Tue Apr 27 17:59:28 CST 2010 /usr/local/freesurfer/subjects/fuzhou_test/bai_hong_jun /usr/local/freesurfer/bin/recon-all -i /mnt/g/fuzhou_gao/pain1/bai_hong_jun_1/MPR/BAI_HONG_JUN.MR.YU_CHUNSHUI_YU.3.1.2008.01.24.18.37.18.31250.304146390.IMA -s bai_hong_jun subjid bai_hong_jun setenv SUBJECTS_DIR /usr/local/freesurfer/subjects/fuzhou_test FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos4-stable-pub-v4.5.0 Linux lijin-desktop 2.6.31-21-generic #59-Ubuntu SMP Wed Mar 24 07:28:56 UTC 2010 i686 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc unlimited total used free shared buffers cached Mem: 3088076 2304160 783916 0 756712 926756 -/+ buffers/cache: 620692 2467384 Swap: 8519672 61832 8457840 ######################################## program versions used $Id: recon-all,v 1.133.2.57 2009/08/06 18:27:48 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.7.2.1 2008/02/29 20:17:11 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/04/27-09:59:28-GMT BuildTimeStamp: Aug 11 2009 08:24:20 CVS: $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ User: root Machine: lijin-desktop Platform: Linux PlatformVersion: 2.6.31-21-generic CompilerName: GCC CompilerVersion: 30400 FLIRT version 5.5 $Id: talairach_avi,v 1.4.2.1 2009/07/30 19:22:07 nicks Exp $ mri_convert --version stable4 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/04/27-09:59:28-GMT BuildTimeStamp: Aug 11 2009 08:24:20 CVS: $Id: tkregister2.c,v 1.86.2.12 2009/03/19 22:04:20 greve Exp $ User: root Machine: lijin-desktop Platform: Linux PlatformVersion: 2.6.31-21-generic CompilerName: GCC CompilerVersion: 30400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@fishie (i686-pc-linux-gnu) on 2007-11-01 at 16:24:51 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/04/27-09:59:28-GMT BuildTimeStamp: Aug 11 2009 08:24:20 CVS: $Id: mri_normalize.c,v 1.52.2.2 2008/05/12 17:34:55 nicks Exp $ User: root Machine: lijin-desktop Platform: Linux PlatformVersion: 2.6.31-21-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/04/27-09:59:29-GMT BuildTimeStamp: Aug 11 2009 08:24:20 CVS: $Id: mri_watershed.cpp,v 1.67.2.5 2009/05/05 19:17:42 nicks Exp $ User: root Machine: lijin-desktop Platform: Linux PlatformVersion: 2.6.31-21-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/04/27-09:59:29-GMT BuildTimeStamp: Aug 11 2009 08:24:20 CVS: $Id: mri_segment.c,v 1.33.2.2 2007/11/21 04:38:38 nicks Exp $ User: root Machine: lijin-desktop Platform: Linux PlatformVersion: 2.6.31-21-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/04/27-09:59:29-GMT BuildTimeStamp: Aug 11 2009 08:24:20 CVS: $Id: mri_label2label.c,v 1.33 2007/08/10 18:23:46 greve Exp $ User: root Machine: lijin-desktop Platform: Linux PlatformVersion: 2.6.31-21-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/04/27-09:59:29-GMT BuildTimeStamp: Aug 11 2009 08:24:20 CVS: $Id: mri_em_register.c,v 1.57.2.2 2008/12/29 17:22:03 nicks Exp $ User: root Machine: lijin-desktop Platform: Linux PlatformVersion: 2.6.31-21-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/04/27-09:59:29-GMT BuildTimeStamp: Aug 11 2009 08:24:20 CVS: $Id: mri_ca_normalize.c,v 