Hi Anil,
On 26. Jun 2006, at 00:08 Uhr, freesurfer-request@nmr.mgh.harvard.edu wrote:
Message: 8 Date: Sun, 25 Jun 2006 17:07:36 -0500 From: "Anil Roy" aroy85@gmail.com Subject: Re: [Freesurfer] recon-all error To: freesurfer@nmr.mgh.harvard.edu Message-ID: 627ebe090606251507s57777571wbd816d66196fc4f5@mail.gmail.com Content-Type: text/plain; charset="iso-8859-1"
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INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects ERROR: /usr/local/freesurfer/subjects/F200 exists, delete or re-run with -force [root@dhcp-129-105-146-220 freesurfer]# recon-all -force -i /root/Desktop/F200.mnc -subjid F200 -sd /usr/local/freesurfer/subjects -all INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects INFO: /usr/local/freesurfer/subjects/F200 exists with -i, but -force specified. Deleting any previous source volumes Actual FREESURFER_HOME /usr/local/freesurfer -rw-rw-r-- 1 root root 9126 Jun 25 15:42 /usr/local/freesurfer/subjects/F200/scripts/recon-all.log Linux dhcp-129-105-146-220.speech.northwestern.edu 2.6.11-1.1369_FC4smp #1 SMP Thu Jun 2 23:08:39 EDT 2005 i686 i686 i386 GNU/Linux WM removal version /usr/local/freesurfer/subjects/F200
mri_convert /root/Desktop/F200.mnc /usr/local/freesurfer/subjects/F200/mri/orig/001.mgz
mri_convert /root/Desktop/F200.mnc /usr/local/freesurfer/subjects/F200/mri/orig/001.mgz reading from /root/Desktop/F200.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to /usr/local/freesurfer/subjects/F200/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Sun Jun 25 15:42:47 CDT 2006 Found 1 runs /usr/local/freesurfer/subjects/F200/mri/orig/001.mgz WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue.
cp /usr/local/freesurfer/subjects/F200/mri/orig/001.mgz /usr/local/freesurfer/subjects/F200/mri/rawavg.mgz
/usr/local/freesurfer/subjects/F200
mri_convert /usr/local/freesurfer/subjects/F200/mri/rawavg.mgz /usr/local/freesurfer/subjects/F200/mri/orig.mgz --conform
mri_convert /usr/local/freesurfer/subjects/F200/mri/rawavg.mgz /usr/local/freesurfer/subjects/F200/mri/orig.mgz --conform reading from /usr/local/freesurfer/subjects/F200/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) Original Data has (1, 1, 1) mm size and (181, 217, 181) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from 4 to 0 (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /usr/local/freesurfer/subjects/F200/mri/orig.mgz...
mri_add_xform_to_header -c /usr/local/freesurfer/subjects/F200/mri/transforms/talairach.xfm /usr/local/freesurfer/subjects/F200/mri/orig.mgz /usr/local/freesurfer/subjects/F200/mri/orig.mgz
INFO: extension is mgz #-------------------------------------------- #@# Nu Intensity Correction Sun Jun 25 15:43:04 CDT 2006
mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2
/usr/local/freesurfer/subjects/F200/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 2005/12/08 01:27:21 greve Exp $ Linux dhcp-129-105-146-220.speech.northwestern.edu 2.6.11-1.1369_FC4smp #1 SMP Thu Jun 2 23:08:39 EDT 2005 i686 i686 i386 GNU/Linux Sun Jun 25 15:43:04 CDT 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.3620 /usr/local/freesurfer/subjects/F200/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.3620/nu0.mnc mri_convert orig.mgz ./tmp.mri_nu_correct.mni.3620/nu0.mnc Can't find the talairach xform '/usr/local/freesurfer/subjects/F200/mri/transforms/talairach.xfm' Transform is not loaded into mri reading from orig.mgz... Talairach transform /usr/local/freesurfer/subjects/F200/mri/transforms/talairach.xfm does not exist ... Cannot load tal xfm file /usr/local/freesurfer/subjects/F200/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.3620/nu0.mnc...
