Dear FreeSurfer group,
I get an error trying to run basic recon-all on a ubuntu 16.04 system.
It finish with errors after a few minutes and I cannot find any help in the recon-all.log (pasted below).
I have made the symbolic links from the installation notes.
Any ideas or thoughts on what the problem might be or how to track it down would be very welcome.
best regards, mads
from bugr: FREESURFER_HOME: /home/XYZ/Toolboxes/freesurfer
Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
Debian version: stretch/sid
Kernel info: Linux 4.4.0-22-generic x86_64
recon-all.log:
Mon May 9 11:12:07 CEST 2016 /home/XYZ/Projects/tmp/fs_test/test /home/XYZ/Toolboxes/freesurfer/bin/recon-all -all -subjid test -i T1.mgz subjid test setenv SUBJECTS_DIR /home/XYZ/Projects/tmp/fs_test FREESURFER_HOME /home/XYZ/Toolboxes/freesurfer Actual FREESURFER_HOME /home/XYZ/Toolboxes/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Linux comp_name 4.4.0-22-generic #39-Ubuntu SMP Thu May 5 16:53:32 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 62044 maxlocks unlimited maxsignal 62044 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited
total used free shared buff/cache available Mem: 15924580 3455984 375968 323648 12092628 11975092 Swap: 16616956 254220 16362736
######################################## program versions used $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:08-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:08-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 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 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:08-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:08-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:08-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:08-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:08-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:08-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400
======= NUMBER OF OPENMP THREADS = 1 ======= ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:08-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:08-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:10-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:10-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:10-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:10-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:10-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:10-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:10-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:10-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:10-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:10-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:11-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $
ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:11-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $
ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:11-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:11-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:11-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:11-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:11-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /home/XYZ/Toolboxes/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /home/XYZ/Toolboxes/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### /home/XYZ/Projects/tmp/fs_test/test
mri_convert /home/XYZ/Projects/tmp/fs_test/T1.mgz /home/XYZ/Projects/tmp/fs_test/test/mri/orig/001.mgz
mri_convert /home/XYZ/Projects/tmp/fs_test/T1.mgz /home/XYZ/Projects/tmp/fs_test/test/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/XYZ/Projects/tmp/fs_test/T1.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 /home/XYZ/Projects/tmp/fs_test/test/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Mon May 9 11:12:13 CEST 2016 Found 1 runs /home/XYZ/Projects/tmp/fs_test/test/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... 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 /home/XYZ/Projects/tmp/fs_test/test/mri/orig/001.mgz /home/XYZ/Projects/tmp/fs_test/test/mri/rawavg.mgz
/home/XYZ/Projects/tmp/fs_test/test
mri_convert /home/XYZ/Projects/tmp/fs_test/test/mri/rawavg.mgz /home/XYZ/Projects/tmp/fs_test/test/mri/orig.mgz --conform
mri_convert /home/XYZ/Projects/tmp/fs_test/test/mri/rawavg.mgz /home/XYZ/Projects/tmp/fs_test/test/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/XYZ/Projects/tmp/fs_test/test/mri/rawavg.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) Original Data has (1, 1, 1) mm size and (256, 256, 256) voxels. Data is conformed to 1 mm size and 256 voxels for all directions writing to /home/XYZ/Projects/tmp/fs_test/test/mri/orig.mgz...
mri_add_xform_to_header -c /home/XYZ/Projects/tmp/fs_test/test/mri/transforms/talairach.xfm /home/XYZ/Projects/tmp/fs_test/test/mri/orig.mgz /home/XYZ/Projects/tmp/fs_test/test/mri/orig.mgz
INFO: extension is mgz #-------------------------------------------- #@# Talairach Mon May 9 11:12:19 CEST 2016 /home/XYZ/Projects/tmp/fs_test/test/mri
mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz
Linux comp_name 4.4.0-22-generic #39-Ubuntu SMP Thu May 5 16:53:32 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s test exited with ERRORS at Mon May 9 11:12:21 CEST 2016
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Hi Mads,
is the file being copied (does /home/XYZ/Projects/tmp/fs_test/test/mri/rawavg.mgz and orig.mgz exist)? If not, maybe some disk space / IO problem. Also what happens when you run
mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz
directly? Maybe something is wrong with the MNI tools.
