Tue Sep 8 18:06:46 CST 2009 /usr/local/freesurfer/subjects/am03 /usr/local/freesurfer/bin/recon-all -s am03 -i /usr/local/freesurfer/subjects/Original-data/structure_am/liuchang/20080623_11_NANY_SYN_LIUCHANG.MR.BNU_CST_NAN_YUN.4.1.2008.06.24.09.14.38.156250.25993470.IMA subjid am03 setenv SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos4-stable-pub-v4.5.0 Linux qq-desktop 2.6.28-15-generic #51-Ubuntu SMP Mon Aug 31 13:33:16 UTC 2009 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: 2060436 1988080 72356 0 4016 149832 -/+ buffers/cache: 1834232 226204 Swap: 2000052 1360160 639892 ######################################## 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: 2009/09/08-10:06:47-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: qq-desktop Platform: Linux PlatformVersion: 2.6.28-15-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: 2009/09/08-10:06:47-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: qq-desktop Platform: Linux PlatformVersion: 2.6.28-15-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: 2009/09/08-10:06:47-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: qq-desktop Platform: Linux PlatformVersion: 2.6.28-15-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/09/08-10:06:47-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: qq-desktop Platform: Linux PlatformVersion: 2.6.28-15-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/09/08-10:06:47-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: qq-desktop Platform: Linux PlatformVersion: 2.6.28-15-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/09/08-10:06:47-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: qq-desktop Platform: Linux PlatformVersion: 2.6.28-15-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/09/08-10:06:47-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: qq-desktop Platform: Linux PlatformVersion: 2.6.28-15-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/09/08-10:06:47-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: qq-desktop Platform: Linux PlatformVersion: 2.6.28-15-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/09/08-10:06:47-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: qq-desktop Platform: Linux PlatformVersion: 2.6.28-15-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/09/08-10:06:47-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: qq-desktop Platform: Linux PlatformVersion: 2.6.28-15-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/09/08-10:06:47-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: qq-desktop Platform: Linux PlatformVersion: 2.6.28-15-generic CompilerName: GCC CompilerVersion: 30400 unknown option -ALL-INFO ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/09/08-10:06:47-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: qq-desktop Platform: Linux PlatformVersion: 2.6.28-15-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/09/08-10:06:47-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: qq-desktop Platform: Linux PlatformVersion: 2.6.28-15-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/09/08-10:06:47-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: qq-desktop Platform: Linux PlatformVersion: 2.6.28-15-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/09/08-10:06:47-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: qq-desktop Platform: Linux PlatformVersion: 2.6.28-15-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/09/08-10:06:47-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: qq-desktop Platform: Linux PlatformVersion: 2.6.28-15-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/09/08-10:06:47-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: qq-desktop Platform: Linux PlatformVersion: 2.6.28-15-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/09/08-10:06:47-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: qq-desktop Platform: Linux PlatformVersion: 2.6.28-15-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/09/08-10:06:47-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: qq-desktop Platform: Linux PlatformVersion: 2.6.28-15-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/09/08-10:06:47-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: qq-desktop Platform: Linux PlatformVersion: 2.6.28-15-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/09/08-10:06:47-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: qq-desktop Platform: Linux PlatformVersion: 2.6.28-15-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/09/08-10:06:47-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: qq-desktop Platform: Linux PlatformVersion: 2.6.28-15-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/09/08-10:06:47-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: qq-desktop Platform: Linux PlatformVersion: 2.6.28-15-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/09/08-10:06:47-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: qq-desktop Platform: Linux PlatformVersion: 2.6.28-15-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/09/08-10:06:47-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: qq-desktop Platform: Linux PlatformVersion: 2.6.28-15-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/09/08-10:06:47-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: qq-desktop Platform: Linux PlatformVersion: 2.6.28-15-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/09/08-10:06:47-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: qq-desktop Platform: Linux PlatformVersion: 2.6.28-15-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/09/08-10:06:47-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: qq-desktop Platform: Linux PlatformVersion: 2.6.28-15-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: 2009/09/08-10:06:47-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: qq-desktop Platform: Linux PlatformVersion: 2.6.28-15-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: 2009/09/08-10:06:47-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: qq-desktop Platform: Linux PlatformVersion: 2.6.28-15-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/09/08-10:06:47-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: qq-desktop Platform: Linux PlatformVersion: 2.6.28-15-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/09/08-10:06:47-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: qq-desktop Platform: Linux PlatformVersion: 2.6.28-15-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/09/08-10:06:47-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: qq-desktop Platform: Linux PlatformVersion: 2.6.28-15-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/am03 mri_convert /usr/local/freesurfer/subjects/Original-data/structure_am/liuchang/20080623_11_NANY_SYN_LIUCHANG.MR.BNU_CST_NAN_YUN.4.1.2008.06.24.09.14.38.156250.25993470.IMA /usr/local/freesurfer/subjects/am03/mri/orig/001.mgz mri_convert /usr/local/freesurfer/subjects/Original-data/structure_am/liuchang/20080623_11_NANY_SYN_LIUCHANG.MR.BNU_CST_NAN_YUN.4.1.2008.06.24.09.14.38.156250.25993470.IMA /usr/local/freesurfer/subjects/am03/mri/orig/001.mgz $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from /usr/local/freesurfer/subjects/Original-data/structure_am/liuchang/20080623_11_NANY_SYN_LIUCHANG.MR.BNU_CST_NAN_YUN.4.1.2008.06.24.09.14.38.156250.25993470.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 130 files in /usr/local/freesurfer/subjects/Original-data/structure_am/liuchang INFO: Scanning for Series Number 4 Scanning Directory INFO: found 128 files in series INFO: loading series header info. RunNo = 3 INFO: sorting. INFO: (256 256 128), 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/freesurfer/subjects/Original-data/structure_am/liuchang/20080623_11_NANY_SYN_LIUCHANG.MR.BNU_CST_NAN_YUN.4.1.2008.06.24.09.14.38.156250.25993470.IMA Identification NumarisVer syngo MR B15 ScannerModel TrioTim PatientName 20080623_11_Nany_SYN_LiuChang Date and time StudyDate 20080623 StudyTime 192715.546000 SeriesTime 194803.281000 AcqTime 193955.147500 Acquisition parameters PulseSeq *tfl3d1_ns Protocol t1_mprage_sag PhEncDir ROW EchoNo 1 FlipAngle 7 EchoTime 3.39 InversionTime 1100 RepetitionTime 2530 PhEncFOV 256 ReadoutFOV 256 Image information RunNo 3 SeriesNo 4 ImageNo 1 NImageRows 256 NImageCols 256 NFrames 1 SliceArraylSize 1 IsMosaic 0 ImgPos 86.4889 142.2373 139.5254 VolRes 1.0000 1.0000 1.3300 VolDim 256 256 128 Vc -0.0000 -1.0000 0.0000 Vr -0.0000 -0.0000 -1.0000 Vs -1.0000 -0.0000 0.0000 VolCenter 1.3689 14.2373 11.5254 TransferSyntaxUID 1.2.840.10008.1.2.1 INFO: no Siemens slice order reversal detected (good!). TR=2530.00, TE=3.39, TI=1100.00, flip angle=7.00 i_ras = (-0, -1, 0) j_ras = (-0, -0, -1) k_ras = (-1, -0, 0) writing to /usr/local/freesurfer/subjects/am03/mri/orig/001.mgz... #------------------------------------------ recon-all finished without error at Tue Sep 8 18:06:58 CST 2009 New invocation of recon-all Wed Sep 9 13:30:27 CST 2009 /usr/local/freesurfer/subjects/am03 /usr/local/freesurfer/bin/recon-all -s am03 -autorecon1 subjid am03 setenv SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos4-stable-pub-v4.5.0 Linux qq-desktop 2.6.28-15-generic #51-Ubuntu SMP Mon Aug 31 13:33:16 UTC 2009 