Iteration 1 Sun Jun 25 15:43:10 CDT 2006 nu_correct -clobber ./tmp.mri_nu_correct.mni.3620/nu0.mnc ./tmp.mri_nu_correct.mni.3620/nu1.mnc [root@dhcp-129-105-146-220.speech.northwestern.edu:/usr/local/ freesurfer/subjects/F200/mri/] [2006-06-25 15:43:11] 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_3670/ ./tmp.mri_nu_correct.mni.3620/nu0.mnc ./tmp.mri_nu_correct.mni.3620/nu1.imp
/usr/local/freesurfer/mni/bin/volume_stats: error while loading shared libraries: libstdc++.so.5: cannot open shared object file: No such file or directory
Here is the part where it breaks; the freesurfer program you use most likely was compiled with gcc 3.x.x, while FC4 is using gcc 4.x.x. The result from the switch in compilers is that you only have a libstdc++.so.6. If you install the following rpm from your installation medium (or any source from the internet) compat-libstdc++-33-3.2.3-47.fc4.i386; it should work. One caveat, I never used FC4, so I might be way off.
Ahoi & good luck Sebastian
nu_estimate_np_and_em: crashed while running volume_stats (termination status=32512) nu_correct: crashed while running nu_estimate_np_and_em (termination status=32512) ERROR: nu_correct Linux dhcp-129-105-146-220.speech.northwestern.edu 2.6.11-1.1369_FC4smp #1 SMP Thu Jun 2 23:08:39 EDT 2005 i686 i686 i386 GNU/Linux
recon-all exited with ERRORS at Sun Jun 25 15:43:11 CDT 2006
Hi Sebastian,
I installed compat-libstdc++-33-3.2.3-47.fc4.i386 and recon-all worked just fine and exited with no errors. It did take 25 hrs though. Thanks a lot.
Anil Roy.
On 6/25/06, Sebastian Moeller sebastian.moeller@lur.rwth-aachen.de wrote:
Hi Anil,
On 26. Jun 2006, at 00:08 Uhr, freesurfer-request@nmr.mgh.harvard.edu wrote:
Message: 8 Date: Sun, 25 Jun 2006 17:07:36 -0500 From: "Anil Roy" aroy85@gmail.com Subject: Re: [Freesurfer] recon-all error To: freesurfer@nmr.mgh.harvard.edu Message-ID: 627ebe090606251507s57777571wbd816d66196fc4f5@mail.gmail.com Content-Type: text/plain; charset="iso-8859-1"
Skipped content of type multipart/alternative-------------- next part
INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects ERROR: /usr/local/freesurfer/subjects/F200 exists, delete or re-run with -force [root@dhcp-129-105-146-220 freesurfer]# recon-all -force -i /root/Desktop/F200.mnc -subjid F200 -sd /usr/local/freesurfer/subjects -all INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects INFO: /usr/local/freesurfer/subjects/F200 exists with -i, but -force specified. Deleting any previous source volumes Actual FREESURFER_HOME /usr/local/freesurfer -rw-rw-r-- 1 root root 9126 Jun 25 15:42 /usr/local/freesurfer/subjects/F200/scripts/recon-all.log Linux dhcp-129-105-146-220.speech.northwestern.edu 2.6.11-1.1369_FC4smp #1 SMP Thu Jun 2 23:08:39 EDT 2005 i686 i686 i386 GNU/Linux WM removal version /usr/local/freesurfer/subjects/F200
mri_convert /root/Desktop/F200.mnc /usr/local/freesurfer/subjects/F200/mri/orig/001.mgz
mri_convert /root/Desktop/F200.mnc /usr/local/freesurfer/subjects/F200/mri/orig/001.mgz reading from /root/Desktop/F200.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to /usr/local/freesurfer/subjects/F200/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Sun Jun 25 15:42:47 CDT 2006 Found 1 runs /usr/local/freesurfer/subjects/F200/mri/orig/001.mgz WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue.
