hi i send you further information of the -nuintensitycor and skullstrip problem,about three control subjects. after running "recon_all -i", i decided to process my data step by step, i run "recon_all -autorecon1" for all of them and it ended with errors. i picked up three cases of the recon-all.log file :
subject 1:
#@# Nu Intensity Correction Mon May 27 18:08:32 CEST 2013
mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2
/home_cluster/mlaouche/freesurf_makh/ctr3/mri /home_cluster/amesse/software/freesurfer5.1/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.18 2011/03/02 20:16:39 nicks Exp $ Linux cn09 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13 00:26:49 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux Mon May 27 18:08:36 CEST 2013 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 tmpdir is ./tmp.mri_nu_correct.mni.12456 /home_cluster/mlaouche/freesurf_makh/ctr3/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.12456/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.12456/nu0.mnc -odt float $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from orig.mgz... TR=7.05, 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) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.12456/nu0.mnc... -------------------------------------------------------- Iteration 1 Mon May 27 18:23:46 CEST 2013 nu_correct -clobber ./tmp.mri_nu_correct.mni.12456/nu0.mnc ./tmp.mri_nu_correct.mni.12456/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.12456/0/ ./tmp.mri_nu_correct.mni.12456/ is a directory but not writeable [mlaouche@cn09:/home_cluster/mlaouche/freesurf_makh/ctr3/mri/] [2013-05-27 18:23:56] running: /home_cluster/amesse/software/freesurfer5.1/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 ./tmp.mri_nu_correct.mni.12456/0/ ./tmp.mri_nu_correct.mni.12456/nu0.mnc ./tmp.mri_nu_correct.mni.12456/nu1.imp
Assertion failed at line 827 in file templates/CachedArray.cc nu_estimate_np_and_em: crashed while running volume_stats (termination status=256) nu_correct: crashed while running nu_estimate_np_and_em (termination status=256) ERROR: nu_correct Linux cn09 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13 00:26:49 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s ctr3 exited with ERRORS at Mon May 27 18:47:13 CEST 2013
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
subject 2:
#@# Nu Intensity Correction Mon May 27 18:08:21 CEST 2013
mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2
/home_cluster/mlaouche/freesurf_makh/ctr5/mri /home_cluster/amesse/software/freesurfer5.1/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.18 2011/03/02 20:16:39 nicks Exp $ Linux cn09 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13 00:26:49 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux Mon May 27 18:08:31 CEST 2013 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 tmpdir is ./tmp.mri_nu_correct.mni.12252 /home_cluster/mlaouche/freesurf_makh/ctr5/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.12252/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.12252/nu0.mnc -odt float $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from orig.mgz... TR=7.07, 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) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.12252/nu0.mnc... tee: ./mri_nu_correct.mni.log: Input/output error -------------------------------------------------------- Iteration 1 Mon May 27 18:23:44 CEST 2013 nu_correct -clobber ./tmp.mri_nu_correct.mni.12252/nu0.mnc ./tmp.mri_nu_correct.mni.12252/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.12252/0/ ./tmp.mri_nu_correct.mni.12252/ is a directory but not writeable [mlaouche@cn09:/home_cluster/mlaouche/freesurf_makh/ctr5/mri/] [2013-05-27 18:23:56] running: /home_cluster/amesse/software/freesurfer5.1/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 ./tmp.mri_nu_correct.mni.12252/0/ ./tmp.mri_nu_correct.mni.12252/nu0.mnc ./tmp.mri_nu_correct.mni.12252/nu1.imp
Computing ranges for each class.: ............................................. Processing:.................................................................Done Fitting splines: .............................................................. Computing ranges for each class.: ............................................. Processing:.................................................................Done Computing ranges for each class.: ............................................. Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Linux cn09 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13 00:26:49 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s ctr5 exited with ERRORS at Mon May 27 19:13:37 CEST 2013
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
subject 3:
#@# Nu Intensity Correction Mon May 27 18:08:34 CEST 2013
mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2
/home_cluster/mlaouche/freesurf_makh/ctr6/mri /home_cluster/amesse/software/freesurfer5.1/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.18 2011/03/02 20:16:39 nicks Exp $ Linux cn09 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13 00:26:49 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux Mon May 27 18:08:38 CEST 2013 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 mkdir: cannot create directory `./tmp.mri_nu_correct.mni.12552': Input/output error tee: ./mri_nu_correct.mni.log: Input/output error tmpdir is ./tmp.mri_nu_correct.mni.12552 Linux cn09 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13 00:26:49 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
Hi Laouchedi
can you send me the rawavg.mgz for one of these? The nu seems to be only a hemisphere with a massive intensity artifact
thanks Bruce
On Mon, 27 May 2013, LAOUCHEDI MAKHLOUF wrote:
hi i send you further information of the -nuintensitycor and skullstrip problem,about three control subjects. after running "recon_all -i", i decided to process my data step by step, i run "recon_all -autorecon1" for all of them and it ended with errors. i picked up three cases of the recon-all.log file :
subject 1:
#@# Nu Intensity Correction Mon May 27 18:08:32 CEST 2013
mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2
/home_cluster/mlaouche/freesurf_makh/ctr3/mri /home_cluster/amesse/software/freesurfer5.1/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.18 2011/03/02 20:16:39 nicks Exp $ Linux cn09 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13 00:26:49 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux Mon May 27 18:08:36 CEST 2013 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 tmpdir is ./tmp.mri_nu_correct.mni.12456 /home_cluster/mlaouche/freesurf_makh/ctr3/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.12456/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.12456/nu0.mnc -odt float $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from orig.mgz... TR=7.05, 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) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.12456/nu0.mnc...