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: 2060436 1668672 391764 0 5124 109972 -/+ buffers/cache: 1553576 506860 Swap: 2000052 1900888 99164 ######################################## 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: 2009/09/09-05:30:27-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: qq-desktop Platform: Linux PlatformVersion: 2.6.28-15-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: 2009/09/09-05:30:27-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: qq-desktop Platform: Linux PlatformVersion: 2.6.28-15-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: 2009/09/09-05:30:28-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: qq-desktop Platform: Linux PlatformVersion: 2.6.28-15-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/09/09-05:30:28-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: qq-desktop Platform: Linux PlatformVersion: 2.6.28-15-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/09/09-05:30:28-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: qq-desktop Platform: Linux PlatformVersion: 2.6.28-15-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/09/09-05:30:28-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: qq-desktop Platform: Linux PlatformVersion: 2.6.28-15-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/09/09-05:30:28-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: qq-desktop Platform: Linux PlatformVersion: 2.6.28-15-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/09/09-05:30:28-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: qq-desktop Platform: Linux PlatformVersion: 2.6.28-15-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/09/09-05:30:28-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: qq-desktop Platform: Linux PlatformVersion: 2.6.28-15-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/09/09-05:30:29-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: qq-desktop Platform: Linux PlatformVersion: 2.6.28-15-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/09/09-05:30:29-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: qq-desktop Platform: Linux PlatformVersion: 2.6.28-15-generic CompilerName: GCC CompilerVersion: 30400 unknown option -ALL-INFO ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/09/09-05:30:29-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: qq-desktop Platform: Linux PlatformVersion: 2.6.28-15-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/09/09-05:30:29-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: qq-desktop Platform: Linux PlatformVersion: 2.6.28-15-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/09/09-05:30:29-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: qq-desktop Platform: Linux PlatformVersion: 2.6.28-15-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/09/09-05:30:29-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: qq-desktop Platform: Linux PlatformVersion: 2.6.28-15-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/09/09-05:30:30-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: qq-desktop Platform: Linux PlatformVersion: 2.6.28-15-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/09/09-05:30:30-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: qq-desktop Platform: Linux PlatformVersion: 2.6.28-15-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/09/09-05:30:30-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: qq-desktop Platform: Linux PlatformVersion: 2.6.28-15-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/09/09-05:30:30-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: qq-desktop Platform: Linux PlatformVersion: 2.6.28-15-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/09/09-05:30:30-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: qq-desktop Platform: Linux PlatformVersion: 2.6.28-15-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/09/09-05:30:30-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: qq-desktop Platform: Linux PlatformVersion: 2.6.28-15-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/09/09-05:30:30-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: qq-desktop Platform: Linux PlatformVersion: 2.6.28-15-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/09/09-05:30:31-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: qq-desktop Platform: Linux PlatformVersion: 2.6.28-15-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/09/09-05:30:31-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: qq-desktop Platform: Linux PlatformVersion: 2.6.28-15-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/09/09-05:30:31-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: qq-desktop Platform: Linux PlatformVersion: 2.6.28-15-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/09/09-05:30:31-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: qq-desktop Platform: Linux PlatformVersion: 2.6.28-15-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/09/09-05:30:31-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: qq-desktop Platform: Linux PlatformVersion: 2.6.28-15-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/09/09-05:30:31-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: qq-desktop Platform: Linux PlatformVersion: 2.6.28-15-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: 2009/09/09-05:30:31-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: qq-desktop Platform: Linux PlatformVersion: 2.6.28-15-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: 2009/09/09-05:30:32-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: qq-desktop Platform: Linux PlatformVersion: 2.6.28-15-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/09/09-05:30:32-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: qq-desktop Platform: Linux PlatformVersion: 2.6.28-15-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/09/09-05:30:32-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: qq-desktop Platform: Linux PlatformVersion: 2.6.28-15-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/09/09-05:30:32-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: qq-desktop Platform: Linux PlatformVersion: 2.6.28-15-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 ####################################### #-------------------------------------------- #@# MotionCor Wed Sep 9 13:30:32 CST 2009 Found 1 runs /usr/local/freesurfer/subjects/am03/mri/orig/001.mgz WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. cp /usr/local/freesurfer/subjects/am03/mri/orig/001.mgz /usr/local/freesurfer/subjects/am03/mri/rawavg.mgz /usr/local/freesurfer/subjects/am03 mri_convert /usr/local/freesurfer/subjects/am03/mri/rawavg.mgz /usr/local/freesurfer/subjects/am03/mri/orig.mgz --conform mri_convert /usr/local/freesurfer/subjects/am03/mri/rawavg.mgz /usr/local/freesurfer/subjects/am03/mri/orig.mgz --conform $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from /usr/local/freesurfer/subjects/am03/mri/rawavg.mgz... TR=2530.00, TE=3.39, TI=1100.00, flip angle=7.00 i_ras = (-0, -1, 0) j_ras = (-0, -0, -1) k_ras = (-1, -0, 0) Original Data has (1, 1, 1.33) mm size and (256, 256, 128) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from 4 to 0 (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /usr/local/freesurfer/subjects/am03/mri/orig.mgz... mri_add_xform_to_header -c /usr/local/freesurfer/subjects/am03/mri/transforms/talairach.xfm /usr/local/freesurfer/subjects/am03/mri/orig.mgz /usr/local/freesurfer/subjects/am03/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Nu Intensity Correction Wed Sep 9 13:30:47 CST 2009 mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2 /usr/local/freesurfer/subjects/am03/mri /usr/local/freesurfer/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.7.2.2 2009/05/04 16:16:27 nicks Exp $ Linux qq-desktop 2.6.28-15-generic #51-Ubuntu SMP Mon Aug 31 13:33:16 UTC 2009 i686 GNU/Linux Wed Sep 9 13:30:48 CST 2009 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 tmpdir is ./tmp.mri_nu_correct.mni.23704 /usr/local/freesurfer/subjects/am03/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.23704/nu0.mnc mri_convert orig.mgz ./tmp.mri_nu_correct.mni.23704/nu0.mnc $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from orig.mgz... TR=2530.00, TE=3.39, TI=1100.00, flip angle=7.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to ./tmp.mri_nu_correct.mni.23704/nu0.mnc... -------------------------------------------------------- Iteration 1 Wed Sep 9 13:30:53 CST 2009 nu_correct -clobber ./tmp.mri_nu_correct.mni.23704/nu0.mnc ./tmp.mri_nu_correct.mni.23704/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.23704/0/ [root@qq-desktop:/usr/local/freesurfer/subjects/am03/mri/] [2009-09-09 13:30:53] running: /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.23704/0/ ./tmp.mri_nu_correct.mni.23704/nu0.mnc ./tmp.mri_nu_correct.mni.23704/nu1.imp Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Number of iterations: 50 CV of field change: 0.00119751 [root@qq-desktop:/usr/local/freesurfer/subjects/am03/mri/] [2009-09-09 13:31:35] running: /usr/local/freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.23704/nu0.mnc ./tmp.mri_nu_correct.mni.23704/0//template.mnc Transforming slices:......................................