Mon Dec 7 15:47:35 CET 2015 /NAS/tupac/matthieu/FS5.3/M0_2013-02-19 /home/global//freesurfer5.3//bin/recon-all -all -sd /NAS/tupac/matthieu/FS5.3/ -subjid M0_2013-02-19 -nuintensitycor-3T -i /NAS/tupac/matthieu/Nifti_IRM//M0_2013-02-19/nii/3DT1.nii.gz subjid M0_2013-02-19 setenv SUBJECTS_DIR /NAS/tupac/matthieu/FS5.3 FREESURFER_HOME /home/global//freesurfer5.3/ Actual FREESURFER_HOME /home/global/freesurfer5.3 build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 Linux kent 3.13.0-24-generic #47-Ubuntu SMP Fri May 2 23:30:00 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize unlimited memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 63694 maxlocks unlimited maxsignal 63694 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 8174420 3267216 4907204 20 175168 2815312 -/+ buffers/cache: 276736 7897684 Swap: 31249404 99532 31149872 ######################################## program versions used $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/07-14:47:35-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: matthieu Machine: kent Platform: Linux PlatformVersion: 3.13.0-24-generic CompilerName: GCC CompilerVersion: 30400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/07-14:47:36-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: matthieu Machine: kent Platform: Linux PlatformVersion: 3.13.0-24-generic CompilerName: GCC CompilerVersion: 30400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/07-14:47:36-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: matthieu Machine: kent Platform: Linux PlatformVersion: 3.13.0-24-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/07-14:47:36-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: matthieu Machine: kent Platform: Linux PlatformVersion: 3.13.0-24-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/07-14:47:36-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: matthieu Machine: kent Platform: Linux PlatformVersion: 3.13.0-24-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/07-14:47:36-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: matthieu Machine: kent Platform: Linux PlatformVersion: 3.13.0-24-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/07-14:47:36-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: matthieu Machine: kent Platform: Linux PlatformVersion: 3.13.0-24-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/07-14:47:36-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: matthieu Machine: kent Platform: Linux PlatformVersion: 3.13.0-24-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/07-14:47:36-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: matthieu Machine: kent Platform: Linux PlatformVersion: 3.13.0-24-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/07-14:47:36-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: matthieu Machine: kent Platform: Linux PlatformVersion: 3.13.0-24-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/07-14:47:36-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: matthieu Machine: kent Platform: Linux PlatformVersion: 3.13.0-24-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/07-14:47:36-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: matthieu Machine: kent Platform: Linux PlatformVersion: 3.13.0-24-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/07-14:47:37-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: matthieu Machine: kent Platform: Linux PlatformVersion: 3.13.0-24-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/07-14:47:37-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: matthieu Machine: kent Platform: Linux PlatformVersion: 3.13.0-24-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/07-14:47:37-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: matthieu Machine: kent Platform: Linux PlatformVersion: 3.13.0-24-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/07-14:47:37-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: matthieu Machine: kent Platform: Linux PlatformVersion: 3.13.0-24-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/07-14:47:37-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: matthieu Machine: kent Platform: Linux PlatformVersion: 3.13.0-24-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/07-14:47:37-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: matthieu Machine: kent Platform: Linux PlatformVersion: 3.13.0-24-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/07-14:47:37-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: matthieu Machine: kent Platform: Linux PlatformVersion: 3.13.0-24-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/07-14:47:37-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: matthieu Machine: kent Platform: Linux PlatformVersion: 3.13.0-24-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/07-14:47:37-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: matthieu Machine: kent Platform: Linux PlatformVersion: 3.13.0-24-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/07-14:47:37-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: matthieu Machine: kent Platform: Linux PlatformVersion: 3.13.0-24-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/07-14:47:37-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: matthieu Machine: kent Platform: Linux PlatformVersion: 3.13.0-24-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/07-14:47:38-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: matthieu Machine: kent Platform: Linux PlatformVersion: 