1.38.2.3 2009/08/02 15:00:46 nicks Exp $ User: root Machine: lijin-desktop Platform: Linux PlatformVersion: 2.6.31-21-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/04/27-09:59:29-GMT BuildTimeStamp: Aug 11 2009 08:24:20 CVS: $Id: mri_ca_register.c,v 1.63.2.3 2009/07/30 22:39:45 nicks Exp $ User: root Machine: lijin-desktop Platform: Linux PlatformVersion: 2.6.31-21-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/04/27-09:59:29-GMT BuildTimeStamp: Aug 11 2009 08:24:20 CVS: $Id: mri_ca_label.c,v 1.80.2.8 2009/07/30 23:22:53 nicks Exp $ User: root Machine: lijin-desktop Platform: Linux PlatformVersion: 2.6.31-21-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/04/27-09:59:29-GMT BuildTimeStamp: Aug 11 2009 08:24:20 CVS: $Id: mri_pretess.c,v 1.16 2007/01/18 20:23:47 nicks Exp $ User: root Machine: lijin-desktop Platform: Linux PlatformVersion: 2.6.31-21-generic CompilerName: GCC CompilerVersion: 30400 unknown option -ALL-INFO ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/04/27-09:59:29-GMT BuildTimeStamp: Aug 11 2009 08:24:20 CVS: $Id: mri_fill.c,v 1.111 2007/07/19 20:16:38 fischl Exp $ User: root Machine: lijin-desktop Platform: Linux PlatformVersion: 2.6.31-21-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/04/27-09:59:29-GMT BuildTimeStamp: Aug 11 2009 08:24:20 CVS: $Id: mri_tessellate.c,v 1.32 2007/04/26 21:44:21 fischl Exp $ User: root Machine: lijin-desktop Platform: Linux PlatformVersion: 2.6.31-21-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/04/27-09:59:29-GMT BuildTimeStamp: Aug 11 2009 08:24:20 CVS: $Id: mri_concatenate_lta.c,v 1.3.2.1 2009/05/06 23:40:38 nicks Exp $ User: root Machine: lijin-desktop Platform: Linux PlatformVersion: 2.6.31-21-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/04/27-09:59:29-GMT BuildTimeStamp: Aug 11 2009 08:24:20 CVS: $Id: mri_normalize_tp2.c,v 1.6 2007/01/08 18:10:12 nicks Exp $ User: root Machine: lijin-desktop Platform: Linux PlatformVersion: 2.6.31-21-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/04/27-09:59:29-GMT BuildTimeStamp: Aug 11 2009 08:24:20 CVS: $Id: mris_smooth.c,v 1.21 2007/01/01 18:16:19 fischl Exp $ User: root Machine: lijin-desktop Platform: Linux PlatformVersion: 2.6.31-21-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/04/27-09:59:30-GMT BuildTimeStamp: Aug 11 2009 08:24:20 CVS: $Id: mris_inflate.c,v 1.33.2.3 2008/04/22 19:47:47 nicks Exp $ User: root Machine: lijin-desktop Platform: Linux PlatformVersion: 2.6.31-21-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/04/27-09:59:30-GMT BuildTimeStamp: Aug 11 2009 08:24:20 CVS: $Id: mris_curvature.c,v 1.25 2007/07/20 16:42:32 fischl Exp $ User: root Machine: lijin-desktop Platform: Linux PlatformVersion: 2.6.31-21-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/04/27-09:59:30-GMT BuildTimeStamp: Aug 11 2009 08:24:20 CVS: $Id: mris_sphere.c,v 1.47 2007/03/08 18:36:08 greve Exp $ User: root Machine: lijin-desktop Platform: Linux PlatformVersion: 2.6.31-21-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/04/27-09:59:30-GMT BuildTimeStamp: Aug 11 2009 08:24:20 CVS: $Id: mris_fix_topology.c,v 1.43 2007/01/05 