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Transforming slices:................................................................................................................................................................................................................................................................Done -------------------------------------------------------- Iteration 2 Wed Sep 9 13:31:40 CST 2009 nu_correct -clobber ./tmp.mri_nu_correct.mni.23704/nu1.mnc ./tmp.mri_nu_correct.mni.23704/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.23704/1/ [root@qq-desktop:/usr/local/freesurfer/subjects/am03/mri/] [2009-09-09 13:31:40] running: /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.23704/1/ ./tmp.mri_nu_correct.mni.23704/nu1.mnc ./tmp.mri_nu_correct.mni.23704/nu2.imp Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Number of iterations: 2 CV of field change: 0.000944589 [root@qq-desktop:/usr/local/freesurfer/subjects/am03/mri/] [2009-09-09 13:31:43] running: /usr/local/freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.23704/nu1.mnc ./tmp.mri_nu_correct.mni.23704/1//template.mnc Transforming slices:......................................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Transforming slices:................................................................................................................................................................................................................................................................Done mri_convert ./tmp.mri_nu_correct.mni.23704/nu2.mnc nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.23704/nu2.mnc nu.mgz --like orig.mgz $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from ./tmp.mri_nu_correct.mni.23704/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... Wed Sep 9 13:31:56 CST 2009 mri_nu_correct.mni done #-------------------------------------------- #@# Talairach Wed Sep 9 13:31:56 CST 2009 /usr/local/freesurfer/subjects/am03/mri talairach_avi --i nu.mgz --xfm transforms/talairach.auto.xfm /usr/local/freesurfer/subjects/am03/mri /usr/local/freesurfer/bin/talairach_avi --i nu.mgz --xfm transforms/talairach.auto.xfm $Id: talairach_avi,v 1.4.2.1 2009/07/30 19:22:07 nicks Exp $ Linux qq-desktop 2.6.28-15-generic #51-Ubuntu SMP Mon Aug 31 13:33:16 UTC 2009 i686 GNU/Linux Wed Sep 9 13:31:56 CST 2009 -------------------------------------------- mri_convert nu.mgz talsrcimg.img $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from nu.mgz... TR=2530.00, TE=3.39, TI=1100.00, flip angle=7.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to talsrcimg.img... Analyze Output Matrix -1.000 0.000 0.000 130.369; 0.000 0.000 1.000 -114.763; 0.000 -1.000 0.000 140.525; 0.000 0.000 0.000 1.000; -------------------- INFO: set hdr.hist.orient to -1 -------------------------------------------- mpr2mni305 talsrcimg Wed Sep 9 13:31:58 CST 2009 /usr/local/freesurfer/bin/mpr2mni305 talsrcimg $Id: mpr2mni305,v 1.3.2.1 2009/07/30 19:21:45 nicks Exp $ target=711-2C_as_mni_average_305 --------------------------------------------------------------------- analyzeto4dfp talsrcimg -O0 -y --------------------------------------------------------------------- $Id: ifh2hdr.c,v 1.3 2007/05/05 10:45:03 nicks Exp $ Wed Sep 9 13:31:59 2009 Writing: talsrcimg.4dfp.hdr $Id: analyzeto4dfp.c,v 1.2 2007/05/05 00:00:06 nicks Exp $ Reading: talsrcimg.hdr header size 348 bytes hdr.dime.datatype offset=70 value=2 hdr.dime.bitpix offset=72 value=8 hdr.hist.orient offset=252 value=-1 dimensionality 4 dimensions 256 256 256 1 Reading: talsrcimg.img Writing: talsrcimg.4dfp.img Writing: talsrcimg.4dfp.ifh ifh2hdr talsrcimg -r0to255 ori=2 --------------------------------------------------------------------- gauss_4dfp talsrcimg 1.1 --------------------------------------------------------------------- $Id: gauss_4dfp.c,v 1.2.2.1 2009/05/15 21:44:49 nicks Exp $ Reading: talsrcimg.4dfp.img Writing: talsrcimg_g11.4dfp.img image dimensions 256 256 256 padded to 288 288 288 processing volume 1$Id: ifh2hdr.c,v 1.3 2007/05/05 10:45:03 nicks Exp $ Wed Sep 9 13:32:19 2009 Writing: talsrcimg_g11.4dfp.hdr Writing: talsrcimg_g11.4dfp.ifh including: talsrcimg.4dfp.img.rec in talsrcimg_g11.4dfp.img.rec --------------------------------------------------------------------- imgreg_4dfp /usr/local/freesurfer/average/711-2C_as_mni_average_305 none talsrcimg_g11 none talsrcimg_to_711-2C_as_mni_average_305_t4 4355 --------------------------------------------------------------------- $Id: imgreg_4dfp.c,v 1.3 2007/08/04 04:19:24 nicks Exp $ /usr/local/freesurfer/average/711-2C_as_mni_average_305.4dfp.img 256 256 256 1 1.000000 1.000000 1.000000 orientation T byte_order littleendian Reading image: /usr/local/freesurfer/average/711-2C_as_mni_average_305.4dfp.img dimensions: 256 256 256 mmppix: 1.0000 -1.0000 -1.0000 center: 128.0000 -129.0000 -129.0000 talsrcimg_g11.4dfp.img 256 256 256 1 1.000000 1.000000 1.000000 orientation T byte_order littleendian Reading image: talsrcimg_g11.4dfp.img dimensions: 256 256 256 mmppix: 1.0000 -1.0000 -1.0000 center: 128.0000 -129.0000 -129.0000 t4_read: talsrcimg_to_711-2C_as_mni_average_305_t4 read error t4_read: transform initialized to I4 rotation matrix determinant 1.000000 image alignment mode 4355 decimal 1103 hex -7.5000 -45.0000 -45.0000 8920.5664 10.2796 0.0000 -45.0000 -45.0000 9300.8369 10.2660 7.5000 -45.0000 -45.0000 8921.5752 10.2422 -7.5000 -37.5000 -45.0000 9146.9648 10.4501 0.0000 -37.5000 -45.0000 9562.0283 10.4319 7.5000 -37.5000 -45.0000 9169.4785 10.4056 -7.5000 -30.0000 -45.0000 9607.7412 10.3708 0.0000 -30.0000 -45.000010054.4326 10.3463 7.5000 -30.0000 -45.0000 9624.6660 10.3152 -7.5000 -22.5000 -45.000010007.1963 10.2935 0.0000 -22.5000 -45.000010492.2939 10.2671 7.5000 -22.5000 -45.000010044.6367 10.2340 -7.5000 -15.0000 -45.000010346.9062 10.2198 0.0000 -15.0000 -45.000010841.2490 10.1976 7.5000 -15.0000 -45.000010383.9736 10.1667 -7.5000 -7.5000 -45.000010616.5459 10.1569 0.0000 -7.5000 -45.000011124.0635 10.1417 7.5000 -7.5000 -45.000010634.8760 10.1162 -7.5000 0.0000 -45.000010833.0967 10.1314 0.0000 0.0000 -45.000011371.6572 10.1182 7.5000 0.0000 -45.000010871.1846 10.0954 -7.5000 7.5000 -45.000010290.1045 10.3559 0.0000 7.5000 -45.000010827.2969 10.3381 7.5000 7.5000 -45.000010359.4678 10.3125 -7.5000 15.0000 -45.0000 9770.3691 10.6790 0.0000 15.0000 -45.000010269.8369 10.6536 7.5000 15.0000 -45.0000 9849.1143 10.6224 -7.5000 22.5000 -45.0000 9288.4971 11.0377 0.0000 22.5000 -45.0000 9763.7490 11.0093 7.5000 22.5000 -45.0000 9377.0205 10.9747 -7.5000 30.0000 -45.0000 8763.0459 11.2806 0.0000 30.0000 -45.0000 9219.0137 11.2558 7.5000 30.0000 -45.0000 8849.8457 11.2208 -7.5000 37.5000 -45.0000 8597.1006 11.6991 0.0000 37.5000 -45.0000 9010.0918 11.6826 7.5000 37.5000 -45.0000 8642.0781 11.6519 -7.5000 45.0000 -45.0000 8119.0762 11.8451 0.0000 45.0000 -45.0000 8528.9453 11.8322 7.5000 45.0000 -45.0000 8165.1123 11.8036 -7.5000 -45.0000 -37.5000 9477.8125 10.1873 0.0000 -45.0000 -37.5000 9900.3770 10.1728 7.5000 -45.0000 -37.5000 9484.7930 10.1527 -7.5000 -37.5000 -37.5000 9743.9463 10.3527 0.0000 -37.5000 -37.500010195.5283 10.3345 7.5000 -37.5000 -37.5000 9770.9531 10.3130 -7.5000 -30.0000 -37.500010245.0791 10.2747 0.0000 -30.0000 -37.500010733.0557 10.2513 7.5000 -30.0000 -37.500010285.1055 10.2245 -7.5000 -22.5000 -37.500010695.7832 10.2009 0.0000 -22.5000 -37.500011209.7354 10.1756 7.5000 -22.5000 -37.500010730.3057 10.1453 -7.5000 -15.0000 -37.500011045.3037 10.1289 0.0000 -15.0000 -37.500011576.0547 10.1068 7.5000 -15.0000 -37.500011075.3262 10.0780 -7.5000 -7.5000 -37.500011289.3623 10.0649 0.0000 -7.5000 -37.500011861.7793 10.0487 7.5000 -7.5000 -37.500011327.5576 10.0257 -7.5000 0.0000 -37.500011501.3643 10.0374 0.0000 0.0000 -37.500012074.7783 10.0233 7.5000 0.0000 -37.500011561.2959 10.0041 -7.5000 7.5000 -37.500010931.0078 10.2565 0.0000 7.5000 -37.500011478.8799 10.2386 7.5000 7.5000 -37.500010987.6602 10.2177 -7.5000 15.0000 -37.500010379.8418 10.5750 0.0000 15.0000 -37.500010887.0898 10.5500 7.5000 15.0000 -37.500010440.0713 10.5229 -7.5000 22.5000 -37.5000 9887.6650 10.9310 0.0000 22.5000 -37.500010364.9297 10.9029 7.5000 22.5000 -37.5000 9937.1611 10.8707 -7.5000 30.0000 -37.5000 9320.9434 11.1683 0.0000 30.0000 -37.5000 9771.4990 11.1433 7.5000 30.0000 -37.5000 9356.3926 11.1117 -7.5000 37.5000 -37.5000 9103.0781 11.5793 0.0000 37.5000 -37.5000 9521.5010 11.5615 7.5000 37.5000 -37.5000 9134.0303 11.5357 -7.5000 45.0000 -37.5000 8587.5234 11.7252 0.0000 45.0000 -37.5000 8992.4941 11.7117 7.5000 45.0000 -37.5000 8628.4785 11.6891 -7.5000 -45.0000 -30.000010267.5068 10.5398 0.0000 -45.0000 -30.000010754.3496 10.5199 7.5000 -45.0000 -30.000010291.7881 10.5032 -7.5000 -37.5000 -30.000010577.6484 10.7084 0.0000 -37.5000 -30.000011081.0127 10.6863 7.5000 -37.5000 -30.000010604.6816 10.6696 -7.5000 -30.0000 -30.000011124.6494 10.6238 0.0000 -30.0000 -30.000011642.9863 10.5992 7.5000 -30.0000 -30.000011143.3145 10.5786 -7.5000 -22.5000 -30.000011594.8672 10.5477 0.0000 -22.5000 -30.000012126.9482 10.5218 7.5000 -22.5000 -30.000011609.4902 10.4972 -7.5000 -15.0000 -30.000011972.7998 10.4749 0.0000 -15.0000 -30.000012518.9424 10.4504 7.5000 -15.0000 -30.000011975.1338 10.4258 -7.5000 -7.5000 -30.000012242.6064 10.4090 0.0000 -7.5000 -30.000012824.1562 10.3881 7.5000 -7.5000 -30.000012254.8389 10.3683 -7.5000 0.0000 -30.000012462.6299 10.3788 0.0000 0.0000 -30.000013029.0303 10.3596 7.5000 0.0000 -30.000012487.5557 10.3438 -7.5000 7.5000 -30.000011833.3848 10.6037 0.0000 7.5000 -30.000012378.3682 10.5821 7.5000 7.5000 -30.000011869.1523 10.5658 -7.5000 15.0000 -30.000011232.4844 10.9342 0.0000 15.0000 -30.000011747.0391 10.9077 7.5000 15.0000 -30.000011255.1611 10.8870 -7.5000 22.5000 -30.000010702.1846 11.3056 0.0000 22.5000 -30.000011183.7295 11.2768 7.5000 22.5000 -30.000010708.3535 11.2506 -7.5000 30.0000 -30.000010053.5449 11.5562 0.0000 30.0000 -30.000010500.1914 11.5287 7.5000 30.0000 -30.000010060.4775 11.5024 -7.5000 37.5000 -30.0000 9769.8291 11.9810 0.0000 37.5000 -30.000010185.3311 11.9582 7.5000 37.5000 -30.0000 9786.3457 11.9357 -7.5000 45.0000 -30.0000 9194.8760 12.1435 0.0000 45.0000 -30.0000 9574.9072 12.1233 7.5000 45.0000 -30.0000 9224.7158 12.1022 -7.5000 -45.0000 -22.500011105.9736 10.8479 0.0000 -45.0000 -22.500011635.5957 10.8235 7.5000 -45.0000 -22.500011145.7539 10.8084 -7.5000 -37.5000 -22.500011447.6191 11.0206 0.0000 -37.5000 -22.500011978.0869 10.9946 7.5000 -37.5000 -22.500011473.3994 10.9794 -7.5000 -30.0000 -22.500012039.5537 10.9295 0.0000 -30.0000 -22.500012581.8281 10.9024 7.5000 -30.0000 -22.500012066.2676 10.8850 -7.5000 -22.5000 -22.500012566.8184 10.8486 0.0000 -22.5000 -22.500013112.1367 10.8215 7.5000 -22.5000 -22.500012576.7373 10.8011 -7.5000 -15.0000 -22.500012968.9189 10.7738 0.0000 -15.0000 -22.500013522.3896 10.7476 7.5000 -15.0000 -22.500012951.9893 10.7263 -7.5000 -7.5000 -22.500013274.5371 10.7071 0.0000 -7.5000 -22.500013851.1182 10.6828 7.5000 -7.5000 -22.500013267.3291 10.6647 -7.5000 0.0000 -22.500013486.4785 10.6752 0.0000 0.0000 -22.500014060.8096 10.6516 7.5000 0.0000 -22.500013503.5166 10.6373 -7.5000 7.5000 -22.500012763.7617 10.9068 0.0000 7.5000 -22.500013306.3662 10.8813 7.5000 7.5000 -22.500012783.0205 10.8666 -7.5000 15.0000 -22.500012074.1152 11.2468 0.0000 15.0000 -22.500012605.7148 11.2184 7.5000 15.0000 -22.500012106.2520 11.2013 -7.5000 22.5000 -22.500011467.7988 11.6289 0.0000 22.5000 -22.500011985.8203 11.5999 7.5000 22.5000 -22.500011500.6133 11.5782 -7.5000 30.0000 -22.500010782.2871 11.8926 0.0000 30.0000 -22.500011236.9316 11.8635 7.5000 30.0000 -22.500010789.4414 11.8402 -7.5000 37.5000 -22.500010465.7686 12.3294 0.0000 37.5000 -22.500010867.4492 12.3033 7.5000 37.5000 -22.500010461.3779 12.2802 -7.5000 45.0000 -22.5000 9837.0439 12.5071 0.0000 45.0000 -22.500010202.7002 12.4808 7.5000 45.0000 -22.5000 9827.5059 12.4564 -7.5000 -45.0000 -15.000011954.0244 11.0618 0.0000 -45.0000 -15.000012547.1836 11.0382 7.5000 -45.0000 -15.000012017.6309 11.0204 -7.5000 -37.5000 -15.000012340.2217 11.2387 0.0000 -37.5000 -15.000012934.3594 11.2126 7.5000 -37.5000 -15.000012385.4570 11.1940 -7.5000 -30.0000 -15.000013004.9443 11.1436 0.0000 -30.0000 -15.000013610.9150 11.1154 7.5000 -30.0000 -15.000013034.2754 11.0953 -7.5000 -22.5000 -15.000013559.1279 11.0573 0.0000 -22.5000 -15.000014173.2832 11.0291 7.5000 -22.5000 -15.000013583.2021 11.0074 -7.5000 -15.0000 -15.000013993.9365 10.9787 0.0000 -15.0000 -15.000014617.3770 10.9527 7.5000 -15.0000 -15.000014002.9639 10.9304 -7.5000 -7.5000 -15.000014308.2627 10.9106 0.0000 -7.5000 -15.000014958.1758 10.8873 7.5000 -7.5000 -15.000014328.3076 10.8675 -7.5000 0.0000 -15.000014505.1885 10.8777 0.0000 0.0000 -15.000015200.1396 10.8549 7.5000 0.0000 -15.000014565.3193 10.8381 -7.5000 7.5000 -15.000013682.2832 11.1155 0.0000 7.5000 -15.000014340.5781 11.0901 7.5000 7.5000 -15.000013738.8770 11.0722 -7.5000 15.0000 -15.000012928.2695 11.4630 0.0000 15.0000 -15.000013540.7734 11.4340 7.5000 15.0000 -15.000012971.9033 11.4143 -7.5000 22.5000 -15.000012271.1006 11.8512 0.0000 22.5000 -15.000012844.5508 11.8220 7.5000 22.5000 -15.000012317.4541 11.7992 -7.5000 30.0000 -15.000011523.4375 12.1250 0.0000 30.0000 -15.000012018.8936 12.0963 7.5000 30.0000 -15.000011540.8516 12.0707 -7.5000 37.5000 -15.000011164.9482 12.5721 0.0000 37.5000 -15.000011586.5088 12.5471 7.5000 37.5000 -15.000011183.5146 12.5198 -7.5000 45.0000 -15.000010461.7471 12.7589 0.0000 45.0000 -15.000010830.1553 12.7328 7.5000 45.0000 -15.000010444.5996 12.7029 -7.5000 -45.0000 -7.500012879.7051 11.1458 0.0000 -45.0000 -7.500013540.5332 11.1274 7.5000 -45.0000 -7.500012988.9941 11.1048 -7.5000 -37.5000 -7.500013285.2373 11.3260 0.0000 -37.5000 -7.500013926.1836 11.3039 7.5000 -37.5000 -7.500013360.2480 11.2793 -7.5000 -30.0000 -7.500013994.6650 11.2309 0.0000 -30.0000 -7.500014662.2002 11.2039 7.5000 -30.0000 -7.500014041.0166 11.1764 -7.5000 -22.5000 -7.500014592.1318 11.1400 0.0000 -22.5000 -7.500015283.8721 11.1117 7.5000 -22.5000 -7.500014629.4854 11.0832 -7.5000 -15.0000 -7.500015051.6660 11.0558 0.0000 -15.0000 -7.500015765.8867 11.0312 7.5000 -15.0000 -7.500015054.1973 11.0038 -7.5000 -7.5000 -7.500015381.9766 10.9842 0.0000 -7.5000 -7.500016120.7500 10.9651 7.5000 -7.5000 -7.500015391.1611 10.9413 -7.5000 0.0000 -7.500015569.8604 10.9513 0.0000 0.0000 -7.500016404.5176 10.9336 7.5000 0.0000 -7.500015625.9648 10.9122 -7.5000 7.5000 -7.500014670.2139 11.1937 0.0000 7.5000 -7.500015478.0156 11.1722 7.5000 7.5000 -7.500014719.8945 11.1484 -7.5000 15.0000 -7.500013836.6621 11.5455 0.0000 15.0000 -7.500014558.5381 11.5179 7.5000 15.0000 -7.500013856.8408 11.4907 -7.5000 22.5000 -7.500013110.2119 11.9345 0.0000 22.5000 -7.500013741.7148 11.9052 7.5000 22.5000 -7.500013116.5869 11.8756 -7.5000 30.0000 -7.500012281.2695 12.2122 0.0000 30.0000 -7.500012819.6094 12.1850 7.5000 30.0000 -7.500012294.9668 12.1534 -7.5000 37.5000 -7.500011868.2910 12.6639 0.0000 37.5000 -7.500012359.1992 12.6434 7.5000 37.5000 -7.500011898.1543 12.6121 -7.5000 45.0000 -7.500011096.4355 12.8525 0.0000 45.0000 -7.500011524.4785 12.8330 7.5000 45.0000 -7.500011096.6787 12.8007 -7.5000 -45.0000 0.000013761.5010 11.1180 0.0000 -45.0000 0.000014474.1533 11.1042 7.5000 -45.0000 0.000013883.5029 11.0803 -7.5000 -37.5000 0.000014152.2285 11.2979 0.0000 -37.5000 0.000014858.3662 11.2794 7.5000 -37.5000 0.000014256.2471 11.2530 -7.5000 -30.0000 0.000014872.5098 11.2042 0.0000 -30.0000 0.000015642.5654 11.1792 7.5000 -30.0000 0.000014939.1641 11.1479 -7.5000 -22.5000 0.000015514.4775 11.1124 0.0000 -22.5000 0.000016327.0957 11.0852 7.5000 -22.5000 0.000015547.6523 11.0519 -7.5000 -15.0000 0.000016041.5449 11.0247 0.0000 -15.0000 0.000016843.3320 11.0018 7.5000 -15.0000 0.000016017.9570 10.9706 -7.5000 -7.5000 0.000016431.4023 10.9489 0.0000 -7.5000 0.000017326.2109 10.9331 7.5000 -7.5000 0.000016450.2422 10.9075 -7.5000 0.0000 0.000016554.2090 10.9148 0.0000 0.0000 0.000017625.2578 10.9012 7.5000 0.0000 0.000016682.2246 10.8787 -7.5000 7.5000 0.000015552.9395 11.1576 0.0000 7.5000 0.000016546.3340 11.1394 7.5000 7.5000 0.000015620.6875 11.1139 -7.5000 15.0000 0.000014620.3828 11.5098 0.0000 15.0000 0.000015474.0801 11.4836 7.5000 15.0000 0.000014644.0693 11.4523 -7.5000 22.5000 0.000013820.4346 11.8991 0.0000 22.5000 0.000014562.6826 11.8697 7.5000 22.5000 0.000013823.6953 11.8348 -7.5000 30.0000 0.000012921.2373 12.1755 0.0000 30.0000 0.000013587.6582 12.1500 7.5000 30.0000 0.000012963.1738 12.1144 -7.5000 37.5000 0.000012493.3770 12.6254 0.0000 37.5000 0.000013114.8623 12.6083 7.5000 37.5000 0.000012533.8564 12.5773 -7.5000 45.0000 0.000011655.5234 12.8127 0.0000 45.0000 0.000012194.0664 12.7990 7.5000 45.0000 0.000011696.0684 12.7699 -7.5000 -45.0000 7.500013514.2148 11.1375 0.0000 -45.0000 7.500014177.2051 11.1219 7.5000 -45.0000 7.500013615.9756 11.1003 -7.5000 -37.5000 7.500013889.0146 11.3149 0.0000 -37.5000 7.500014593.4277 11.2954 7.5000 -37.5000 7.500013995.0166 11.2725 -7.5000 -30.0000 7.500014603.9541 11.2226 0.0000 -30.0000 7.500015369.0703 11.1979 7.5000 -30.0000 7.500014683.8877 11.1696 -7.5000 -22.5000 7.500015237.9873 11.1350 0.0000 -22.5000 7.500016026.6455 11.1083 7.5000 -22.5000 7.500015238.1758 11.0765 -7.5000 -15.0000 7.500015846.9717 11.0496 0.0000 -15.0000 7.500016743.9238 11.0261 7.5000 -15.0000 7.500015840.6025 10.9957 -7.5000 -7.5000 7.500016333.6396 10.9729 0.0000 -7.5000 7.500017506.2422 10.9555 7.5000 -7.5000 7.500016465.3145 10.9310 -7.5000 0.0000 7.500016473.5586 10.9373 0.0000 0.0000 7.500017883.6797 10.9221 7.5000 0.0000 7.500016668.5469 10.9016 -7.5000 7.5000 7.500015378.0615 11.1773 0.0000 7.5000 7.500016562.3438 11.1581 7.5000 7.5000 7.500015491.5166 11.1360 -7.5000 15.0000 7.500014373.4814 11.5283 0.0000 15.0000 7.500015317.1855 11.5017 7.5000 15.0000 7.500014411.2598 11.4733 -7.5000 22.5000 7.500013500.0176 11.9188 0.0000 22.5000 7.500014336.9268 11.8890 7.5000 22.5000 7.500013553.5010 11.8553 -7.5000 30.0000 7.500012602.4639 12.1927 0.0000 30.0000 7.500013379.0430 12.1663 7.5000 30.0000 7.500012675.1895 12.1327 -7.5000 37.5000 7.500012203.0469 12.6403 0.0000 37.5000 7.500012916.8945 12.6212 7.5000 37.5000 7.500012232.0674 12.5937 -7.5000 45.0000 7.500011406.4141 12.8282 0.0000 45.0000 7.500012019.2236 12.8132 7.5000 45.0000 7.500011407.1182 12.7888 -7.5000 -45.0000 15.000013100.5605 11.1862 0.0000 -45.0000 15.000013748.9443 11.1644 7.5000 -45.0000 