Best, Martin
On 05/11/2016 07:43 AM, Mads Jensen wrote:
Dear FreeSurfer group,
I get an error trying to run basic recon-all on a ubuntu 16.04 system.
It finish with errors after a few minutes and I cannot find any help in the recon-all.log (pasted below).
I have made the symbolic links from the installation notes.
Any ideas or thoughts on what the problem might be or how to track it down would be very welcome.
best regards, mads
from bugr: FREESURFER_HOME: /home/XYZ/Toolboxes/freesurfer
Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
Debian version: stretch/sid
Kernel info: Linux 4.4.0-22-generic x86_64
recon-all.log:
Mon May 9 11:12:07 CEST 2016 /home/XYZ/Projects/tmp/fs_test/test /home/XYZ/Toolboxes/freesurfer/bin/recon-all -all -subjid test -i T1.mgz subjid test setenv SUBJECTS_DIR /home/XYZ/Projects/tmp/fs_test FREESURFER_HOME /home/XYZ/Toolboxes/freesurfer Actual FREESURFER_HOME /home/XYZ/Toolboxes/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Linux comp_name 4.4.0-22-generic #39-Ubuntu SMP Thu May 5 16:53:32 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 62044 maxlocks unlimited maxsignal 62044 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited
total used free shared buff/cacheavailable Mem: 15924580 3455984 375968 323648 12092628 11975092 Swap: 16616956 254220 16362736
######################################## program versions used $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:08-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:08-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 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 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:08-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:08-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:08-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:08-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:08-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:08-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400
======= NUMBER OF OPENMP THREADS = 1 ======= ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:08-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:08-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:10-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:10-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:10-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:10-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:10-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:10-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:10-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:10-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:10-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:10-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:11-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $
ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:11-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $
ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:11-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:11-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:11-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:11-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:11-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /home/XYZ/Toolboxes/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /home/XYZ/Toolboxes/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### /home/XYZ/Projects/tmp/fs_test/test
mri_convert /home/XYZ/Projects/tmp/fs_test/T1.mgz /home/XYZ/Projects/tmp/fs_test/test/mri/orig/001.mgz
mri_convert /home/XYZ/Projects/tmp/fs_test/T1.mgz /home/XYZ/Projects/tmp/fs_test/test/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/XYZ/Projects/tmp/fs_test/T1.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 /home/XYZ/Projects/tmp/fs_test/test/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Mon May 9 11:12:13 CEST 2016 Found 1 runs /home/XYZ/Projects/tmp/fs_test/test/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... 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 /home/XYZ/Projects/tmp/fs_test/test/mri/orig/001.mgz /home/XYZ/Projects/tmp/fs_test/test/mri/rawavg.mgz
/home/XYZ/Projects/tmp/fs_test/test
mri_convert /home/XYZ/Projects/tmp/fs_test/test/mri/rawavg.mgz /home/XYZ/Projects/tmp/fs_test/test/mri/orig.mgz --conform
mri_convert /home/XYZ/Projects/tmp/fs_test/test/mri/rawavg.mgz /home/XYZ/Projects/tmp/fs_test/test/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/XYZ/Projects/tmp/fs_test/test/mri/rawavg.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) Original Data has (1, 1, 1) mm size and (256, 256, 256) voxels. Data is conformed to 1 mm size and 256 voxels for all directions writing to /home/XYZ/Projects/tmp/fs_test/test/mri/orig.mgz...
