Hi Yawu
where did you get that dicom from? Does the file you are pointing to exist?
cheers Bruce
On Fri, 27 Jul 2012, Liu Yawu wrote:
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
- 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
- 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
- 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 cachedMem: 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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