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12.9557 0.0000 22.5000 52.5000 2508.6958 12.7466 7.5000 22.5000 52.5000 2506.0913 12.7777 -7.5000 30.0000 52.5000 2400.0547 13.6880 0.0000 30.0000 52.5000 2426.0002 13.4412 7.5000 30.0000 52.5000 2427.3252 13.4562 -7.5000 37.5000 52.5000 2305.2764 14.5782 0.0000 37.5000 52.5000 2333.4036 14.3432 7.5000 37.5000 52.5000 2330.5044 14.3605 -7.5000 45.0000 52.5000 2190.0745 15.7372 0.0000 45.0000 52.5000 2217.5437 15.5102 7.5000 45.0000 52.5000 2212.4604 15.5580 --------------------------------------------------------------------- imgreg_4dfp /usr/local/freesurfer/average/711-2C_as_mni_average_305 /usr/local/freesurfer/average/711-2B_as_mni_average_305_mask talsrcimg_g11 none talsrcimg_to_711-2C_as_mni_average_305_t4 1283 --------------------------------------------------------------------- $Id: imgreg_4dfp.c,v 1.3 2007/08/04 04:19:24 nicks Exp $ /usr/local/freesurfer/average/711-2C_as_mni_average_305.4dfp.img 256 256 256 1 1.000000 1.000000 1.000000 orientation T byte_order littleendian Reading image: /usr/local/freesurfer/average/711-2C_as_mni_average_305.4dfp.img dimensions: 256 256 256 mmppix: 1.0000 -1.0000 -1.0000 center: 128.0000 -129.0000 -129.0000 /usr/local/freesurfer/average/711-2B_as_mni_average_305_mask.4dfp.img 256 256 256 1 1.000000 1.000000 1.000000 orientation T byte_order littleendian Reading mask: /usr/local/freesurfer/average/711-2B_as_mni_average_305_mask.4dfp.img (2306576 pixels) talsrcimg_g11.4dfp.img 256 256 256 1 1.000000 1.000000 1.000000 orientation T byte_order littleendian Reading image: talsrcimg_g11.4dfp.img dimensions: 256 256 256 mmppix: 1.0000 -1.0000 -1.0000 center: 128.0000 -129.0000 -129.0000 rotation matrix determinant 1.000000 $Id: fimgreg.f,v 1.1 2007/05/04 22:33:59 nicks Exp $ image alignment mode 1283 decimal 503 hex parameters 0.0000 0.0000 15.0000 0.0000 0.0000 0.0000 eta,q 0.94637 9.88886 niter,ni,del,rscale 5 3 12.0000 1.2000 parameters 1.1845 0.5235 15.1747 -1.8992 1.7760 -1.2424 eta,q 0.94802 9.88727 0.0746 0.0626 0.0609 0.0556 0.0624 0.0553 0.0650 0.0588 0.0565 0.0537 0.0585 0.0532 0.0579 0.0564 0.0542 0.0534 0.0560 0.0521 0.0551 0.0548 0.0543 0.0542 0.0534 0.0522 0.0555 0.0547 0.0557 0.0555 0.0522 0.0537 0.0579 0.0566 0.0571 0.0570 0.0535 0.0561 0.0632 0.0609 0.0590 0.0590 0.0562 0.0594 niter,ni,del,rscale 4 3 12.0000 1.2000 parameters 0.9014 1.0691 14.6805 -1.7404 1.7796 -1.4018 eta,q 0.94878 9.88351 0.0657 0.0635 0.0573 0.0577 0.0583 0.0561 0.0572 0.0590 0.0525 0.0545 0.0554 0.0539 0.0526 0.0550 0.0508 0.0520 0.0526 0.0519 0.0520 0.0519 0.0516 0.0512 0.0512 0.0512 0.0546 0.0525 0.0535 0.0521 0.0524 0.0521 0.0601 0.0561 0.0555 0.0544 0.0550 0.0540 0.0675 0.0607 0.0575 0.0568 0.0586 0.0568 niter,ni,del,rscale 3 3 12.0000 1.2000 parameters 0.8875 1.0094 14.7296 -1.6819 1.7638 -1.4039 eta,q 0.94873 9.88369 0.0666 0.0615 0.0591 0.0575 0.0582 0.0563 0.0579 0.0572 0.0534 0.0543 0.0554 0.0541 0.0527 0.0534 0.0510 0.0519 0.0526 0.0521 0.0512 0.0512 0.0512 0.0513 0.0513 0.0513 0.0533 0.0531 0.0531 0.0523 0.0525 0.0521 0.0588 0.0572 0.0552 0.0546 0.0551 0.0539 0.0661 0.0622 0.0569 0.0569 0.0586 0.0565 registration optimization eta report parameter search radius 6.0000 6.0000 6.0000 6.0000 6.0000 6.0000 100000*second partial in parameter space 42. 28. 19. 16. 19. 14. 0.0666 0.0615 0.0591 0.0575 0.0582 0.0563 0.0579 0.0572 0.0534 0.0543 0.0554 0.0541 0.0527 0.0534 0.0510 0.0519 0.0526 0.0521 0.0512 0.0512 0.0512 0.0513 0.0513 0.0513 0.0533 0.0531 0.0531 0.0523 0.0525 0.0521 0.0588 0.0572 0.0552 0.0546 0.0551 0.0539 0.0661 0.0622 0.0569 0.0569 0.0586 0.0565 0.8875 1.0094 14.7296 -1.6819 1.7638 -1.4039 eta,q 0.94873 9.88369 --------------------------------------------------------------------- imgreg_4dfp /usr/local/freesurfer/average/711-2C_as_mni_average_305 /usr/local/freesurfer/average/711-2B_as_mni_average_305_mask talsrcimg_g11 none talsrcimg_to_711-2C_as_mni_average_305_t4 3335 --------------------------------------------------------------------- $Id: imgreg_4dfp.c,v 1.3 2007/08/04 04:19:24 nicks Exp $ /usr/local/freesurfer/average/711-2C_as_mni_average_305.4dfp.img 256 256 256 1 1.000000 1.000000 1.000000 orientation T byte_order littleendian Reading image: /usr/local/freesurfer/average/711-2C_as_mni_average_305.4dfp.img dimensions: 256 256 256 mmppix: 1.0000 -1.0000 -1.0000 center: 128.0000 -129.0000 -129.0000 /usr/local/freesurfer/average/711-2B_as_mni_average_305_mask.4dfp.img 256 256 256 1 1.000000 1.000000 1.000000 orientation T byte_order littleendian Reading mask: /usr/local/freesurfer/average/711-2B_as_mni_average_305_mask.4dfp.img (2306576 pixels) talsrcimg_g11.4dfp.img 256 256 256 1 1.000000 1.000000 1.000000 orientation T byte_order littleendian Reading image: talsrcimg_g11.4dfp.img dimensions: 256 256 256 mmppix: 1.0000 -1.0000 -1.0000 center: 128.0000 -129.0000 -129.0000 $Id: fimgreg.f,v 1.1 2007/05/04 22:33:59 nicks Exp $ image alignment mode 3335 decimal D07 hex parameters 0.8875 1.0094 14.7296 -0.0774 -0.0753 -0.0904 2.5392 -3.0037 -2.4488 3.0095 3.0779 -2.9336 eta,q 0.94992 9.89146 niter,ni,del,rscale 5 3 5.0000 1.2000 parameter 4 0.556656 -> 0.500000 qaram 1.1500 parameter 5 2.589555 -> 0.500000 qaram 1.1500 parameter 6 2.130325 -> 0.500000 qaram 1.1500 parameter 10 0.503611 -> 0.500000 qaram 1.1500 parameter 12 0.952960 -> 0.500000 qaram 1.1500 parameters 1.0532 1.2549 14.9244 -4.2174 -4.2153 -4.2304 2.9438 -1.1261 -2.1022 -1.1305 3.6894 -7.0736 eta,q 0.96247 9.51338 0.0534 0.0522 0.0520 0.0498 0.0446 0.0373 0.0429 0.0463 0.0415 0.0398 0.0405 0.0375 0.0517 0.0511 0.0509 0.0494 0.0457 0.0392 0.0415 0.0436 0.0405 0.0388 0.0396 0.0374 0.0506 0.0504 0.0503 0.0495 0.0474 0.0424 0.0404 0.0414 0.0399 0.0388 0.0390 0.0379 0.0501 0.0501 0.0500 0.0500 0.0494 0.0462 0.0400 0.0400 0.0396 0.0396 0.0387 0.0387 0.0503 0.0501 0.0501 0.0511 0.0516 0.0506 0.0402 0.0397 0.0398 0.0412 0.0388 0.0399 0.0511 0.0506 0.0506 0.0528 0.0540 0.0557 0.0410 0.0404 0.0403 0.0433 0.0392 0.0414 0.0526 0.0515 0.0514 0.0549 0.0565 0.0606 0.0424 0.0422 0.0412 0.0457 0.0400 0.0430 niter,ni,del,rscale 7 3 5.0000 1.2000 parameter 5 0.988317 -> 0.500000 qaram 1.3225 parameter 6 0.651207 -> 0.500000 qaram 1.3225 parameters 1.0447 1.4802 15.0407 -3.5808 -8.9763 -8.9914 2.9454 -1.1547 -2.4076 0.5983 4.3924 -7.6116 eta,q 0.96701 9.17416 0.0410 0.0408 0.0403 0.0409 0.0349 0.0334 0.0361 0.0375 0.0351 0.0389 0.0345 0.0349 0.0391 0.0392 0.0388 0.0393 0.0349 0.0332 0.0346 0.0352 0.0340 0.0362 0.0336 0.0338 0.0379 0.0381 0.0379 0.0381 0.0357 0.0334 0.0335 0.0337 0.0334 0.0342 0.0332 0.0331 0.0375 0.0375 0.0375 0.0375 0.0374 0.0351 0.0332 0.0332 0.0332 0.0332 0.0330 0.0330 0.0379 0.0377 0.0377 0.0375 0.0398 0.0389 0.0335 0.0336 0.0335 0.0331 0.0330 0.0333 0.0391 0.0385 0.0385 0.0384 0.0425 0.0436 0.0345 0.0351 0.0343 0.0339 0.0333 0.0342 0.0410 0.0398 0.0398 0.0403 0.0455 0.0495 0.0361 0.0377 0.0354 0.0356 0.0340 0.0354 niter,ni,del,rscale 7 3 5.0000 1.2000 parameters 1.2086 1.9936 13.9428 -1.8732 -11.5549 -12.2500 2.8956 -0.9514 -3.0066 1.2908 4.7932 -7.9452 eta,q 0.96801 8.95341 0.0368 0.0369 0.0331 0.0356 0.0337 0.0335 0.0346 0.0361 0.0334 0.0358 0.0331 0.0340 0.0348 0.0350 0.0324 0.0342 0.0326 0.0323 0.0332 0.0340 0.0325 0.0336 0.0325 0.0329 0.0335 0.0337 0.0324 0.0331 0.0320 0.0320 0.0323 0.0325 0.0321 0.0324 0.0321 0.0322 0.0330 0.0330 0.0328 0.0323 0.0320 0.0319 0.0320 0.0320 0.0320 0.0320 0.0320 0.0320 0.0332 0.0329 0.0337 0.0320 0.0331 0.0334 0.0323 0.0322 0.0322 0.0323 0.0321 0.0323 0.0341 0.0334 0.0349 0.0324 0.0352 0.0374 0.0333 0.0335 0.0329 0.0331 0.0324 0.0331 0.0359 0.0345 0.0364 0.0339 0.0380 0.0428 0.0347 0.0358 0.0339 0.0345 0.0329 0.0343 niter,ni,del,rscale 6 3 5.0000 1.2000 parameters 1.3065 2.6845 13.4179 -2.3194 -13.0281 -13.7185 2.6352 -0.7822 -3.8758 2.7393 5.4375 -8.0999 eta,q 0.96841 8.78323 0.0354 0.0358 0.0328 0.0333 0.0336 0.0345 0.0340 0.0354 0.0328 0.0354 0.0327 0.0336 0.0336 0.0340 0.0320 0.0324 0.0326 0.0326 0.0327 0.0335 0.0321 0.0335 0.0321 0.0325 0.0324 0.0328 0.0316 0.0319 0.0319 0.0317 0.0319 0.0322 0.0317 0.0322 0.0317 0.0318 0.0320 0.0320 0.0317 0.0316 0.0317 0.0317 0.0317 0.0317 0.0317 0.0316 0.0316 0.0316 0.0322 0.0317 0.0322 0.0316 0.0322 0.0320 0.0321 0.0319 0.0320 0.0317 0.0317 0.0319 0.0332 0.0321 0.0331 0.0324 0.0336 0.0340 0.0330 0.0331 0.0326 0.0323 0.0319 0.0326 0.0349 0.0330 0.0342 0.0341 0.0357 0.0381 0.0344 0.0352 0.0334 0.0334 0.0324 0.0337 niter,ni,del,rscale 5 3 5.0000 1.2000 parameters 1.3867 3.3298 13.0295 -3.3639 -15.2464 -14.9666 2.2137 -0.5952 -5.0176 4.5826 5.7229 -8.1038 eta,q 0.96901 8.56016 0.0348 0.0351 0.0326 0.0326 0.0326 0.0343 0.0334 0.0349 0.0322 0.0350 0.0320 0.0330 0.0331 0.0334 0.0318 0.0318 0.0318 0.0323 0.0322 0.0330 0.0315 0.0332 0.0314 0.0319 0.0320 0.0323 0.0314 0.0315 0.0314 0.0312 0.0314 0.0317 0.0311 0.0319 0.0311 0.0312 0.0316 0.0316 0.0314 0.0314 0.0314 0.0314 0.0312 0.0312 0.0312 0.0311 0.0310 0.0310 0.0318 0.0314 0.0318 0.0315 0.0319 0.0318 0.0317 0.0315 0.0316 0.0310 0.0311 0.0312 0.0328 0.0318 0.0326 0.0322 0.0332 0.0334 0.0326 0.0327 0.0322 0.0316 0.0314 0.0320 0.0345 0.0327 0.0337 0.0337 0.0352 0.0370 0.0339 0.0346 0.0329 0.0327 0.0318 0.0329 niter,ni,del,rscale 4 3 5.0000 1.2000 parameters 1.4502 4.1496 12.5872 -4.7687 -17.9612 -16.3426 