mri_add_xform_to_header -c /home/XYZ/Projects/tmp/fs_test/test/mri/transforms/talairach.xfm /home/XYZ/Projects/tmp/fs_test/test/mri/orig.mgz /home/XYZ/Projects/tmp/fs_test/test/mri/orig.mgz
INFO: extension is mgz #-------------------------------------------- #@# Talairach Mon May 9 11:12:19 CEST 2016 /home/XYZ/Projects/tmp/fs_test/test/mri
mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz
Linux comp_name 4.4.0-22-generic #39-Ubuntu SMP Thu May 5 16:53:32 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s test exited with ERRORS at Mon May 9 11:12:21 CEST 2016
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Martin,
Thanks for your reply.
rawavg.mgz and orig.mgz does exist. When I run the command I get the following error:
mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz /home/XYZ/Projects/tmp/fs_test/test/mri /home/XYZ/Toolboxes/freesurfer/bin/mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz nIters 1 $Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $ Linux comp_name 4.4.0-22-generic #39-Ubuntu SMP Thu May 5 16:53:32 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux Wed May 11 16:03:55 CEST 2016 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.3509 /home/XYZ/Projects/tmp/fs_test/test/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.3509/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.3509/nu0.mnc -odt float $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ 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) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.3509/nu0.mnc...
-------------------------------------------------------- Iteration 1 Wed May 11 16:03:57 CEST 2016 nu_correct -clobber ./tmp.mri_nu_correct.mni.3509/nu0.mnc ./tmp.mri_nu_correct.mni.3509/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.3509/0/ -iterations 1000 -distance 50 Can't use 'defined(@array)' (Maybe you should just omit the defined()?) at /home/XYZ/Toolboxes/freesurfer/mni/bin/nu_estimate_np_and_em line 165. nu_correct: crashed while running nu_estimate_np_and_em (termination status=65280) ERROR: nu_correct
best, mads
On 05/11/2016 03:32 PM, Martin Reuter wrote:
Hi Mads,
is the file being copied (does /home/XYZ/Projects/tmp/fs_test/test/mri/rawavg.mgz and orig.mgz exist)? If not, maybe some disk space / IO problem. Also what happens when you run
mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz
directly? Maybe something is wrong with the MNI tools.
Best, Martin
On 05/11/2016 07:43 AM, Mads Jensen wrote:
Dear FreeSurfer group,
I get an error trying to run basic recon-all on a ubuntu 16.04 system.
It finish with errors after a few minutes and I cannot find any help in the recon-all.log (pasted below).
I have made the symbolic links from the installation notes.
Any ideas or thoughts on what the problem might be or how to track it down would be very welcome.
best regards, mads
from bugr: FREESURFER_HOME: /home/XYZ/Toolboxes/freesurfer
Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
Debian version: stretch/sid
Kernel info: Linux 4.4.0-22-generic x86_64
recon-all.log:
Mon May 9 11:12:07 CEST 2016 /home/XYZ/Projects/tmp/fs_test/test /home/XYZ/Toolboxes/freesurfer/bin/recon-all -all -subjid test -i T1.mgz subjid test setenv SUBJECTS_DIR /home/XYZ/Projects/tmp/fs_test FREESURFER_HOME /home/XYZ/Toolboxes/freesurfer Actual FREESURFER_HOME /home/XYZ/Toolboxes/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Linux comp_name 4.4.0-22-generic #39-Ubuntu SMP Thu May 5 16:53:32 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 62044 maxlocks unlimited maxsignal 62044 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited
total used free shared buff/cacheavailable Mem: 15924580 3455984 375968 323648 12092628 11975092 Swap: 16616956 254220 16362736
######################################## program versions used $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:08-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:08-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 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 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:08-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:08-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:08-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:08-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:08-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:08-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400
