Hi,
I recently install Freesurfer under ubuntu. I tested two own data. It works in
one our own case, but did not work for other cases. The problem is the
Freesurfer "not found or unknown file type for file
/home/d4201z/Desktop/im_4/20001108150735000005086.dcm" when convert convert dcm
to mgz. Any helps are appreciated!
Here are detailed inf:
FREESURFER_HOME: /usr/local/src/freesurfer
Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0
Debian version: wheezy/sid
Kernel info: Linux 3.2.0-27-generic x86_64
1. the entire command-line executed
recon-all -s APauli \
-i
/home/d4201z/Desktop/im_3/1.3.12.2.1107.5.2.4.7668.20000829111709000005084.dcm
2. the error message generated
file not found or unknown file type for file
/home/d4201z/Desktop/im_3/1.3.12.2.1107.5.2.4.7668.20000829111709000005084.dcm
3. the subject's /script/recon-all.log
Fri Jul 27 12:20:31 EEST 2012
/usr/local/src/freesurfer/subjects/APauli
/usr/local/src/freesurfer/bin/recon-all
-s APauli -i
/home/d4201z/Desktop/im_3/1.3.12.2.1107.5.2.4.7668.20000829111709000005084.dcm
subjid APauli
setenv SUBJECTS_DIR /usr/local/src/freesurfer/subjects
FREESURFER_HOME /usr/local/src/freesurfer
Actual FREESURFER_HOME /usr/local/src/freesurfer
build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0
Linux d4201z-CELSIUS-M470-2 3.2.0-27-generic #43-Ubuntu SMP Fri Jul 6 14:25:57
UTC 2012 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 95900
maxlocks unlimited
maxsignal 95900
maxmessage 819200
maxnice 0
maxrtprio 0
maxrttime unlimited
total used free shared buffers cached
Mem: 12298252 2880484 9417768 0 127152 973356
-/+ buffers/cache: 1779976 10518276
Swap: 19529724 0 19529724
########################################
program versions used
$Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 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: 2012/07/27-09:20:31-GMT BuildTimeStamp: May 22 2011
08:23:31 CVS: $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $
User: d4201z Machine: d4201z-CELSIUS-M470-2 Platform: Linux PlatformVersion:
3.2.0-27-generic 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: 2012/07/27-09:20:31-GMT BuildTimeStamp: May 22
2011 08:23:31 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve
Exp $ User: d4201z Machine: d4201z-CELSIUS-M470-2 Platform: Linux
PlatformVersion: 3.2.0-27-generic 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: 2012/07/27-09:20:31-GMT BuildTimeStamp: May 22
2011 08:23:31 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $
User: d4201z Machine: d4201z-CELSIUS-M470-2 Platform: Linux
PlatformVersion: 3.2.0-27-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name:
stable5 $ TimeStamp: 2012/07/27-09:20:31-GMT BuildTimeStamp: May 22 2011
08:23:31 CVS: $Id: mri_normalize.c,v 1.73 2011/03/11 20:55:38 fischl Exp $
User: d4201z Machine: d4201z-CELSIUS-M470-2 Platform: Linux PlatformVersion:
3.2.0-27-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name:
stable5 $ TimeStamp: 2012/07/27-09:20:31-GMT BuildTimeStamp: May 22 2011
08:23:31 CVS: $Id: mri_watershed.cpp,v 1.96 2011/03/16 21:23:49 nicks Exp $
User: d4201z Machine: d4201z-CELSIUS-M470-2 Platform: Linux PlatformVersion:
3.2.0-27-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name:
stable5 $ TimeStamp: 2012/07/27-09:20:31-GMT BuildTimeStamp: May 22 2011
08:23:31 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User:
d4201z Machine: d4201z-CELSIUS-M470-2 Platform: Linux PlatformVersion:
3.2.0-27-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name:
stable5 $ TimeStamp: 2012/07/27-09:20:32-GMT BuildTimeStamp: May 22 2011
08:23:31 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User:
d4201z Machine: d4201z-CELSIUS-M470-2 Platform: Linux PlatformVersion:
3.2.0-27-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2012/07/27-09:20:32-GMT BuildTimeStamp: May 22
2011 08:23:31 CVS: $Id: mri_label2label.c,v 1.40.2.1 2011/05/19 17:21:56 greve
Exp $ User: d4201z Machine: d4201z-CELSIUS-M470-2 Platform: Linux
PlatformVersion: 3.2.0-27-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2012/07/27-09:20:32-GMT BuildTimeStamp: May 22
2011 08:23:31 CVS: $Id: mri_em_register.c,v 1.84 2011/03/16 21:23:48 nicks Exp
$ User: d4201z Machine: d4201z-CELSIUS-M470-2 Platform: Linux
PlatformVersion: 3.2.0-27-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2012/07/27-09:20:32-GMT BuildTimeStamp: May 22
2011 08:23:31 CVS: $Id: mri_ca_normalize.c,v 1.52 2011/03/02 00:04:14 nicks
Exp $ User: d4201z Machine: d4201z-CELSIUS-M470-2 Platform: Linux
