Hi Bruce, As you wanted i attached the log file.
and by the way /usr/local/139942/I0000000 is a image file which is in dicom format and high res T1-Weighted 1*1*1. It is sagital series in the folder 139942 which contains about 165 images. If you need i can send files too!!!!!!!! Kind Regards -------------------------------------------------------------------------------- Hi Hassan first, you need to send us the screen output and the recon-all.log. The info you sent is not sufficient for us to help you. Second, is /usr/local/139942/I0000000 a directory or a file? It needs to be a file, and should be a single slice in the correct (i.e. high res T1-weighted) series. Is it in dicom format? cheers Bruce On Sat, 7 Mar 2015, Hassan bakhshi wrote: > Hi? > I'm still stopped at the recon-all stage.? > I use the command correctly and there it is: > > recon-all -i /usr/local/139942/I0000000 -subject test -all > > > the data is a sagital series. I think the command cant be execute at the > mri_convert step, because i dont have .mgz files in the test directory.? > > > The error is segfault !!!!!!! > > What can I do to solve it??? > >
recon-all.error
Description: Binary data
یکشنبه ۰۸ مارس ۱۵، ساعت ۰۹:۳۷:۳۲ (IRST)
/usr/local/freesurfer/subjects/test
/usr/local/freesurfer/bin/recon-all
-i /usr/local/139942/I0000000 -subject test -all
subjid test
setenv SUBJECTS_DIR /usr/local/freesurfer/subjects
FREESURFER_HOME /usr/local/freesurfer
Actual FREESURFER_HOME /usr/local/freesurfer
build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
Linux circle-Ubuntu 3.13.0-32-generic #57-Ubuntu SMP Tue Jul 15 03:51:08 UTC 2014 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 47440
maxlocks unlimited
maxsignal 47440
maxmessage 819200
maxnice 0
maxrtprio 0
maxrttime unlimited
total used free shared buffers cached
Mem: 6094032 2117176 3976856 30228 83636 1075816
-/+ buffers/cache: 957724 5136308
Swap: 102396 0 102396
########################################
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: 2015/03/08-06:07:32-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: root Machine: circle-Ubuntu Platform: Linux PlatformVersion: 3.13.0-32-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: 2015/03/08-06:07:32-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: root Machine: circle-Ubuntu Platform: Linux PlatformVersion: 3.13.0-32-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: 2015/03/08-06:07:32-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: root Machine: circle-Ubuntu Platform: Linux PlatformVersion: 3.13.0-32-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/03/08-06:07:32-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: root Machine: circle-Ubuntu Platform: Linux PlatformVersion: 3.13.0-32-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/03/08-06:07:32-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: root Machine: circle-Ubuntu Platform: Linux PlatformVersion: 3.13.0-32-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/03/08-06:07:32-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: root Machine: circle-Ubuntu Platform: Linux PlatformVersion: 3.13.0-32-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/03/08-06:07:32-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: root Machine: circle-Ubuntu Platform: Linux PlatformVersion: 3.13.0-32-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/03/08-06:07:32-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: root Machine: circle-Ubuntu Platform: Linux PlatformVersion: 3.13.0-32-generic CompilerName: GCC CompilerVersion: 40400
======= NUMBER OF OPENMP THREADS = 1 =======
ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/03/08-06:07:32-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: root Machine: circle-Ubuntu Platform: Linux PlatformVersion: 3.13.0-32-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/03/08-06:07:33-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: root Machine: circle-Ubuntu Platform: Linux PlatformVersion: 3.13.0-32-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/03/08-06:07:33-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: root Machine: circle-Ubuntu Platform: Linux PlatformVersion: 3.13.0-32-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/03/08-06:07:33-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: root Machine: circle-Ubuntu Platform: Linux PlatformVersion: 3.13.0-32-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/03/08-06:07:33-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: root Machine: circle-Ubuntu Platform: Linux PlatformVersion: 3.13.0-32-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/03/08-06:07:33-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: root Machine: circle-Ubuntu Platform: Linux PlatformVersion: 3.13.0-32-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/03/08-06:07:33-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: root Machine: circle-Ubuntu Platform: Linux PlatformVersion: 3.13.0-32-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/03/08-06:07:33-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: root Machine: circle-Ubuntu Platform: Linux PlatformVersion: 3.13.0-32-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/03/08-06:07:33-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: root Machine: circle-Ubuntu Platform: Linux PlatformVersion: 3.13.0-32-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/03/08-06:07:33-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: root Machine: circle-Ubuntu Platform: Linux PlatformVersion: 3.13.0-32-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/03/08-06:07:33-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: root Machine: circle-Ubuntu Platform: Linux PlatformVersion: 3.13.0-32-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/03/08-06:07:33-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: root Machine: circle-Ubuntu Platform: Linux PlatformVersion: 3.13.0-32-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/03/08-06:07:33-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: root Machine: circle-Ubuntu Platform: Linux PlatformVersion: 3.13.0-32-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/03/08-06:07:34-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: root Machine: circle-Ubuntu Platform: Linux PlatformVersion: 3.13.0-32-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/03/08-06:07:34-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: root Machine: circle-Ubuntu Platform: Linux PlatformVersion: 3.13.0-32-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/03/08-06:07:34-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: root Machine: circle-Ubuntu Platform: Linux PlatformVersion: 3.13.0-32-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/03/08-06:07:34-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: root Machine: circle-Ubuntu Platform: Linux PlatformVersion: 3.13.0-32-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/03/08-06:07:34-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: root Machine: circle-Ubuntu Platform: Linux PlatformVersion: 3.13.0-32-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/03/08-06:07:34-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: root Machine: circle-Ubuntu Platform: Linux PlatformVersion: 3.13.0-32-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/03/08-06:07:34-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: root Machine: circle-Ubuntu Platform: Linux PlatformVersion: 3.13.0-32-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/03/08-06:07:34-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: root Machine: circle-Ubuntu Platform: Linux PlatformVersion: 3.13.0-32-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/03/08-06:07:34-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: root Machine: circle-Ubuntu Platform: Linux PlatformVersion: 3.13.0-32-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/03/08-06:07:34-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: root Machine: circle-Ubuntu Platform: Linux PlatformVersion: 3.13.0-32-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/03/08-06:07:34-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: root Machine: circle-Ubuntu Platform: Linux PlatformVersion: 3.13.0-32-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: 2015/03/08-06:07:34-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: root Machine: circle-Ubuntu Platform: Linux PlatformVersion: 3.13.0-32-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: 2015/03/08-06:07:35-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: root Machine: circle-Ubuntu Platform: Linux PlatformVersion: 3.13.0-32-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/03/08-06:07:35-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: root Machine: circle-Ubuntu Platform: Linux PlatformVersion: 3.13.0-32-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/03/08-06:07:35-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: root Machine: circle-Ubuntu Platform: Linux PlatformVersion: 3.13.0-32-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/03/08-06:07:35-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: root Machine: circle-Ubuntu Platform: Linux PlatformVersion: 3.13.0-32-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/03/08-06:07:35-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: root Machine: circle-Ubuntu Platform: Linux PlatformVersion: 3.13.0-32-generic CompilerName: GCC CompilerVersion: 40400
#######################################
GCADIR /usr/local/freesurfer/average
GCA RB_all_2008-03-26.gca
GCASkull RB_all_withskull_2008-03-26.gca
AvgCurvTif average.curvature.filled.buckner40.tif
GCSDIR /usr/local/freesurfer/average
GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs
#######################################
/usr/local/freesurfer/subjects/test
mri_convert /usr/local/139942/I0000000 /usr/local/freesurfer/subjects/test/mri/orig/001.mgz
mri_convert /usr/local/139942/I0000000 /usr/local/freesurfer/subjects/test/mri/orig/001.mgz
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /usr/local/139942/I0000000...
Getting Series No
INFO: Found 167 files in /usr/local/139942
INFO: Scanning for Series Number 1
Scanning Directory
INFO: found 3 files in series
INFO: loading series header info.
RunNo = 0
INFO: sorting.
INFO: (512 512 3), nframes = 1, ismosaic=0
PE Dir ROW ROW
AutoAlign matrix detected
AutoAlign Matrix ---------------------
1.000 0.000 0.000 0.000;
0.000 1.000 0.000 0.000;
0.000 0.000 1.000 0.000;
0.000 0.000 0.000 1.000;
FileName /usr/local/139942/I0000001
Identification
NumarisVer syngo MR B17
ScannerModel Avanto
PatientName TEST 2^S-F
Date and time
StudyDate 20130222
StudyTime 094632.750000
SeriesTime 094741.578000
AcqTime 094743.167500
Acquisition parameters
PulseSeq *fl2d1
Protocol localizer
PhEncDir ROW
EchoNo 1
FlipAngle 20
EchoTime 2.95
InversionTime -1
RepetitionTime 7
PhEncFOV 260
ReadoutFOV 260
Image information
RunNo 0
SeriesNo 1
ImageNo 2
NImageRows 512
NImageCols 512
NFrames 1
SliceArraylSize 3
IsMosaic 0
ImgPos 130.0000 -0.0000 130.0000
VolRes 0.5078 0.5078 9.6000
VolDim 512 512 3
Vc -1.0000 -0.0000 0.0000
Vr -0.0000 -0.0000 -1.0000
Vs -1.0000 -0.0000 0.0000
VolCenter -14.4000 -0.0000 0.0000
TransferSyntaxUID 1.2.840.10008.1.2.4.90
UseSliceScaleFactor 0 (slice 0: 1)
Linux circle-Ubuntu 3.13.0-32-generic #57-Ubuntu SMP Tue Jul 15 03:51:08 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s test exited with ERRORS at یکشنبه ۰۸ مارس ۱۵، ساعت ۰۹:۳۷:۳۸ (IRST)
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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