2.1782 -0.7188 -4.7261 6.4274 4.2644 -7.9293 eta,q 0.97011 8.29586 0.0341 0.0347 0.0318 0.0317 0.0316 0.0333 0.0326 0.0337 0.0319 0.0346 0.0306 0.0319 0.0324 0.0330 0.0311 0.0309 0.0307 0.0314 0.0314 0.0319 0.0310 0.0327 0.0301 0.0309 0.0314 0.0317 0.0307 0.0306 0.0304 0.0303 0.0305 0.0306 0.0304 0.0312 0.0299 0.0302 0.0310 0.0310 0.0307 0.0307 0.0306 0.0304 0.0302 0.0302 0.0302 0.0302 0.0300 0.0299 0.0313 0.0307 0.0311 0.0310 0.0313 0.0312 0.0305 0.0307 0.0304 0.0300 0.0302 0.0301 0.0322 0.0310 0.0319 0.0316 0.0325 0.0327 0.0314 0.0320 0.0308 0.0307 0.0307 0.0308 0.0338 0.0317 0.0330 0.0329 0.0343 0.0361 0.0327 0.0340 0.0316 0.0320 0.0313 0.0317 niter,ni,del,rscale 3 3 5.0000 1.2000 parameters 1.3579 4.9270 12.0846 -5.8877 -19.3345 -17.4738 2.4767 -0.9740 -3.7689 7.5594 3.3331 -7.9866 eta,q 0.97097 8.13031 0.0326 0.0337 0.0306 0.0309 0.0314 0.0326 0.0319 0.0327 0.0317 0.0336 0.0300 0.0309 0.0311 0.0320 0.0300 0.0299 0.0301 0.0306 0.0306 0.0308 0.0305 0.0315 0.0294 0.0299 0.0302 0.0307 0.0296 0.0294 0.0294 0.0294 0.0296 0.0296 0.0296 0.0300 0.0291 0.0292 0.0299 0.0299 0.0296 0.0296 0.0295 0.0294 0.0292 0.0292 0.0292 0.0292 0.0291 0.0290 0.0303 0.0296 0.0301 0.0300 0.0301 0.0303 0.0294 0.0298 0.0293 0.0292 0.0294 0.0293 0.0314 0.0299 0.0309 0.0306 0.0312 0.0318 0.0302 0.0312 0.0298 0.0301 0.0298 0.0299 0.0331 0.0307 0.0321 0.0317 0.0328 0.0347 0.0316 0.0332 0.0307 0.0318 0.0305 0.0309 niter,ni,del,rscale 2 3 5.0000 1.2000 parameters 1.2400 5.3093 11.7513 -6.1369 -19.6788 -18.0413 2.5519 -1.0633 -3.4138 8.0683 3.1457 -8.1256 eta,q 0.97117 8.08061 0.0318 0.0322 0.0302 0.0310 0.0316 0.0326 0.0314 0.0326 0.0312 0.0328 0.0300 0.0306 0.0302 0.0306 0.0295 0.0298 0.0301 0.0306 0.0302 0.0307 0.0299 0.0309 0.0293 0.0296 0.0293 0.0295 0.0290 0.0290 0.0292 0.0292 0.0292 0.0293 0.0292 0.0295 0.0289 0.0290 0.0290 0.0290 0.0290 0.0289 0.0289 0.0289 0.0289 0.0289 0.0289 0.0289 0.0288 0.0288 0.0295 0.0291 0.0293 0.0295 0.0294 0.0297 0.0291 0.0294 0.0290 0.0291 0.0290 0.0291 0.0306 0.0296 0.0301 0.0301 0.0304 0.0311 0.0300 0.0308 0.0297 0.0302 0.0295 0.0297 0.0324 0.0306 0.0311 0.0310 0.0320 0.0337 0.0314 0.0328 0.0307 0.0320 0.0301 0.0307 niter,ni,del,rscale 1 3 5.0000 1.2000 parameters 1.2180 5.4767 11.5760 -6.1733 -19.7687 -18.3179 2.5581 -1.0806 -3.3426 8.3174 3.1095 -8.1976 eta,q 0.97121 8.06485 0.0319 0.0315 0.0302 0.0311 0.0317 0.0328 0.0313 0.0326 0.0309 0.0326 0.0300 0.0305 0.0302 0.0301 0.0294 0.0298 0.0301 0.0307 0.0301 0.0307 0.0298 0.0306 0.0293 0.0296 0.0292 0.0292 0.0290 0.0290 0.0291 0.0292 0.0291 0.0293 0.0290 0.0293 0.0289 0.0290 0.0288 0.0288 0.0288 0.0288 0.0288 0.0288 0.0288 0.0288 0.0288 0.0288 0.0288 0.0288 0.0292 0.0290 0.0291 0.0293 0.0292 0.0296 0.0291 0.0293 0.0290 0.0291 0.0290 0.0290 0.0303 0.0297 0.0297 0.0300 0.0302 0.0309 0.0300 0.0306 0.0298 0.0303 0.0294 0.0296 0.0320 0.0308 0.0308 0.0308 0.0317 0.0333 0.0314 0.0327 0.0308 0.0322 0.0300 0.0306 registration optimization eta report parameter search radius 2.4000 2.4000 2.4000 8.2800 9.5220 9.5220 7.2000 7.2000 7.2000 8.2800 7.2000 8.2800 100000*second partial in parameter space 53. 41. 29. 3. 3. 5. 5. 7. 4. 5. 2. 3. 0.0319 0.0315 0.0302 0.0311 0.0317 0.0328 0.0313 0.0326 0.0309 0.0326 0.0300 0.0305 0.0302 0.0301 0.0294 0.0298 0.0301 0.0307 0.0301 0.0307 0.0298 0.0306 0.0293 0.0296 0.0292 0.0292 0.0290 0.0290 0.0291 0.0292 0.0291 0.0293 0.0290 0.0293 0.0289 0.0290 0.0288 0.0288 0.0288 0.0288 0.0288 0.0288 0.0288 0.0288 0.0288 0.0288 0.0288 0.0288 0.0292 0.0290 0.0291 0.0293 0.0292 0.0296 0.0291 0.0293 0.0290 0.0291 0.0290 0.0290 0.0303 0.0297 0.0297 0.0300 0.0302 0.0309 0.0300 0.0306 0.0298 0.0303 0.0294 0.0296 0.0320 0.0308 0.0308 0.0308 0.0317 0.0333 0.0314 0.0327 0.0308 0.0322 0.0300 0.0306 1.2180 5.4767 11.5760 -6.1733 -19.7687 -18.3179 2.5581 -1.0806 -3.3426 8.3174 3.1095 -8.1976 eta,q 0.97121 8.06485 --------------------------------------------------------------------- imgreg_4dfp /usr/local/freesurfer/average/711-2C_as_mni_average_305 /usr/local/freesurfer/average/711-2B_as_mni_average_305_mask talsrcimg_g11 none talsrcimg_to_711-2C_as_mni_average_305_t4 2311 --------------------------------------------------------------------- $Id: imgreg_4dfp.c,v 1.3 2007/08/04 04:19:24 nicks Exp $ /usr/local/freesurfer/average/711-2C_as_mni_average_305.4dfp.img 256 256 256 1 1.000000 1.000000 1.000000 orientation T byte_order littleendian Reading image: /usr/local/freesurfer/average/711-2C_as_mni_average_305.4dfp.img dimensions: 256 256 256 mmppix: 1.0000 -1.0000 -1.0000 center: 128.0000 -129.0000 -129.0000 /usr/local/freesurfer/average/711-2B_as_mni_average_305_mask.4dfp.img 256 256 256 1 1.000000 1.000000 1.000000 orientation T byte_order littleendian Reading mask: /usr/local/freesurfer/average/711-2B_as_mni_average_305_mask.4dfp.img (2306576 pixels) talsrcimg_g11.4dfp.img 256 256 256 1 1.000000 1.000000 1.000000 orientation T byte_order littleendian Reading image: talsrcimg_g11.4dfp.img dimensions: 256 256 256 mmppix: 1.0000 -1.0000 -1.0000 center: 128.0000 -129.0000 -129.0000 $Id: fimgreg.f,v 1.1 2007/05/04 22:33:59 nicks Exp $ image alignment mode 2311 decimal 907 hex parameters 1.2180 5.4767 11.5760 -6.1733 -19.7687 -18.3179 2.5581 -1.0806 -3.3426 8.3174 3.1095 -8.1976 eta,q 0.97121 8.06485 niter,ni,del,rscale 5 3 5.0000 0.8000 parameters 1.2210 5.5201 11.5193 -6.7224 -19.8831 -18.5261 2.6606 -1.0935 -3.4033 8.4140 3.0365 -8.2195 eta,q 0.97126 8.02988 0.0302 0.0299 0.0295 0.0295 0.0296 0.0299 0.0300 0.0306 0.0297 0.0301 0.0293 0.0294 0.0294 0.0293 0.0291 0.0290 0.0291 0.0292 0.0294 0.0296 0.0292 0.0293 0.0290 0.0290 0.0290 0.0289 0.0289 0.0288 0.0288 0.0288 0.0289 0.0289 0.0288 0.0289 0.0288 0.0288 0.0288 0.0288 0.0288 0.0288 0.0288 0.0288 0.0287 0.0288 0.0287 0.0287 0.0287 0.0287 0.0290 0.0289 0.0289 0.0290 0.0289 0.0290 0.0289 0.0290 0.0289 0.0289 0.0288 0.0288 0.0294 0.0292 0.0292 0.0294 0.0292 0.0295 0.0293 0.0296 0.0292 0.0293 0.0290 0.0290 0.0302 0.0298 0.0296 0.0298 0.0296 0.0300 0.0299 0.0306 0.0297 0.0300 0.0293 0.0294 niter,ni,del,rscale 4 3 5.0000 0.7000 parameters 1.2157 5.5420 11.4643 -6.8102 -19.9091 -18.6739 2.6917 -1.0960 -3.4009 8.4814 3.0117 -8.2141 eta,q 0.97127 8.01995 0.0298 0.0296 0.0293 0.0295 0.0294 0.0297 0.0297 0.0302 0.0295 0.0297 0.0292 0.0292 0.0292 0.0291 0.0290 0.0291 0.0290 0.0292 0.0292 0.0294 0.0291 0.0292 0.0289 0.0289 0.0289 0.0288 0.0288 0.0288 0.0288 0.0288 0.0289 0.0289 0.0288 0.0289 0.0288 0.0288 0.0287 0.0287 0.0287 0.0287 0.0287 0.0287 0.0287 0.0287 0.0287 0.0287 0.0287 0.0287 0.0289 0.0288 0.0288 0.0289 0.0288 0.0289 0.0289 0.0289 0.0288 0.0288 0.0288 0.0288 0.0292 0.0291 0.0290 0.0292 0.0290 0.0293 0.0292 0.0294 0.0291 0.0291 0.0290 0.0289 0.0299 0.0295 0.0294 0.0295 0.0294 0.0297 0.0297 0.0302 0.0295 0.0297 0.0292 0.0292 niter,ni,del,rscale 3 3 5.0000 0.6000 parameters 1.2172 5.5603 11.4219 -6.8576 -19.9306 -18.8055 2.6979 -1.1018 -3.3932 8.5361 2.9857 -8.2117 eta,q 0.97127 8.01256 0.0296 0.0293 0.0291 0.0293 0.0292 0.0295 0.0295 0.0298 0.0293 0.0295 0.0291 0.0291 0.0291 0.0290 0.0289 0.0290 0.0289 0.0291 0.0291 0.0292 0.0290 0.0291 0.0289 0.0289 0.0288 0.0288 0.0288 0.0288 0.0288 0.0288 0.0288 0.0288 0.0288 0.0288 0.0288 0.0288 0.0287 0.0287 0.0287 0.0287 0.0287 0.0287 0.0287 0.0287 0.0287 0.0287 0.0287 0.0287 0.0288 0.0288 0.0288 0.0288 0.0288 0.0289 0.0288 0.0289 0.0288 0.0288 0.0288 0.0288 0.0291 0.0290 0.0289 0.0290 0.0290 0.0292 0.0291 0.0292 0.0290 0.0290 0.0289 0.0289 0.0295 0.0293 0.0292 0.0293 0.0292 0.0295 0.0294 0.0298 0.0293 0.0294 0.0291 0.0291 niter,ni,del,rscale 2 3 5.0000 0.5000 parameters 1.2202 5.5724 11.3919 -6.8842 -19.9535 -18.9093 2.6829 -1.1111 -3.3947 8.5726 2.9726 -8.1886 eta,q 0.97127 8.00695 0.0293 0.0292 0.0290 0.0292 0.0291 0.0293 0.0292 0.0295 0.0291 0.0292 0.0290 0.0290 0.0290 0.0289 0.0289 0.0289 0.0289 0.0290 0.0290 0.0291 0.0289 0.0290 0.0288 0.0288 0.0288 0.0288 0.0288 0.0288 0.0288 0.0288 0.0288 0.0288 0.0288 0.0288 0.0288 0.0288 0.0287 0.0287 0.0287 0.0287 0.0287 0.0287 0.0287 0.0287 0.0287 0.0287 0.0287 0.0287 0.0288 0.0288 0.0288 0.0288 0.0288 0.0288 0.0288 0.0288 0.0288 0.0288 0.0288 0.0288 0.0290 0.0289 0.0289 0.0289 0.0289 0.0290 0.0290 0.0291 0.0289 0.0289 0.0288 0.0288 0.0293 0.0291 0.0290 0.0292 0.0291 0.0293 0.0292 0.0295 0.0291 0.0292 0.0290 0.0290 niter,ni,del,rscale 1 3 5.0000 0.4000 parameters 1.2237 5.5822 11.3749 -6.9018 -19.9792 -18.9729 2.6675 -1.1397 -3.3886 8.5958 2.9531 -8.1813 eta,q 0.97127 8.00308 0.0291 0.0290 0.0289 0.0290 0.0289 0.0291 0.0291 0.0292 0.0290 0.0290 0.0289 0.0289 0.0289 0.0288 0.0288 0.0288 0.0288 0.0289 0.0289 0.0289 0.0288 0.0289 0.0288 0.0288 0.0288 0.0288 0.0287 0.0288 0.0287 0.0288 0.0288 0.0288 0.0288 0.0288 0.0287 0.0287 0.0287 0.0287 0.0287 0.0287 0.0287 0.0287 0.0287 0.0287 0.0287 0.0287 0.0287 0.0287 0.0288 0.0288 0.0288 0.0288 0.0288 0.0288 0.0288 0.0288 0.0288 0.0288 0.0287 0.0287 0.0289 0.0288 0.0288 0.0289 0.0288 0.0289 0.0289 0.0290 0.0288 0.0289 0.0288 0.0288 0.0291 0.0290 0.0289 0.0290 0.0289 0.0291 0.0291 0.0292 0.0290 0.0290 0.0289 0.0289 registration optimization eta report parameter search radius 0.8000 0.8000 0.8000 2.4000 2.4000 2.4000 2.4000 2.4000 2.4000 2.4000 2.4000 2.4000 100000*second partial in parameter space 57. 41. 30. 5. 4. 7. 6. 9. 4. 5. 3. 3. 