======= NUMBER OF OPENMP THREADS = 1 =======ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:08-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:08-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:10-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:10-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:10-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:10-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:10-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:10-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:10-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:10-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:10-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:10-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:11-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $
ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:11-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $
ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:11-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:11-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:11-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:11-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:11-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /home/XYZ/Toolboxes/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /home/XYZ/Toolboxes/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### /home/XYZ/Projects/tmp/fs_test/test
mri_convert /home/XYZ/Projects/tmp/fs_test/T1.mgz/home/XYZ/Projects/tmp/fs_test/test/mri/orig/001.mgz
mri_convert /home/XYZ/Projects/tmp/fs_test/T1.mgz /home/XYZ/Projects/tmp/fs_test/test/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/XYZ/Projects/tmp/fs_test/T1.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 /home/XYZ/Projects/tmp/fs_test/test/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Mon May 9 11:12:13 CEST 2016 Found 1 runs /home/XYZ/Projects/tmp/fs_test/test/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... 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 /home/XYZ/Projects/tmp/fs_test/test/mri/orig/001.mgz/home/XYZ/Projects/tmp/fs_test/test/mri/rawavg.mgz
/home/XYZ/Projects/tmp/fs_test/test
mri_convert /home/XYZ/Projects/tmp/fs_test/test/mri/rawavg.mgz/home/XYZ/Projects/tmp/fs_test/test/mri/orig.mgz --conform
mri_convert /home/XYZ/Projects/tmp/fs_test/test/mri/rawavg.mgz /home/XYZ/Projects/tmp/fs_test/test/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/XYZ/Projects/tmp/fs_test/test/mri/rawavg.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) Original Data has (1, 1, 1) mm size and (256, 256, 256) voxels. Data is conformed to 1 mm size and 256 voxels for all directions writing to /home/XYZ/Projects/tmp/fs_test/test/mri/orig.mgz...
mri_add_xform_to_header -c/home/XYZ/Projects/tmp/fs_test/test/mri/transforms/talairach.xfm /home/XYZ/Projects/tmp/fs_test/test/mri/orig.mgz /home/XYZ/Projects/tmp/fs_test/test/mri/orig.mgz
INFO: extension is mgz #-------------------------------------------- #@# Talairach Mon May 9 11:12:19 CEST 2016 /home/XYZ/Projects/tmp/fs_test/test/mri
mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale--i orig.mgz --o orig_nu.mgz
Linux comp_name 4.4.0-22-generic #39-Ubuntu SMP Thu May 5 16:53:32 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s test exited with ERRORS at Mon May 9 11:12:21 CEST 2016
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hello Mads,
This is a recently discovered issue with the mni tools that ship with freesurfer v5.3 and the latest version of perl (which probably comes with Ubuntu 16). I know the issue exists with perl version 5.22 but I dont know with what version the issue started.
This has been fixed in the dev version of freesurfer and thus will be fixed in the upcoming release of freesurfer version 6.0. Unfortunately, you only have 2 options if you want to use freesurfer v5.3 on your Ubuntu 16 machine:
1) Update to the newest Development Version of freesurfer:
https://surfer.nmr.mgh.harvard.edu/fswiki/Download
2) Use the "sudo apt-get" tools to install a pre 5.22 version of perl on your machine.
Hope this helps.
-Zeke
On 05/11/2016 10:06 AM, Mads Jensen wrote:
Hi Martin,
Thanks for your reply.
rawavg.mgz and orig.mgz does exist. When I run the command I get the following error:
mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz /home/XYZ/Projects/tmp/fs_test/test/mri /home/XYZ/Toolboxes/freesurfer/bin/mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz nIters 1 $Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $ Linux comp_name 4.4.0-22-generic #39-Ubuntu SMP Thu May 5 16:53:32 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux Wed May 11 16:03:55 CEST 2016 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.3509 /home/XYZ/Projects/tmp/fs_test/test/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.3509/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.3509/nu0.mnc -odt float $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ 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) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.3509/nu0.mnc...
