Dear freesurfer experts:
I am trying to process an MRI using recon-all -autorecon1 -autorecon2
-autorecon3
and exited with errors. Apparently the encoded image data is not supported
(below you can see the recon-all.log)
Is there a way to process this study?
Thank you very much for your help,
Katica
Here is the recon-all.log:
Tue Oct 8 14:06:54 PDT 2013
/home/spaz/Cat/subjects/MGH020_SurferOutput
/usr/local/freesurfer/bin/recon-all
-autorecon1 -autorecon2 -autorecon3 -subject MGH020_SurferOutput -i
/home/spaz/Cat/subjects/MGH020/Mribrnwo/SAG_FSPGR_3D_3/IM-0003-0001.dcm
subjid MGH020_SurferOutput
setenv SUBJECTS_DIR /home/spaz/Cat/subjects
FREESURFER_HOME /usr/local/freesurfer
Actual FREESURFER_HOME /usr/local/freesurfer
build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0
Linux localhost.localdomain 3.6.11-4.fc16.x86_64 #1 SMP Tue Jan 8 20:57:42 UTC
2013 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 1024
total used free shared buffers cached
Mem: 1012544 931236 81308 0 42064 556144
-/+ buffers/cache: 333028 679516
Swap: 2030588 126356 1904232
########################################
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: 2013/10/08-21:06:54-GMT BuildTimeStamp: May 13 2013
18:45:07 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
User: spaz Machine: localhost.localdomain Platform: Linux PlatformVersion:
3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400
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: 2013/10/08-21:06:54-GMT BuildTimeStamp: May 13
2013 18:45:07 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve
Exp $ User: spaz Machine: localhost.localdomain Platform: Linux
PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400
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: 2013/10/08-21:06:54-GMT BuildTimeStamp: May 13
2013 18:45:07 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $
User: spaz Machine: localhost.localdomain Platform: Linux PlatformVersion:
3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name:
stable5 $ TimeStamp: 2013/10/08-21:06:54-GMT BuildTimeStamp: May 13 2013
18:45:07 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $
User: spaz Machine: localhost.localdomain Platform: Linux PlatformVersion:
3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name:
stable5 $ TimeStamp: 2013/10/08-21:06:54-GMT BuildTimeStamp: May 13 2013
18:45:07 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp
$ User: spaz Machine: localhost.localdomain Platform: Linux
PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name:
stable5 $ TimeStamp: 2013/10/08-21:06:54-GMT BuildTimeStamp: May 13 2013
18:45:07 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User:
spaz Machine: localhost.localdomain Platform: Linux PlatformVersion:
3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name:
stable5 $ TimeStamp: 2013/10/08-21:06:55-GMT BuildTimeStamp: May 13 2013
18:45:07 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User:
spaz Machine: localhost.localdomain Platform: Linux PlatformVersion:
3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2013/10/08-21:06:55-GMT BuildTimeStamp: May 13
2013 18:45:07 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve
Exp $ User: spaz Machine: localhost.localdomain Platform: Linux
PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2013/10/08-21:06:55-GMT BuildTimeStamp: May 13
2013 18:45:07 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks
Exp $ User: spaz Machine: localhost.localdomain Platform: Linux
PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2013/10/08-21:06:55-GMT BuildTimeStamp: May 13
2013 18:45:07 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32
nicks Exp $ User: spaz Machine: localhost.localdomain Platform: Linux
PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2013/10/08-21:06:55-GMT BuildTimeStamp: May 13
2013 18:45:07 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks
Exp $ User: spaz Machine: localhost.localdomain Platform: Linux
PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name:
stable5 $ TimeStamp: 2013/10/08-21:06:55-GMT BuildTimeStamp: May 13 2013
18:45:07 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $
User: spaz Machine: localhost.localdomain Platform: Linux PlatformVersion:
3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name:
stable5 $ TimeStamp: 2013/10/08-21:06:55-GMT BuildTimeStamp: May 13 2013
18:45:07 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User:
spaz Machine: localhost.localdomain Platform: Linux PlatformVersion:
3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name:
stable5 $ TimeStamp: 2013/10/08-21:06:55-GMT BuildTimeStamp: May 13 2013
18:45:07 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User:
spaz Machine: localhost.localdomain Platform: Linux PlatformVersion:
3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2013/10/08-21:06:55-GMT BuildTimeStamp: May 13
2013 18:45:07 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp
$ User: spaz Machine: localhost.localdomain Platform: Linux
PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2013/10/08-21:06:55-GMT BuildTimeStamp: May 13
2013 18:45:07 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks
Exp $ User: spaz Machine: localhost.localdomain Platform: Linux
PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2013/10/08-21:06:55-GMT BuildTimeStamp: May 13
2013 18:45:07 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks
Exp $ User: spaz Machine: localhost.localdomain Platform: Linux
PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name:
stable5 $ TimeStamp: 2013/10/08-21:06:55-GMT BuildTimeStamp: May 13 2013
18:45:07 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User:
spaz Machine: localhost.localdomain Platform: Linux PlatformVersion:
3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name:
stable5 $ TimeStamp: 2013/10/08-21:06:55-GMT BuildTimeStamp: May 13 2013
18:45:07 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $
User: spaz Machine: localhost.localdomain Platform: Linux PlatformVersion:
3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2013/10/08-21:06:55-GMT BuildTimeStamp: May 13
2013 18:45:07 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp
$ User: spaz Machine: localhost.localdomain Platform: Linux
PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name:
stable5 $ TimeStamp: 2013/10/08-21:06:55-GMT BuildTimeStamp: May 13 2013
18:45:07 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User:
spaz Machine: localhost.localdomain Platform: Linux PlatformVersion:
3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2013/10/08-21:06:56-GMT BuildTimeStamp: May 13
2013 18:45:07 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks
Exp $ User: spaz Machine: localhost.localdomain Platform: Linux
PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2013/10/08-21:06:56-GMT BuildTimeStamp: May 13
2013 18:45:07 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks
Exp $ User: spaz Machine: localhost.localdomain Platform: Linux
PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name:
stable5 $ TimeStamp: 2013/10/08-21:06:56-GMT BuildTimeStamp: May 13 2013
18:45:07 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $
User: spaz Machine: localhost.localdomain Platform: Linux PlatformVersion:
3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2013/10/08-21:06:56-GMT BuildTimeStamp: May 13
2013 18:45:07 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07
greve Exp $ User: spaz Machine: localhost.localdomain Platform: Linux
PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2013/10/08-21:06:56-GMT BuildTimeStamp: May 13
2013 18:45:07 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01
nicks Exp $ User: spaz Machine: localhost.localdomain Platform: Linux
PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name:
stable5 $ TimeStamp: 2013/10/08-21:06:56-GMT BuildTimeStamp: May 13 2013
18:45:07 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $
User: spaz Machine: localhost.localdomain Platform: Linux PlatformVersion:
3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name:
stable5 $ TimeStamp: 2013/10/08-21:06:56-GMT BuildTimeStamp: May 13 2013
18:45:07 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $
User: spaz Machine: localhost.localdomain Platform: Linux PlatformVersion:
3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_anatomical_stats ProgramArguments: -all-info
ProgramVersion: $Name: stable5 $ TimeStamp: 2013/10/08-21:06:56-GMT
BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_anatomical_stats.c,v 1.72
2011/03/02 00:04:26 nicks Exp $ User: spaz Machine: localhost.localdomain
Platform: Linux PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC
CompilerVersion: 30400
ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name:
stable5 $ TimeStamp: 2013/10/08-21:06:56-GMT BuildTimeStamp: May 13 2013
18:45:07 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User:
spaz Machine: localhost.localdomain Platform: Linux PlatformVersion:
3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2013/10/08-21:06:56-GMT BuildTimeStamp: May 13
2013 18:45:07 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30
nicks Exp $ User: spaz Machine: localhost.localdomain Platform: Linux
PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name:
stable5 $ TimeStamp: 2013/10/08-21:06:56-GMT BuildTimeStamp: May 13 2013
18:45:07 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $
User: spaz Machine: localhost.localdomain Platform: Linux PlatformVersion:
3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400
$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: 2013/10/08-21:06:56-GMT BuildTimeStamp: May 13
2013 18:45:07 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47
mreuter Exp $ User: spaz Machine: localhost.localdomain Platform: Linux
PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400
$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: 2013/10/08-21:06:56-GMT BuildTimeStamp: May 13
2013 18:45:07 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06
mreuter Exp $ User: spaz Machine: localhost.localdomain Platform: Linux
PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name:
stable5 $ TimeStamp: 2013/10/08-21:06:56-GMT BuildTimeStamp: May 13 2013
18:45:07 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: spaz
Machine: localhost.localdomain Platform: Linux PlatformVersion:
3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name:
stable5 $ TimeStamp: 2013/10/08-21:06:57-GMT BuildTimeStamp: May 13 2013
18:45:07 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: spaz
Machine: localhost.localdomain Platform: Linux PlatformVersion:
3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_fuse_segmentations ProgramArguments: -all-info
ProgramVersion: $Name: stable5 $ TimeStamp: 2013/10/08-21:06:57-GMT
BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_fuse_segmentations.c,v 1.8
2011/03/02 00:04:15 nicks Exp $ User: spaz Machine: localhost.localdomain
Platform: Linux PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC
CompilerVersion: 30400
ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name:
stable5 $ TimeStamp: 2013/10/08-21:06:57-GMT BuildTimeStamp: May 13 2013
18:45:07 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $
User: spaz Machine: localhost.localdomain Platform: Linux PlatformVersion:
3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400
#######################################
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
#######################################
/home/spaz/Cat/subjects/MGH020_SurferOutput
mri_convert
/home/spaz/Cat/subjects/MGH020/Mribrnwo/SAG_FSPGR_3D_3/IM-0003-0001.dcm
/home/spaz/Cat/subjects/MGH020_SurferOutput/mri/orig/001.mgz
mri_convert
/home/spaz/Cat/subjects/MGH020/Mribrnwo/SAG_FSPGR_3D_3/IM-0003-0001.dcm
/home/spaz/Cat/subjects/MGH020_SurferOutput/mri/orig/001.mgz
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from
/home/spaz/Cat/subjects/MGH020/Mribrnwo/SAG_FSPGR_3D_3/IM-0003-0001.dcm...
Starting DICOMRead2()
dcmfile =
/home/spaz/Cat/subjects/MGH020/Mribrnwo/SAG_FSPGR_3D_3/IM-0003-0001.dcm
dcmdir = /home/spaz/Cat/subjects/MGH020/Mribrnwo/SAG_FSPGR_3D_3
ERROR: RLL-encoded image data not supported!
(Transfer Syntax UID: 1.2.840.10008.1.2.5)
Linux localhost.localdomain 3.6.11-4.fc16.x86_64 #1 SMP Tue Jan 8 20:57:42 UTC
2013 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s MGH020_SurferOutput exited with ERRORS at Tue Oct 8 14:06:57 PDT
2013
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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