0.0291 0.0290 0.0289 0.0290 0.0289 0.0291 0.0291 0.0292 0.0290 0.0290 0.0289 0.0289 0.0289 0.0288 0.0288 0.0288 0.0288 0.0289 0.0289 0.0289 0.0288 0.0289 0.0288 0.0288 0.0288 0.0288 0.0287 0.0288 0.0287 0.0288 0.0288 0.0288 0.0288 0.0288 0.0287 0.0287 0.0287 0.0287 0.0287 0.0287 0.0287 0.0287 0.0287 0.0287 0.0287 0.0287 0.0287 0.0287 0.0288 0.0288 0.0288 0.0288 0.0288 0.0288 0.0288 0.0288 0.0288 0.0288 0.0287 0.0287 0.0289 0.0288 0.0288 0.0289 0.0288 0.0289 0.0289 0.0290 0.0288 0.0289 0.0288 0.0288 0.0291 0.0290 0.0289 0.0290 0.0289 0.0291 0.0291 0.0292 0.0290 0.0290 0.0289 0.0289 1.2237 5.5822 11.3749 -6.9018 -19.9792 -18.9729 2.6675 -1.1397 -3.3886 8.5958 2.9531 -8.1813 eta,q 0.97127 8.00308 --------------------------------------------------------------------- imgreg_4dfp /usr/local/freesurfer/average/711-2C_as_mni_average_305 /usr/local/freesurfer/average/711-2B_as_mni_average_305_mask talsrcimg_g11 none talsrcimg_to_711-2C_as_mni_average_305_t4 2311 --------------------------------------------------------------------- $Id: imgreg_4dfp.c,v 1.3 2007/08/04 04:19:24 nicks Exp $ /usr/local/freesurfer/average/711-2C_as_mni_average_305.4dfp.img 256 256 256 1 1.000000 1.000000 1.000000 orientation T byte_order littleendian Reading image: /usr/local/freesurfer/average/711-2C_as_mni_average_305.4dfp.img dimensions: 256 256 256 mmppix: 1.0000 -1.0000 -1.0000 center: 128.0000 -129.0000 -129.0000 /usr/local/freesurfer/average/711-2B_as_mni_average_305_mask.4dfp.img 256 256 256 1 1.000000 1.000000 1.000000 orientation T byte_order littleendian Reading mask: /usr/local/freesurfer/average/711-2B_as_mni_average_305_mask.4dfp.img (2306576 pixels) talsrcimg_g11.4dfp.img 256 256 256 1 1.000000 1.000000 1.000000 orientation T byte_order littleendian Reading image: talsrcimg_g11.4dfp.img dimensions: 256 256 256 mmppix: 1.0000 -1.0000 -1.0000 center: 128.0000 -129.0000 -129.0000 $Id: fimgreg.f,v 1.1 2007/05/04 22:33:59 nicks Exp $ image alignment mode 2311 decimal 907 hex parameters 1.2237 5.5822 11.3749 -6.9018 -19.9792 -18.9729 2.6675 -1.1397 -3.3886 8.5958 2.9531 -8.1813 eta,q 0.97127 8.00308 niter,ni,del,rscale 5 3 5.0000 0.8000 parameters 1.2195 5.6118 11.3303 -6.7301 -19.9088 -18.8445 2.6798 -1.0689 -3.3693 8.5866 3.0017 -8.2275 eta,q 0.97126 8.01666 0.0301 0.0298 0.0294 0.0298 0.0296 0.0301 0.0300 0.0307 0.0297 0.0300 0.0293 0.0293 0.0294 0.0292 0.0290 0.0292 0.0291 0.0294 0.0293 0.0296 0.0292 0.0293 0.0290 0.0290 0.0289 0.0288 0.0288 0.0289 0.0288 0.0289 0.0289 0.0290 0.0288 0.0289 0.0288 0.0288 0.0287 0.0287 0.0287 0.0287 0.0287 0.0287 0.0287 0.0287 0.0287 0.0287 0.0287 0.0287 0.0289 0.0288 0.0288 0.0289 0.0288 0.0289 0.0289 0.0290 0.0288 0.0289 0.0288 0.0288 0.0294 0.0292 0.0291 0.0292 0.0291 0.0294 0.0293 0.0296 0.0292 0.0293 0.0290 0.0290 0.0302 0.0297 0.0295 0.0296 0.0295 0.0299 0.0300 0.0305 0.0297 0.0300 0.0293 0.0294 niter,ni,del,rscale 4 3 5.0000 0.7000 parameters 1.2242 5.6100 11.3642 -6.7868 -19.9331 -18.8421 2.6836 -1.0786 -3.3837 8.5887 2.9794 -8.2312 eta,q 0.97127 8.01385 0.0298 0.0295 0.0293 0.0295 0.0294 0.0298 0.0297 0.0302 0.0295 0.0297 0.0292 0.0292 0.0292 0.0291 0.0290 0.0291 0.0290 0.0292 0.0292 0.0294 0.0291 0.0292 0.0289 0.0289 0.0289 0.0288 0.0288 0.0288 0.0288 0.0288 0.0288 0.0289 0.0288 0.0288 0.0288 0.0288 0.0287 0.0287 0.0287 0.0287 0.0287 0.0287 0.0287 0.0287 0.0287 0.0287 0.0287 0.0287 0.0289 0.0288 0.0288 0.0289 0.0288 0.0289 0.0289 0.0289 0.0288 0.0288 0.0288 0.0288 0.0292 0.0291 0.0290 0.0291 0.0290 0.0293 0.0292 0.0294 0.0291 0.0292 0.0289 0.0289 0.0298 0.0295 0.0293 0.0295 0.0294 0.0297 0.0297 0.0302 0.0295 0.0297 0.0292 0.0292 niter,ni,del,rscale 3 3 5.0000 0.6000 parameters 1.2230 5.5972 11.3721 -6.8313 -19.9474 -18.8923 2.6918 -1.0945 -3.3884 8.6007 2.9745 -8.2212 eta,q 0.97127 8.01000 0.0295 0.0293 0.0292 0.0293 0.0292 0.0295 0.0294 0.0298 0.0293 0.0294 0.0291 0.0291 0.0291 0.0290 0.0289 0.0290 0.0289 0.0291 0.0291 0.0292 0.0290 0.0290 0.0289 0.0289 0.0288 0.0288 0.0288 0.0288 0.0288 0.0288 0.0288 0.0288 0.0288 0.0288 0.0288 0.0288 0.0287 0.0287 0.0287 0.0287 0.0287 0.0287 0.0287 0.0287 0.0287 0.0287 0.0287 0.0287 0.0288 0.0288 0.0288 0.0288 0.0288 0.0289 0.0288 0.0289 0.0288 0.0288 0.0288 0.0288 0.0291 0.0290 0.0289 0.0290 0.0290 0.0292 0.0291 0.0292 0.0290 0.0290 0.0289 0.0289 0.0295 0.0293 0.0292 0.0293 0.0292 0.0295 0.0294 0.0298 0.0293 0.0294 0.0291 0.0291 niter,ni,del,rscale 2 3 5.0000 0.5000 parameters 1.2248 5.5933 11.3626 -6.8739 -19.9620 -18.9512 2.6829 -1.1068 -3.3956 8.6098 2.9662 -8.1954 eta,q 0.97127 8.00564 0.0293 0.0291 0.0290 0.0292 0.0291 0.0293 0.0292 0.0295 0.0291 0.0292 0.0290 0.0290 0.0290 0.0289 0.0289 0.0289 0.0289 0.0290 0.0290 0.0291 0.0289 0.0289 0.0288 0.0288 0.0288 0.0288 0.0288 0.0288 0.0288 0.0288 0.0288 0.0288 0.0288 0.0288 0.0288 0.0288 0.0287 0.0287 0.0287 0.0287 0.0287 0.0287 0.0287 0.0287 0.0287 0.0287 0.0287 0.0287 0.0288 0.0288 0.0288 0.0288 0.0288 0.0288 0.0288 0.0288 0.0288 0.0288 0.0288 0.0287 0.0290 0.0289 0.0289 0.0289 0.0289 0.0290 0.0290 0.0291 0.0289 0.0289 0.0288 0.0288 0.0293 0.0291 0.0290 0.0292 0.0291 0.0293 0.0292 0.0295 0.0291 0.0292 0.0290 0.0290 niter,ni,del,rscale 1 3 5.0000 0.4000 parameters 1.2279 5.5953 11.3528 -6.9006 -19.9813 -19.0093 2.6658 -1.1360 -3.3899 8.6211 2.9540 -8.1788 eta,q 0.97127 8.00181 0.0291 0.0290 0.0289 0.0290 0.0289 0.0291 0.0291 0.0292 0.0290 0.0290 0.0289 0.0289 0.0289 0.0288 0.0288 0.0289 0.0288 0.0289 0.0289 0.0289 0.0288 0.0289 0.0288 0.0288 0.0288 0.0288 0.0287 0.0288 0.0287 0.0288 0.0288 0.0288 0.0288 0.0288 0.0287 0.0287 0.0287 0.0287 0.0287 0.0287 0.0287 0.0287 0.0287 0.0287 0.0287 0.0287 0.0287 0.0287 0.0288 0.0288 0.0288 0.0288 0.0288 0.0288 0.0288 0.0288 0.0288 0.0288 0.0288 0.0287 0.0289 0.0288 0.0288 0.0289 0.0288 0.0289 0.0289 0.0290 0.0288 0.0289 0.0288 0.0288 0.0291 0.0290 0.0289 0.0290 0.0289 0.0291 0.0291 0.0292 0.0290 0.0290 0.0289 0.0289 registration optimization eta report parameter search radius 0.8000 0.8000 0.8000 2.4000 2.4000 2.4000 2.4000 2.4000 2.4000 2.4000 2.4000 2.4000 100000*second partial in parameter space 56. 40. 30. 5. 4. 7. 6. 9. 4. 5. 3. 3. 0.0291 0.0290 0.0289 0.0290 0.0289 0.0291 0.0291 0.0292 0.0290 0.0290 0.0289 0.0289 0.0289 0.0288 0.0288 0.0289 0.0288 0.0289 0.0289 0.0289 0.0288 0.0289 0.0288 0.0288 0.0288 0.0288 0.0287 0.0288 0.0287 0.0288 0.0288 0.0288 0.0288 0.0288 0.0287 0.0287 0.0287 0.0287 0.0287 0.0287 0.0287 0.0287 0.0287 0.0287 0.0287 0.0287 0.0287 0.0287 0.0288 0.0288 0.0288 0.0288 0.0288 0.0288 0.0288 0.0288 0.0288 0.0288 0.0288 0.0287 0.0289 0.0288 0.0288 0.0289 0.0288 0.0289 0.0289 0.0290 0.0288 0.0289 0.0288 0.0288 0.0291 0.0290 0.0289 0.0290 0.0289 0.0291 0.0291 0.0292 0.0290 0.0290 0.0289 0.0289 1.2279 5.5953 11.3528 -6.9006 -19.9813 -19.0093 2.6658 -1.1360 -3.3899 8.6211 2.9540 -8.1788 eta,q 0.97127 8.00181 --------------------------------------------------------------------- compute_vox2vox talsrcimg talsrcimg_to_711-2C_as_mni_average_305_t4 /usr/local/freesurfer/average/711-2C_as_mni_average_305 --------------------------------------------------------------------- $Id: compute_vox2vox.c,v 1.2 2007/05/05 00:00:06 nicks Exp $ Reading: talsrcimg.4dfp.ifh Reading: talsrcimg_to_711-2C_as_mni_average_305_t4 Reading: /usr/local/freesurfer/average/711-2C_as_mni_average_305.4dfp.ifh Writing: talsrcimg_to_711-2C_as_mni_average_305_t4_vox2vox.txt start time Wed Sep 9 13:31:58 CST 2009 end time Wed Sep 9 13:32:55 CST 2009 mpr2mni305 success -------------------------------------------- tkregister2_cmdl --mov nu.mgz --targ /usr/local/freesurfer/average/mni305.cor.mgz --xfmout transforms/talairach.auto.xfm --vox2vox talsrcimg_to_711-2C_as_mni_average_305_t4_vox2vox.txt --noedit --reg talsrcimg.reg.tmp.dat tkregister_tcl /usr/local/freesurfer/lib/tcl/tkregister2.tcl Vox2Vox Matrix 0.931 0.027 0.011 2.750; -0.034 0.800 -0.086 35.269; -0.030 0.082 0.810 28.807; 0.000 0.000 0.000 1.000; target volume /usr/local/freesurfer/average/mni305.cor.mgz movable volume nu.mgz reg file talsrcimg.reg.tmp.