Iteration 1 Wed May 11 16:03:57 CEST 2016 nu_correct -clobber ./tmp.mri_nu_correct.mni.3509/nu0.mnc ./tmp.mri_nu_correct.mni.3509/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.3509/0/ -iterations 1000 -distance 50 Can't use 'defined(@array)' (Maybe you should just omit the defined()?) at /home/XYZ/Toolboxes/freesurfer/mni/bin/nu_estimate_np_and_em line 165. nu_correct: crashed while running nu_estimate_np_and_em (termination status=65280) ERROR: nu_correct
best, mads
On 05/11/2016 03:32 PM, Martin Reuter wrote:
Hi Mads,
is the file being copied (does /home/XYZ/Projects/tmp/fs_test/test/mri/rawavg.mgz and orig.mgz exist)? If not, maybe some disk space / IO problem. Also what happens when you run
mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgzdirectly? Maybe something is wrong with the MNI tools.
Best, Martin
On 05/11/2016 07:43 AM, Mads Jensen wrote:
Dear FreeSurfer group,
I get an error trying to run basic recon-all on a ubuntu 16.04 system.
It finish with errors after a few minutes and I cannot find any help in the recon-all.log (pasted below).
I have made the symbolic links from the installation notes.
Any ideas or thoughts on what the problem might be or how to track it down would be very welcome.
best regards, mads
from bugr: FREESURFER_HOME: /home/XYZ/Toolboxes/freesurfer
Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
Debian version: stretch/sid
Kernel info: Linux 4.4.0-22-generic x86_64
recon-all.log:
Mon May 9 11:12:07 CEST 2016 /home/XYZ/Projects/tmp/fs_test/test /home/XYZ/Toolboxes/freesurfer/bin/recon-all -all -subjid test -i T1.mgz subjid test setenv SUBJECTS_DIR /home/XYZ/Projects/tmp/fs_test FREESURFER_HOME /home/XYZ/Toolboxes/freesurfer Actual FREESURFER_HOME /home/XYZ/Toolboxes/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Linux comp_name 4.4.0-22-generic #39-Ubuntu SMP Thu May 5 16:53:32 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 62044 maxlocks unlimited maxsignal 62044 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited
total used free shared buff/cacheavailable Mem: 15924580 3455984 375968 323648 12092628 11975092 Swap: 16616956 254220 16362736
######################################## program versions used $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:08-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:08-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 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 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:08-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:08-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:08-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:08-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:08-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:08-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400
======= NUMBER OF OPENMP THREADS = 1 =======ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:08-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:08-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:10-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:10-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:10-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:10-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:10-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:10-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:10-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:10-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:10-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:10-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:11-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $
ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:11-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $
ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:11-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:11-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:11-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:11-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:11-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /home/XYZ/Toolboxes/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /home/XYZ/Toolboxes/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### /home/XYZ/Projects/tmp/fs_test/test
mri_convert /home/XYZ/Projects/tmp/fs_test/T1.mgz/home/XYZ/Projects/tmp/fs_test/test/mri/orig/001.mgz
mri_convert /home/XYZ/Projects/tmp/fs_test/T1.mgz /home/XYZ/Projects/tmp/fs_test/test/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/XYZ/Projects/tmp/fs_test/T1.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 /home/XYZ/Projects/tmp/fs_test/test/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Mon May 9 11:12:13 CEST 2016 Found 1 runs /home/XYZ/Projects/tmp/fs_test/test/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... 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 /home/XYZ/Projects/tmp/fs_test/test/mri/orig/001.mgz/home/XYZ/Projects/tmp/fs_test/test/mri/rawavg.mgz
/home/XYZ/Projects/tmp/fs_test/test
mri_convert /home/XYZ/Projects/tmp/fs_test/test/mri/rawavg.mgz/home/XYZ/Projects/tmp/fs_test/test/mri/orig.mgz --conform
mri_convert /home/XYZ/Projects/tmp/fs_test/test/mri/rawavg.mgz /home/XYZ/Projects/tmp/fs_test/test/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/XYZ/Projects/tmp/fs_test/test/mri/rawavg.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) Original Data has (1, 1, 1) mm size and (256, 256, 256) voxels. Data is conformed to 1 mm size and 256 voxels for all directions writing to /home/XYZ/Projects/tmp/fs_test/test/mri/orig.mgz...