PlatformVersion: 3.2.0-27-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2012/07/27-09:20:32-GMT BuildTimeStamp: May 22
2011 08:23:31 CVS: $Id: mri_ca_register.c,v 1.78 2011/03/02 14:27:40 fischl
Exp $ User: d4201z Machine: d4201z-CELSIUS-M470-2 Platform: Linux
PlatformVersion: 3.2.0-27-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name:
stable5 $ TimeStamp: 2012/07/27-09:20:32-GMT BuildTimeStamp: May 22 2011
08:23:31 CVS: $Id: mri_ca_label.c,v 1.96 2011/03/02 00:04:13 nicks Exp $
User: d4201z Machine: d4201z-CELSIUS-M470-2 Platform: Linux PlatformVersion:
3.2.0-27-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name:
stable5 $ TimeStamp: 2012/07/27-09:20:32-GMT BuildTimeStamp: May 22 2011
08:23:31 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User:
d4201z Machine: d4201z-CELSIUS-M470-2 Platform: Linux PlatformVersion:
3.2.0-27-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name:
stable5 $ TimeStamp: 2012/07/27-09:20:32-GMT BuildTimeStamp: May 22 2011
08:23:31 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User:
d4201z Machine: d4201z-CELSIUS-M470-2 Platform: Linux PlatformVersion:
3.2.0-27-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2012/07/27-09:20:32-GMT BuildTimeStamp: May 22
2011 08:23:31 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp
$ User: d4201z Machine: d4201z-CELSIUS-M470-2 Platform: Linux
PlatformVersion: 3.2.0-27-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2012/07/27-09:20:32-GMT BuildTimeStamp: May 22
2011 08:23:31 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks
Exp $ User: d4201z Machine: d4201z-CELSIUS-M470-2 Platform: Linux
PlatformVersion: 3.2.0-27-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2012/07/27-09:20:32-GMT BuildTimeStamp: May 22
2011 08:23:31 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks
Exp $ User: d4201z Machine: d4201z-CELSIUS-M470-2 Platform: Linux
PlatformVersion: 3.2.0-27-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name:
stable5 $ TimeStamp: 2012/07/27-09:20:32-GMT BuildTimeStamp: May 22 2011
08:23:31 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User:
d4201z Machine: d4201z-CELSIUS-M470-2 Platform: Linux PlatformVersion:
3.2.0-27-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name:
stable5 $ TimeStamp: 2012/07/27-09:20:32-GMT BuildTimeStamp: May 22 2011
08:23:31 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $
User: d4201z Machine: d4201z-CELSIUS-M470-2 Platform: Linux PlatformVersion:
3.2.0-27-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2012/07/27-09:20:32-GMT BuildTimeStamp: May 22
2011 08:23:31 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp
$ User: d4201z Machine: d4201z-CELSIUS-M470-2 Platform: Linux
PlatformVersion: 3.2.0-27-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name:
stable5 $ TimeStamp: 2012/07/27-09:20:32-GMT BuildTimeStamp: May 22 2011
08:23:31 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User:
d4201z Machine: d4201z-CELSIUS-M470-2 Platform: Linux PlatformVersion:
3.2.0-27-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2012/07/27-09:20:32-GMT BuildTimeStamp: May 22
2011 08:23:31 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks
Exp $ User: d4201z Machine: d4201z-CELSIUS-M470-2 Platform: Linux
PlatformVersion: 3.2.0-27-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2012/07/27-09:20:32-GMT BuildTimeStamp: May 22
2011 08:23:31 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks
Exp $ User: d4201z Machine: d4201z-CELSIUS-M470-2 Platform: Linux
PlatformVersion: 3.2.0-27-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name:
stable5 $ TimeStamp: 2012/07/27-09:20:33-GMT BuildTimeStamp: May 22 2011
08:23:31 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $
User: d4201z Machine: d4201z-CELSIUS-M470-2 Platform: Linux PlatformVersion:
3.2.0-27-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2012/07/27-09:20:33-GMT BuildTimeStamp: May 22
2011 08:23:31 CVS: $Id: mris_euler_number.c,v 1.8 2011/03/02 00:04:32 nicks
Exp $ User: d4201z Machine: d4201z-CELSIUS-M470-2 Platform: Linux
PlatformVersion: 3.2.0-27-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2012/07/27-09:20:33-GMT BuildTimeStamp: May 22
2011 08:23:31 CVS: $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks
Exp $ User: d4201z Machine: d4201z-CELSIUS-M470-2 Platform: Linux
PlatformVersion: 3.2.0-27-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name:
stable5 $ TimeStamp: 2012/07/27-09:20:33-GMT BuildTimeStamp: May 22 2011
08:23:31 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $
User: d4201z Machine: d4201z-CELSIUS-M470-2 Platform: Linux PlatformVersion:
