiatry University of Oslo
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