cp /usr/local/freesurfer/subjects/F200/mri/orig/001.mgz /usr/local/freesurfer/subjects/F200/mri/rawavg.mgz
/usr/local/freesurfer/subjects/F200
mri_convert /usr/local/freesurfer/subjects/F200/mri/rawavg.mgz /usr/local/freesurfer/subjects/F200/mri/orig.mgz --conform
mri_convert /usr/local/freesurfer/subjects/F200/mri/rawavg.mgz /usr/local/freesurfer/subjects/F200/mri/orig.mgz --conform reading from /usr/local/freesurfer/subjects/F200/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) Original Data has (1, 1, 1) mm size and (181, 217, 181) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from 4 to 0 (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /usr/local/freesurfer/subjects/F200/mri/orig.mgz...
mri_add_xform_to_header -c /usr/local/freesurfer/subjects/F200/mri/transforms/talairach.xfm /usr/local/freesurfer/subjects/F200/mri/orig.mgz /usr/local/freesurfer/subjects/F200/mri/orig.mgz
INFO: extension is mgz #-------------------------------------------- #@# Nu Intensity Correction Sun Jun 25 15:43:04 CDT 2006
mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2
/usr/local/freesurfer/subjects/F200/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 2005/12/08 01:27:21 greve Exp $ Linux dhcp-129-105-146-220.speech.northwestern.edu 2.6.11-1.1369_FC4smp #1 SMP Thu Jun 2 23:08:39 EDT 2005 i686 i686 i386 GNU/Linux Sun Jun 25 15:43:04 CDT 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.3620 /usr/local/freesurfer/subjects/F200/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.3620/nu0.mnc mri_convert orig.mgz ./tmp.mri_nu_correct.mni.3620/nu0.mnc Can't find the talairach xform '/usr/local/freesurfer/subjects/F200/mri/transforms/talairach.xfm' Transform is not loaded into mri reading from orig.mgz... Talairach transform /usr/local/freesurfer/subjects/F200/mri/transforms/talairach.xfm does not exist ... Cannot load tal xfm file /usr/local/freesurfer/subjects/F200/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.3620/nu0.mnc...
Iteration 1 Sun Jun 25 15:43:10 CDT 2006 nu_correct -clobber ./tmp.mri_nu_correct.mni.3620/nu0.mnc ./tmp.mri_nu_correct.mni.3620/nu1.mnc [root@dhcp-129-105-146-220.speech.northwestern.edu:/usr/local/ freesurfer/subjects/F200/mri/] [2006-06-25 15:43:11] 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_3670/ ./tmp.mri_nu_correct.mni.3620/nu0.mnc ./tmp.mri_nu_correct.mni.3620/nu1.imp
/usr/local/freesurfer/mni/bin/volume_stats: error while loading shared libraries: libstdc++.so.5: cannot open shared object file: No such file or directory
Here is the part where it breaks; the freesurfer program you usemost likely was compiled with gcc 3.x.x, while FC4 is using gcc 4.x.x. The result from the switch in compilers is that you only have a libstdc++.so.6. If you install the following rpm from your installation medium (or any source from the internet) compat-libstdc++-33-3.2.3-47.fc4.i386; it should work. One caveat, I never used FC4, so I might be way off.
Ahoi & good luck Sebastian
nu_estimate_np_and_em: crashed while running volume_stats (termination status=32512) nu_correct: crashed while running nu_estimate_np_and_em (termination status=32512) ERROR: nu_correct Linux dhcp-129-105-146-220.speech.northwestern.edu 2.6.11-1.1369_FC4smp #1 SMP Thu Jun 2 23:08:39 EDT 2005 i686 i686 i386 GNU/Linux
recon-all exited with ERRORS at Sun Jun 25 15:43:11 CDT 2006
-- Sebastian Moeller
Tel.: 04 21 - 2 18 - 78 38 oder 96 91 Fax.: 04 21 - 2 18 - 90 04 GSM: 01 62 - 3 25 45 59 moeller@brain.uni-bremen.de
AG Kreiter / FB 2 Institut fuer Hirnforschung III Abteilung Theoretische Neurobiologie Universitaet Bremen Biogarten Hochschulring 16a Postfach 33 04 40 28359 Bremen
freesurfer@nmr.mgh.harvard.edu
-
Anil Roy -
Sebastian Moeller