mri_add_xform_to_header -c/home/XYZ/Projects/tmp/fs_test/test/mri/transforms/talairach.xfm /home/XYZ/Projects/tmp/fs_test/test/mri/orig.mgz /home/XYZ/Projects/tmp/fs_test/test/mri/orig.mgz
INFO: extension is mgz #-------------------------------------------- #@# Talairach Mon May 9 11:12:19 CEST 2016 /home/XYZ/Projects/tmp/fs_test/test/mri
mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale--i orig.mgz --o orig_nu.mgz
Linux comp_name 4.4.0-22-generic #39-Ubuntu SMP Thu May 5 16:53:32 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s test exited with ERRORS at Mon May 9 11:12:21 CEST 2016
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Hi Zeke,
Thank you for clarifying this, it did help. You are right the perl version is 5.22
I will give the development version a try.
best, mads
On 05/11/2016 04:51 PM, Z K wrote:
Hello Mads,
This is a recently discovered issue with the mni tools that ship with freesurfer v5.3 and the latest version of perl (which probably comes with Ubuntu 16). I know the issue exists with perl version 5.22 but I dont know with what version the issue started.
This has been fixed in the dev version of freesurfer and thus will be fixed in the upcoming release of freesurfer version 6.0. Unfortunately, you only have 2 options if you want to use freesurfer v5.3 on your Ubuntu 16 machine:
Update to the newest Development Version of freesurfer:
Use the "sudo apt-get" tools to install a pre 5.22 version of perl on
your machine.
Hope this helps.
-Zeke
On 05/11/2016 10:06 AM, Mads Jensen wrote:
Hi Martin,
Thanks for your reply.
rawavg.mgz and orig.mgz does exist. When I run the command I get the following error:
mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz /home/XYZ/Projects/tmp/fs_test/test/mri /home/XYZ/Toolboxes/freesurfer/bin/mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz nIters 1 $Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $ Linux comp_name 4.4.0-22-generic #39-Ubuntu SMP Thu May 5 16:53:32 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux Wed May 11 16:03:55 CEST 2016 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.3509 /home/XYZ/Projects/tmp/fs_test/test/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.3509/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.3509/nu0.mnc -odt float $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ 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) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.3509/nu0.mnc...
Iteration 1 Wed May 11 16:03:57 CEST 2016 nu_correct -clobber ./tmp.mri_nu_correct.mni.3509/nu0.mnc ./tmp.mri_nu_correct.mni.3509/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.3509/0/ -iterations 1000 -distance 50 Can't use 'defined(@array)' (Maybe you should just omit the defined()?) at /home/XYZ/Toolboxes/freesurfer/mni/bin/nu_estimate_np_and_em line 165. nu_correct: crashed while running nu_estimate_np_and_em (termination status=65280) ERROR: nu_correct
best, mads
On 05/11/2016 03:32 PM, Martin Reuter wrote:
Hi Mads,
is the file being copied (does /home/XYZ/Projects/tmp/fs_test/test/mri/rawavg.mgz and orig.mgz exist)? If not, maybe some disk space / IO problem. Also what happens when you run
mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50--no-rescale --i orig.mgz --o orig_nu.mgz
directly? Maybe something is wrong with the MNI tools.
Best, Martin
On 05/11/2016 07:43 AM, Mads Jensen wrote:
Dear FreeSurfer group,
I get an error trying to run basic recon-all on a ubuntu 16.04 system.
It finish with errors after a few minutes and I cannot find any help in the recon-all.log (pasted below).