3.13.0-24-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/07-14:47:38-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: matthieu Machine: kent Platform: Linux PlatformVersion: 3.13.0-24-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/07-14:47:38-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: matthieu Machine: kent Platform: Linux PlatformVersion: 3.13.0-24-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/07-14:47:38-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: matthieu Machine: kent Platform: Linux PlatformVersion: 3.13.0-24-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/07-14:47:38-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: matthieu Machine: kent Platform: Linux PlatformVersion: 3.13.0-24-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/07-14:47:38-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: matthieu Machine: kent Platform: Linux PlatformVersion: 3.13.0-24-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/07-14:47:38-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: matthieu Machine: kent Platform: Linux PlatformVersion: 3.13.0-24-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/07-14:47:38-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: matthieu Machine: kent Platform: Linux PlatformVersion: 3.13.0-24-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/07-14:47:38-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: matthieu Machine: kent Platform: Linux PlatformVersion: 3.13.0-24-generic CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/07-14:47:38-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: matthieu Machine: kent Platform: Linux PlatformVersion: 3.13.0-24-generic CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/07-14:47:38-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: matthieu Machine: kent Platform: Linux PlatformVersion: 3.13.0-24-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/07-14:47:39-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: matthieu Machine: kent Platform: Linux PlatformVersion: 3.13.0-24-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/07-14:47:39-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: matthieu Machine: kent Platform: Linux PlatformVersion: 3.13.0-24-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/07-14:47:39-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: matthieu Machine: kent Platform: Linux PlatformVersion: 3.13.0-24-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/07-14:47:39-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: matthieu Machine: kent Platform: Linux PlatformVersion: 3.13.0-24-generic CompilerName: GCC CompilerVersion: 30400 ####################################### GCADIR /home/global//freesurfer5.3//average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /home/global//freesurfer5.3//average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### /NAS/tupac/matthieu/FS5.3/M0_2013-02-19 mri_convert /NAS/tupac/matthieu/Nifti_IRM/M0_2013-02-19/nii/3DT1.nii.gz /NAS/tupac/matthieu/FS5.3/M0_2013-02-19/mri/orig/001.mgz mri_convert /NAS/tupac/matthieu/Nifti_IRM/M0_2013-02-19/nii/3DT1.nii.gz /NAS/tupac/matthieu/FS5.3/M0_2013-02-19/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /NAS/tupac/matthieu/Nifti_IRM/M0_2013-02-19/nii/3DT1.nii.gz... TR=9.87, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.132389, -0.979278, -0.153257) j_ras = (0.0398541, -0.149233, 0.987998) k_ras = (0.990396, 0.136908, -0.0192714) writing to /NAS/tupac/matthieu/FS5.3/M0_2013-02-19/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Mon Dec 7 15:47:48 CET 2015 Found 1 runs /NAS/tupac/matthieu/FS5.3/M0_2013-02-19/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... 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 /NAS/tupac/matthieu/FS5.3/M0_2013-02-19/mri/orig/001.mgz /NAS/tupac/matthieu/FS5.3/M0_2013-02-19/mri/rawavg.mgz /NAS/tupac/matthieu/FS5.3/M0_2013-02-19 mri_convert /NAS/tupac/matthieu/FS5.3/M0_2013-02-19/mri/rawavg.mgz /NAS/tupac/matthieu/FS5.3/M0_2013-02-19/mri/orig.mgz --conform mri_convert /NAS/tupac/matthieu/FS5.3/M0_2013-02-19/mri/rawavg.mgz /NAS/tupac/matthieu/FS5.3/M0_2013-02-19/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /NAS/tupac/matthieu/FS5.3/M0_2013-02-19/mri/rawavg.mgz... TR=9.87, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.132389, -0.979278, -0.153257) j_ras = (0.0398541, -0.149233, 0.987998) k_ras = (0.990396, 0.136908, -0.0192714) Original Data has (1, 1, 1.00001) mm size and (256, 256, 160) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /NAS/tupac/matthieu/FS5.3/M0_2013-02-19/mri/orig.mgz... mri_add_xform_to_header -c /NAS/tupac/matthieu/FS5.3/M0_2013-02-19/mri/transforms/talairach.xfm /NAS/tupac/matthieu/FS5.3/M0_2013-02-19/mri/orig.mgz /NAS/tupac/matthieu/FS5.3/M0_2013-02-19/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Mon Dec 7 15:48:04 CET 2015 /NAS/tupac/matthieu/FS5.3/M0_2013-02-19/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Mon Dec 7 15:54:04 CET 2015 /NAS/tupac/matthieu/FS5.3/M0_2013-02-19/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.3451, pval=0.0406 >= threshold=0.0050) awk -f /home/global//freesurfer5.3//bin/extract_talairach_avi_QA.awk /NAS/tupac/matthieu/FS5.3/M0_2013-02-19/mri/transforms/talairach_avi.log tal_QC_AZS /NAS/tupac/matthieu/FS5.3/M0_2013-02-19/mri/transforms/talairach_avi.log TalAviQA: 0.95090 z-score: -6 #-------------------------------------------- #@# Nu Intensity Correction Mon Dec 7 15:54:04 CET 2015 