16:57:16 nicks Exp $ User: root Machine: lijin-desktop Platform: Linux PlatformVersion: 2.6.31-21-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/04/27-09:59:30-GMT BuildTimeStamp: Aug 11 2009 08:24:20 CVS: $Id: mris_topo_fixer.cpp,v 1.26.2.1 2007/11/18 03:06:20 nicks Exp $ User: root Machine: lijin-desktop Platform: Linux PlatformVersion: 2.6.31-21-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/04/27-09:59:30-GMT BuildTimeStamp: Aug 11 2009 08:24:20 CVS: $Id: mris_ca_label.c,v 1.23 2007/03/23 20:00:07 fischl Exp $ User: root Machine: lijin-desktop Platform: Linux PlatformVersion: 2.6.31-21-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/04/27-09:59:30-GMT BuildTimeStamp: Aug 11 2009 08:24:20 CVS: $Id: mris_euler_number.c,v 1.5 2006/12/29 02:09:10 nicks Exp $ User: root Machine: lijin-desktop Platform: Linux PlatformVersion: 2.6.31-21-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/04/27-09:59:30-GMT BuildTimeStamp: Aug 11 2009 08:24:20 CVS: $Id: mris_make_surfaces.c,v 1.99.2.5 2008/08/21 22:48:22 nicks Exp $ User: root Machine: lijin-desktop Platform: Linux PlatformVersion: 2.6.31-21-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/04/27-09:59:30-GMT BuildTimeStamp: Aug 11 2009 08:24:20 CVS: $Id: mris_register.c,v 1.48 2007/07/19 15:58:50 fischl Exp $ User: root Machine: lijin-desktop Platform: Linux PlatformVersion: 2.6.31-21-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/04/27-09:59:30-GMT BuildTimeStamp: Aug 11 2009 08:24:20 CVS: $Id: mris_anatomical_stats.c,v 1.54.2.7 2009/06/08 23:45:06 nicks Exp $ User: root Machine: lijin-desktop Platform: Linux PlatformVersion: 2.6.31-21-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/04/27-09:59:30-GMT BuildTimeStamp: Aug 11 2009 08:24:20 CVS: $Id: mrisp_paint.c,v 1.8 2007/02/13 16:57:23 fischl Exp $ User: root Machine: lijin-desktop Platform: Linux PlatformVersion: 2.6.31-21-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/04/27-09:59:30-GMT BuildTimeStamp: Aug 11 2009 08:24:20 CVS: $Id: mris_curvature_stats.c,v 1.28.2.5 2009/02/04 21:12:59 nicks Exp $ User: root Machine: lijin-desktop Platform: Linux PlatformVersion: 2.6.31-21-generic CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_register.cpp,v 1.22.2.1 2009/05/22 00:58:19 nicks Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/04/27-09:59:31-GMT BuildTimeStamp: Aug 11 2009 08:24:20 CVS: $Id: mri_robust_register.cpp,v 1.22.2.1 2009/05/22 00:58:19 nicks Exp $ User: root Machine: lijin-desktop Platform: Linux PlatformVersion: 2.6.31-21-generic CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_template.cpp,v 1.6.2.4 2009/08/05 16:30:00 nicks Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/04/27-09:59:31-GMT BuildTimeStamp: Aug 11 2009 08:24:20 CVS: $Id: mri_robust_template.cpp,v 1.6.2.4 2009/08/05 16:30:00 nicks Exp $ User: root Machine: lijin-desktop Platform: Linux PlatformVersion: 2.6.31-21-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/04/27-09:59:31-GMT BuildTimeStamp: Aug 11 2009 08:24:20 CVS: $Id: mri_and.c,v 1.2.2.1 2009/05/22 00:58:19 nicks Exp $ User: root Machine: lijin-desktop Platform: Linux