I have made the symbolic links from the installation notes.
Any ideas or thoughts on what the problem might be or how to track it down would be very welcome.
best regards, mads
from bugr: FREESURFER_HOME: /home/XYZ/Toolboxes/freesurfer
Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
Debian version: stretch/sid
Kernel info: Linux 4.4.0-22-generic x86_64
recon-all.log:
Mon May 9 11:12:07 CEST 2016 /home/XYZ/Projects/tmp/fs_test/test /home/XYZ/Toolboxes/freesurfer/bin/recon-all -all -subjid test -i T1.mgz subjid test setenv SUBJECTS_DIR /home/XYZ/Projects/tmp/fs_test FREESURFER_HOME /home/XYZ/Toolboxes/freesurfer Actual FREESURFER_HOME /home/XYZ/Toolboxes/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Linux comp_name 4.4.0-22-generic #39-Ubuntu SMP Thu May 5 16:53:32 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 62044 maxlocks unlimited maxsignal 62044 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited
total used free shared buff/cacheavailable Mem: 15924580 3455984 375968 323648 12092628 11975092 Swap: 16616956 254220 16362736
######################################## program versions used $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:08-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:08-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 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 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:08-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:08-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:08-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:08-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:08-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:08-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400
======= NUMBER OF OPENMP THREADS = 1 =======ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:08-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:08-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:10-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:10-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:10-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:10-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:10-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:10-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:10-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:10-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:10-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:10-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:11-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $
ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:11-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $
ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:11-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:11-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:11-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:11-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:11-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /home/XYZ/Toolboxes/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /home/XYZ/Toolboxes/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### /home/XYZ/Projects/tmp/fs_test/test
mri_convert /home/XYZ/Projects/tmp/fs_test/T1.mgz/home/XYZ/Projects/tmp/fs_test/test/mri/orig/001.mgz
mri_convert /home/XYZ/Projects/tmp/fs_test/T1.mgz /home/XYZ/Projects/tmp/fs_test/test/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/XYZ/Projects/tmp/fs_test/T1.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 /home/XYZ/Projects/tmp/fs_test/test/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Mon May 9 11:12:13 CEST 2016 Found 1 runs /home/XYZ/Projects/tmp/fs_test/test/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... 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 /home/XYZ/Projects/tmp/fs_test/test/mri/orig/001.mgz/home/XYZ/Projects/tmp/fs_test/test/mri/rawavg.mgz
/home/XYZ/Projects/tmp/fs_test/test
mri_convert /home/XYZ/Projects/tmp/fs_test/test/mri/rawavg.mgz/home/XYZ/Projects/tmp/fs_test/test/mri/orig.mgz --conform
mri_convert /home/XYZ/Projects/tmp/fs_test/test/mri/rawavg.mgz /home/XYZ/Projects/tmp/fs_test/test/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/XYZ/Projects/tmp/fs_test/test/mri/rawavg.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) Original Data has (1, 1, 1) mm size and (256, 256, 256) voxels. Data is conformed to 1 mm size and 256 voxels for all directions writing to /home/XYZ/Projects/tmp/fs_test/test/mri/orig.mgz...
mri_add_xform_to_header -c/home/XYZ/Projects/tmp/fs_test/test/mri/transforms/talairach.xfm /home/XYZ/Projects/tmp/fs_test/test/mri/orig.mgz /home/XYZ/Projects/tmp/fs_test/test/mri/orig.mgz
INFO: extension is mgz #-------------------------------------------- #@# Talairach Mon May 9 11:12:19 CEST 2016 /home/XYZ/Projects/tmp/fs_test/test/mri
mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50--no-rescale --i orig.mgz --o orig_nu.mgz
Linux comp_name 4.4.0-22-generic #39-Ubuntu SMP Thu May 5 16:53:32 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s test exited with ERRORS at Mon May 9 11:12:21 CEST 2016
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Mads Jensen -
Martin Reuter -
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