3.2.0-27-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name:
stable5 $ TimeStamp: 2012/07/27-09:20:33-GMT BuildTimeStamp: May 22 2011
08:23:31 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $
User: d4201z Machine: d4201z-CELSIUS-M470-2 Platform: Linux PlatformVersion:
3.2.0-27-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_anatomical_stats ProgramArguments: -all-info
ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/27-09:20:33-GMT
BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_anatomical_stats.c,v 1.72
2011/03/02 00:04:26 nicks Exp $ User: d4201z Machine: d4201z-CELSIUS-M470-2
Platform: Linux PlatformVersion: 3.2.0-27-generic CompilerName: GCC
CompilerVersion: 30400
ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name:
stable5 $ TimeStamp: 2012/07/27-09:20:33-GMT BuildTimeStamp: May 22 2011
08:23:31 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User:
d4201z Machine: d4201z-CELSIUS-M470-2 Platform: Linux PlatformVersion:
3.2.0-27-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2012/07/27-09:20:33-GMT BuildTimeStamp: May 22
2011 08:23:31 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30
nicks Exp $ User: d4201z Machine: d4201z-CELSIUS-M470-2 Platform: Linux
PlatformVersion: 3.2.0-27-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name:
stable5 $ TimeStamp: 2012/07/27-09:20:33-GMT BuildTimeStamp: May 22 2011
08:23:31 CVS: $Id: mris_calc.c,v 1.37.2.4 2011/04/04 00:53:08 nicks Exp $
User: d4201z Machine: d4201z-CELSIUS-M470-2 Platform: Linux PlatformVersion:
3.2.0-27-generic CompilerName: GCC CompilerVersion: 30400
$Id: mri_robust_register.cpp,v 1.52 2011/03/16 21:23:49 nicks Exp $
ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2012/07/27-09:20:33-GMT BuildTimeStamp: May 22
2011 08:23:31 CVS: $Id: mri_robust_register.cpp,v 1.52 2011/03/16 21:23:49
nicks Exp $ User: d4201z Machine: d4201z-CELSIUS-M470-2 Platform: Linux
PlatformVersion: 3.2.0-27-generic CompilerName: GCC CompilerVersion: 30400
$Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $
ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2012/07/27-09:20:33-GMT BuildTimeStamp: May 22
2011 08:23:31 CVS: $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24
nicks Exp $ User: d4201z Machine: d4201z-CELSIUS-M470-2 Platform: Linux
PlatformVersion: 3.2.0-27-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name:
stable5 $ TimeStamp: 2012/07/27-09:20:33-GMT BuildTimeStamp: May 22 2011
08:23:31 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User:
d4201z Machine: d4201z-CELSIUS-M470-2 Platform: Linux PlatformVersion:
3.2.0-27-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name:
stable5 $ TimeStamp: 2012/07/27-09:20:33-GMT BuildTimeStamp: May 22 2011
08:23:31 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User:
d4201z Machine: d4201z-CELSIUS-M470-2 Platform: Linux PlatformVersion:
3.2.0-27-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_fuse_segmentations ProgramArguments: -all-info
ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/27-09:20:33-GMT
BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_fuse_segmentations.c,v 1.8
2011/03/02 00:04:15 nicks Exp $ User: d4201z Machine: d4201z-CELSIUS-M470-2
Platform: Linux PlatformVersion: 3.2.0-27-generic CompilerName: GCC
CompilerVersion: 30400
ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name:
stable5 $ TimeStamp: 2012/07/27-09:20:33-GMT BuildTimeStamp: May 22 2011
08:23:31 CVS: $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $
User: d4201z Machine: d4201z-CELSIUS-M470-2 Platform: Linux PlatformVersion:
3.2.0-27-generic CompilerName: GCC CompilerVersion: 30400
#######################################
GCADIR /usr/local/src/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/src/freesurfer/average
GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs
#######################################
/usr/local/src/freesurfer/subjects/APauli
mri_convert
/home/d4201z/Desktop/im_3/1.3.12.2.1107.5.2.4.7668.20000829111709000005084.dcm
/usr/local/src/freesurfer/subjects/APauli/mri/orig/001.mgz
mri_convert
/home/d4201z/Desktop/im_3/1.3.12.2.1107.5.2.4.7668.20000829111709000005084.dcm
/usr/local/src/freesurfer/subjects/APauli/mri/orig/001.mgz
file not found or unknown file type for file
/home/d4201z/Desktop/im_3/1.3.12.2.1107.5.2.4.7668.20000829111709000005084.dcm
#------------------------------------------
recon-all -s APauli finished without error at Fri Jul 27 12:20:34 EEST 2012
Regards,
Yawu
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