Iteration 1 Mon May 27 18:23:46 CEST 2013 nu_correct -clobber ./tmp.mri_nu_correct.mni.12456/nu0.mnc ./tmp.mri_nu_correct.mni.12456/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.12456/0/ ./tmp.mri_nu_correct.mni.12456/ is a directory but not writeable [mlaouche@cn09:/home_cluster/mlaouche/freesurf_makh/ctr3/mri/] [2013-05-27 18:23:56] running: /home_cluster/amesse/software/freesurfer5.1/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 ./tmp.mri_nu_correct.mni.12456/0/ ./tmp.mri_nu_correct.mni.12456/nu0.mnc ./tmp.mri_nu_correct.mni.12456/nu1.imp
Assertion failed at line 827 in file templates/CachedArray.cc nu_estimate_np_and_em: crashed while running volume_stats (termination status=256) nu_correct: crashed while running nu_estimate_np_and_em (termination status=256) ERROR: nu_correct Linux cn09 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13 00:26:49 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s ctr3 exited with ERRORS at Mon May 27 18:47:13 CEST 2013
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
subject 2:
#@# Nu Intensity Correction Mon May 27 18:08:21 CEST 2013
mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2
/home_cluster/mlaouche/freesurf_makh/ctr5/mri /home_cluster/amesse/software/freesurfer5.1/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.18 2011/03/02 20:16:39 nicks Exp $ Linux cn09 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13 00:26:49 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux Mon May 27 18:08:31 CEST 2013 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 tmpdir is ./tmp.mri_nu_correct.mni.12252 /home_cluster/mlaouche/freesurf_makh/ctr5/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.12252/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.12252/nu0.mnc -odt float $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from orig.mgz... TR=7.07, 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) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.12252/nu0.mnc... tee: ./mri_nu_correct.mni.log: Input/output error
Iteration 1 Mon May 27 18:23:44 CEST 2013 nu_correct -clobber ./tmp.mri_nu_correct.mni.12252/nu0.mnc ./tmp.mri_nu_correct.mni.12252/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.12252/0/ ./tmp.mri_nu_correct.mni.12252/ is a directory but not writeable [mlaouche@cn09:/home_cluster/mlaouche/freesurf_makh/ctr5/mri/] [2013-05-27 18:23:56] running: /home_cluster/amesse/software/freesurfer5.1/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 ./tmp.mri_nu_correct.mni.12252/0/ ./tmp.mri_nu_correct.mni.12252/nu0.mnc ./tmp.mri_nu_correct.mni.12252/nu1.imp
Computing ranges for each class.: ............................................. Processing:.................................................................Done Fitting splines: .............................................................. Computing ranges for each class.: ............................................. Processing:.................................................................Done Computing ranges for each class.: ............................................. Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Linux cn09 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13 00:26:49 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s ctr5 exited with ERRORS at Mon May 27 19:13:37 CEST 2013
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
subject 3:
#@# Nu Intensity Correction Mon May 27 18:08:34 CEST 2013
mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2
/home_cluster/mlaouche/freesurf_makh/ctr6/mri /home_cluster/amesse/software/freesurfer5.1/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.18 2011/03/02 20:16:39 nicks Exp $ Linux cn09 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13 00:26:49 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux Mon May 27 18:08:38 CEST 2013 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 mkdir: cannot create directory `./tmp.mri_nu_correct.mni.12552': Input/output error tee: ./mri_nu_correct.mni.log: Input/output error tmpdir is ./tmp.mri_nu_correct.mni.12552 Linux cn09 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13 00:26:49 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
LAOUCHEDI MAKHLOUF