PlatformVersion: 2.6.31-21-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/04/27-09:59:31-GMT BuildTimeStamp: Aug 11 2009 08:24:20 CVS: $Id: mri_or.c,v 1.1.2.1 2009/06/09 19:52:43 nicks Exp $ User: root Machine: lijin-desktop Platform: Linux PlatformVersion: 2.6.31-21-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/04/27-09:59:31-GMT BuildTimeStamp: Aug 11 2009 08:24:20 CVS: $Id: mri_fuse_segmentations.c,v 1.5.2.2 2009/06/10 19:42:00 nicks Exp $ User: root Machine: lijin-desktop Platform: Linux PlatformVersion: 2.6.31-21-generic CompilerName: GCC CompilerVersion: 30400 ####################################### GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCS curvature.buckner40.filled.desikan_killiany.2009-03-04.gcs ####################################### /usr/local/freesurfer/subjects/fuzhou_test/bai_hong_jun mri_convert /mnt/g/fuzhou_gao/pain1/bai_hong_jun_1/MPR/BAI_HONG_JUN.MR.YU_CHUNSHUI_YU.3.1.2008.01.24.18.37.18.31250.304146390.IMA /usr/local/freesurfer/subjects/fuzhou_test/bai_hong_jun/mri/orig/001.mgz mri_convert /mnt/g/fuzhou_gao/pain1/bai_hong_jun_1/MPR/BAI_HONG_JUN.MR.YU_CHUNSHUI_YU.3.1.2008.01.24.18.37.18.31250.304146390.IMA /usr/local/freesurfer/subjects/fuzhou_test/bai_hong_jun/mri/orig/001.mgz $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from /mnt/g/fuzhou_gao/pain1/bai_hong_jun_1/MPR/BAI_HONG_JUN.MR.YU_CHUNSHUI_YU.3.1.2008.01.24.18.37.18.31250.304146390.IMA... INFO: this looks like a dicom, not an old Siemens .ima file, so I'm going to unpack it as a dicom. If this fails, run mri_convert with -it dicom Getting Series No INFO: Found 178 files in /mnt/g/fuzhou_gao/pain1/bai_hong_jun_1/MPR INFO: Scanning for Series Number 3 Scanning Directory INFO: found 176 files in series INFO: loading series header info. RunNo = 2 INFO: sorting. INFO: (224 256 176), 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 /mnt/g/fuzhou_gao/pain1/bai_hong_jun_1/MPR/BAI_HONG_JUN.MR.YU_CHUNSHUI_YU.3.1.2008.01.24.18.37.18.31250.304146390.IMA Identification NumarisVer syngo MR B13 4VB13A ScannerModel TrioTim PatientName BAI HONG JUN Date and time StudyDate 20080124 StudyTime 180716.765000 SeriesTime 181648.078000 AcqTime 180906.302500 Acquisition parameters PulseSeq *tfl3d1_ns Protocol t1_mpr_ns_sag_iso PhEncDir ROW EchoNo 1 FlipAngle 9 EchoTime 2.19 InversionTime 900 RepetitionTime 2000 PhEncFOV 224 ReadoutFOV 256 Image information RunNo 2 SeriesNo 3 ImageNo 1 NImageRows 256 NImageCols 224 NFrames 1 SliceArraylSize 1 IsMosaic 0 ImgPos 108.9795 117.0079 111.5134 VolRes 1.0000 1.0000 1.0000 VolDim 224 256 176 Vc -0.0473 -0.9989 0.0000 Vr -0.0905 0.0043 -0.9959 Vs -0.9948 0.0471 0.0906 VolCenter 4.5646 9.8240 -7.9903 TransferSyntaxUID 1.2.840.10008.1.2.1 INFO: no Siemens slice order reversal detected (good!). TR=2000.00, TE=2.19, TI=900.00, flip angle=9.00 i_ras = (-0.047272, -0.998882, 8.65441e-10) j_ras = (-0.0904694, 0.00428146, -0.99589) k_ras = (-0.994777, 0.0470778, 0.0905707) writing to /usr/local/freesurfer/subjects/fuzhou_test/bai_hong_jun/mri/orig/001.mgz... #------------------------------------------ recon-all finished without error at Tue Apr 27 17:59:42 CST 2010