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.86.2.12 2009/03/19 22:04:20 greve Exp $ Diagnostic Level -1 INFO: loading target /usr/local/freesurfer/average/mni305.cor.mgz Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable nu.mgz Tmov: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) -------- 0.931 -0.011 0.027 1.217; 0.030 0.810 -0.082 11.163; -0.034 0.086 0.800 5.682; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 0.931 -0.011 0.027 1.217; 0.030 0.810 -0.082 11.163; -0.034 0.086 0.800 5.682; 0.000 0.000 0.000 1.000; Determinant 0.610957 subject = subject-unknown RegMat --------------------------- 0.931 -0.011 0.027 1.217; 0.030 0.810 -0.082 11.163; -0.034 0.086 0.800 5.682; 0.000 0.000 0.000 1.000; register: file talsrcimg.reg.tmp.dat written `talsrcimg_to_711-2C_as_mni_average_305_t4_vox2vox.txt' -> `transforms/talsrcimg_to_711-2C_as_mni_average_305_t4_vox2vox.txt' removed `talsrcimg.4dfp.hdr' removed `talsrcimg.4dfp.ifh' removed `talsrcimg.4dfp.img' removed `talsrcimg.4dfp.img.rec' removed `talsrcimg.hdr' removed `talsrcimg.img' removed `talsrcimg.mat' removed `talsrcimg.reg.tmp.dat' removed `talsrcimg_g11.4dfp.hdr' removed `talsrcimg_g11.4dfp.ifh' removed `talsrcimg_g11.4dfp.img' removed `talsrcimg_g11.4dfp.img.rec' removed `talsrcimg_to_711-2C_as_mni_average_305_t4' -------------------------------------------- Wed Sep 9 13:32:57 CST 2009 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Wed Sep 9 13:32:58 CST 2009 /usr/local/freesurfer/subjects/am03/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7921, pval=0.8469 >= threshold=0.0050) awk -f /usr/local/freesurfer/bin/extract_talairach_avi_QA.awk /usr/local/freesurfer/subjects/am03/mri/transforms/talairach_avi.log TalAviQA: 0.97127 z-score: -1 #-------------------------------------------- #@# Intensity Normalization Wed Sep 9 13:32:58 CST 2009 /usr/local/freesurfer/subjects/am03/mri mri_normalize -g 1 nu.mgz T1.mgz using max gradient = 1.000 reading from nu.mgz... normalizing image... talairach transform 1.072 0.019 -0.034 -2.664; -0.034 1.221 0.126 -33.087; 0.049 -0.131 1.235 -18.052; 0.000 0.000 0.000 1.000; INFO: Modifying talairach volume c_(r,a,s) based on average_305 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 1 of 2 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 2 of 2 building Voronoi diagram... performing soap bubble smoothing... writing output to T1.mgz 3D bias adjustment took 4 minutes and 37 seconds. MRIsplineNormalize(): npeaks = 14 Starting OpenSpline(): npoints = 14 white matter peak found at 111 gm peak at 63 (63), valley at 36 (36) csf peak at 32, setting threshold to 52 white matter peak found at 111 gm peak at 64 (64), valley at 37 (37) csf peak at 32, setting threshold to 53 #-------------------------------------------- #@# Skull Stripping Wed Sep 9 13:37:37 CST 2009 /usr/local/freesurfer/subjects/am03/mri mri_em_register -skull nu.mgz /usr/local/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 5 reading 1 input volumes... logging results to talairach_with_skull.log reading '/usr/local/freesurfer/average/RB_all_withskull_2008-03-26.gca'... average std = 23.1 using min determinant for regularization = 53.4 0 singular and 5702 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 20.2 or > 943.7 total sample mean = 92.0 (1443 zeros) ************************************************ spacing=8, using 3481 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3481, passno 0, spacing 8 resetting wm mean[0]: 117 --> 126 resetting gm mean[0]: 74 --> 74 input volume #1 is the most T1-like using real data threshold=9.0 skull bounding box = (42, 36, 37) --> (211, 255, 221) using (98, 109, 129) as brain centroid... mean wm in atlas = 126, using box (77,82,106) --> (118, 136,151) to find MRI wm before smoothing, mri peak at 158 after smoothing, mri peak at 158, scaling input intensities by 0.797 scaling channel 0 by 0.797468 initial log_p = -22984.3 ************************************************ First Search limited to translation only. ************************************************ using real data threshold=18.0 Found translation: (0.6, -1.7, -10.8): log p = -16659.5 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-14471.0, old_max_log_p =-16659.5 (thresh=-16642.8) 0.996 -0.070 -0.071 17.894; 0.069 1.189 0.082 -43.226; 0.069 -0.061 1.059 -26.438; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-14312.6, old_max_log_p =-14471.0 (thresh=-14456.5) 0.996 -0.070 -0.071 17.894; 0.069 1.189 0.082 -43.226; 0.074 -0.065 1.125 -34.717; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-14312.6, old_max_log_p =-14312.6 (thresh=-14298.3) 0.996 -0.070 -0.071 17.894; 0.069 1.189 0.082 -43.226; 0.074 -0.065 1.125 -34.717; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-13940.9, old_max_log_p =-14312.6 (thresh=-14298.3) 1.015 -0.057 0.004 2.901; 0.055 1.225 0.123 -48.852; 0.007 -0.100 1.106 -18.011; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-13917.4, old_max_log_p =-13940.9 (thresh=-13927.0) 1.015 -0.057 0.004 2.901; 0.055 1.225 0.123 -48.852; 0.007 -0.098 1.089 -16.073; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 5 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-13917.4, old_max_log_p =-13917.4 (thresh=-13903.5) 1.015 -0.057 0.004 2.901; 0.055 1.225 0.123 -48.852; 0.007 -0.098 1.089 -16.073; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-13863.0, old_max_log_p =-13917.4 (thresh=-13903.5) 1.010 -0.066 -0.002 5.739; 0.064 1.225 0.114 -48.843; 0.012 -0.089 1.099 -18.925; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-13863.0, old_max_log_p =-13863.0 (thresh=-13849.1) 1.010 -0.066 -0.002 5.739; 0.064 1.225 0.114 -48.843; 0.012 -0.089 1.099 -18.925; 0.000 0.000 0.000 1.000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 3481 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.01046 -0.06639 -0.00156 5.73923; 0.06374 1.22507 0.11370 -48.84271; 0.01168 -0.08902 1.09863 -18.92546; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.01046 -0.06639 -0.00156 5.73923; 0.06374 1.22507 0.11370 -48.84271; 0.01168 -0.08902 1.09863 -18.92546; 0.00000 0.00000 0.00000 1.00000; v3p/netlib/opt/lbfgs.c: lb3_1.lp > 0 outof QuasiNewtonEMA: 008: -log(p) = 13863.0 tol 0.000010 Resulting transform: 1.010 -0.066 -0.002 5.739; 0.064 1.225 0.114 -48.843; 0.012 -0.089 1.099 -18.925; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -13863.0 (old=-22984.3) transform before final EM align: 1.010 -0.066 -0.002 5.739; 0.064 1.225 0.114 -48.843; 0.012 -0.089 1.099 -18.925; 0.000 0.000 0.000 1.000; ************************************************** EM alignment process ... Computing final MAP estimate using 382743 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.01046 -0.06639 -0.00156 5.73923; 0.06374 1.22507 0.11370 -48.84271; 0.01168 -0.08902 1.09863 -18.92546; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.01046 -0.06639 -0.00156 5.73923; 0.06374 1.22507 0.11370 -48.84271; 0.01168 -0.08902 1.09863 -18.92546; 0.00000 0.00000 0.00000 1.00000; v3p/netlib/opt/lbfgs.c: lb3_1.lp > 0 outof QuasiNewtonEMA: 008: -log(p) = 1781208.9 tol 0.000000 final transform: 1.010 -0.066 -0.002 5.739; 0.064 1.225 0.114 -48.843; 0.012 -0.089 1.099 -18.925; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull.lta... registration took 88 minutes and 47 seconds. mri_watershed -T1 -brain_atlas /usr/local/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details) ********************************************************* The input file is T1.mgz The output file is brainmask.auto.mgz If this is incorrect, please exit with CTL-C Weighting the input with atlas information before watershed *************************WATERSHED************************** Sorting... first estimation of the COG coord: x=127 y=112 z=127 r=80 first estimation of the main basin volume: 2219863 voxels Looking for seedpoints 2 found in the cerebellum 16 found in the rest of the brain global maximum in x=95, y=110, z=89, Imax=255 CSF=12, WM_intensity=110, WM_VARIANCE=5 WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110 preflooding height equal to 10 percent done Analyze main basin size=-1162767544 voxels, voxel volume =1.000 = 3132199752 mmm3 = 3132199.752 cm3 done PostAnalyze...Basin Prior 17 basins merged thanks to atlas ***** 0 basin(s) merged in 1 iteration(s) ***** 0 voxel(s) added to the main basin done Weighting the input with prior template ****************TEMPLATE DEFORMATION**************** second estimation of the COG coord: x=126,y=119, z=120, r=9251 iterations GLOBAL CSF_MIN=0, CSF_intensity=9, CSF_MAX=28 , nb = 21996 RIGHT_CER CSF_MIN=0, CSF_intensity=5, CSF_MAX=20 , nb = 1566 LEFT_CER CSF_MIN=0, CSF_intensity=4, CSF_MAX=16 , nb = 1494 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=26 , nb = 9612 LEFT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=29 , nb = 9189 OTHER CSF_MIN=0, CSF_intensity=4, CSF_MAX=35 , nb = 135 Problem with the least square interpolation in GM_MIN calculation. CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 28, 31, 37, 62 after analyzing : 28, 35, 37, 41 RIGHT_CER before analyzing : 20, 27, 43, 72 after analyzing : 20, 37, 43, 45 LEFT_CER before analyzing : 16, 31, 50, 64 after analyzing : 16, 43, 50, 48 RIGHT_BRAIN before analyzing : 26, 32, 40, 58 after analyzing : 26, 37, 40, 42 LEFT_BRAIN before analyzing : 29, 32, 37, 60 after analyzing : 29, 35, 37, 41 OTHER before analyzing : 35, 36, 37, 62 after analyzing : 35, 36, 37, 42 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...65 iterations *********************VALIDATION********************* curvature mean = -0.013, std = 0.011 curvature mean = 69.689, std = 6.775 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 5.87, sigma = 8.62 after rotation: sse = 5.87, sigma = 8.62 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 6.10, its var is 6.78 before Erosion-Dilatation 2.55% of inacurate vertices after Erosion-Dilatation 3.43% of inacurate vertices Validation of the shape of the surface done. Scaling of atlas fields onto current surface fields ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...40 iterations mghRead: encountered error executing: 'zcat /usr/local/freesurfer/subjects/am03/mri/T1.mgz',frame -1, errno 12 mri_strip_skull: done peeling brain Brain Size = 1657531 voxels, voxel volume = 1.000 mm3 = 1657531 mmm3 = 1657.531 cm3 mri_watershed Error: read failed Linux qq-desktop 2.6.28-15-generic #51-Ubuntu SMP Mon Aug 31 13:33:16 UTC 2009 i686 GNU/Linux recon-all exited with ERRORS at Wed Sep 9 15:08:15 CST 2009