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --proto-iters 1000 --distance 50 --n 1 /NAS/tupac/matthieu/FS5.3/M0_2013-02-19/mri /home/global//freesurfer5.3//bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --proto-iters 1000 --distance 50 --n 1 nIters 1 $Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $ Linux kent 3.13.0-24-generic #47-Ubuntu SMP Fri May 2 23:30:00 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux Mon Dec 7 15:54:04 CET 2015 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 tmpdir is ./tmp.mri_nu_correct.mni.4297 /NAS/tupac/matthieu/FS5.3/M0_2013-02-19/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.4297/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.4297/nu0.mnc -odt float $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from orig.mgz... TR=9.87, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -2.98023e-08, 3.53903e-08) j_ras = (1.80677e-07, 5.42495e-08, -1) k_ras = (2.98023e-08, 1, -2.84053e-08) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.4297/nu0.mnc... -------------------------------------------------------- Iteration 1 Mon Dec 7 15:54:10 CET 2015 nu_correct -clobber ./tmp.mri_nu_correct.mni.4297/nu0.mnc ./tmp.mri_nu_correct.mni.4297/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.4297/0/ -iterations 1000 -distance 50 defined(@array) is deprecated at /home/global//freesurfer5.3//mni/bin/nu_estimate_np_and_em line 165. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /home/global//freesurfer5.3//mni/bin/nu_estimate_np_and_em line 170. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /home/global//freesurfer5.3//mni/bin/nu_estimate_np_and_em line 211. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /home/global//freesurfer5.3//mni/bin/nu_estimate_np_and_em line 1051. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /home/global//freesurfer5.3//mni/bin/nu_estimate_np_and_em line 1054. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /home/global//freesurfer5.3//mni/bin/nu_estimate_np_and_em line 1449. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /home/global//freesurfer5.3//mni/bin/nu_estimate_np_and_em line 1455. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /home/global//freesurfer5.3//mni/bin/nu_estimate_np_and_em line 1457. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /home/global//freesurfer5.3//mni/bin/nu_estimate_np_and_em line 1481. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /home/global//freesurfer5.3//mni/bin/nu_estimate_np_and_em line 1631. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /home/global//freesurfer5.3//mni/bin/nu_estimate_np_and_em line 1633. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /home/global//freesurfer5.3//mni/bin/nu_estimate_np_and_em line 1635. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /home/global//freesurfer5.3//mni/bin/nu_estimate_np_and_em line 1637. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /home/global//freesurfer5.3//mni/bin/nu_estimate_np_and_em line 1639. (Maybe you should just omit the defined()?) [matthieu@kent:/NAS/tupac/matthieu/FS5.3/M0_2013-02-19/mri/] [2015-12-07 15:54:10] running: /home/global//freesurfer5.3//mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.4297/0/ ./tmp.mri_nu_correct.mni.4297/nu0.mnc ./tmp.mri_nu_correct.mni.4297/nu1.imp Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/global//freesurfer5.3//mni/bin/sharpen_volume line 153. Processing:.................................................................Done Number of iterations: 131 CV of field change: 0.000998488 [matthieu@kent:/NAS/tupac/matthieu/FS5.3/M0_2013-02-19/mri/] [2015-12-07 15:57:56] running: /home/global//freesurfer5.3//mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.4297/nu0.mnc ./tmp.mri_nu_correct.mni.4297/0//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done mri_binarize --i ./tmp.mri_nu_correct.mni.4297/nu1.mnc --min -1 --o ./tmp.mri_nu_correct.mni.4297/ones.mgz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /NAS/tupac/matthieu/FS5.3/M0_2013-02-19/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.4297/nu1.mnc --min -1 --o ./tmp.mri_nu_correct.mni.4297/ones.mgz sysname Linux hostname kent machine x86_64 user matthieu input ./tmp.mri_nu_correct.mni.4297/nu1.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.4297/ones.mgz Binarizing based on threshold min -1 max +infinity binval 1 binvalnot 0 Found 16777216 values in range Counting number of voxels Found 16777216 voxels in final mask mri_binarize done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.4297/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.4297/sum.junk --avgwf ./tmp.mri_nu_correct.mni.4297/input.mean.dat $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.4297/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.4297/sum.junk --avgwf ./tmp.mri_nu_correct.mni.4297/input.mean.dat sysname Linux hostname kent machine x86_64 user matthieu UseRobust 0 Loading ./tmp.mri_nu_correct.mni.4297/ones.mgz Loading orig.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 16777216 16777216.000 Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.4297/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.4297/ones.mgz --i ./tmp.mri_nu_correct.mni.4297/nu1.mnc --sum ./tmp.mri_nu_correct.mni.4297/sum.junk --avgwf ./tmp.mri_nu_correct.mni.4297/output.mean.dat $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.4297/ones.mgz --i ./tmp.mri_nu_correct.mni.4297/nu1.mnc --sum ./tmp.mri_nu_correct.mni.4297/sum.junk --avgwf ./tmp.mri_nu_correct.mni.4297/output.mean.dat sysname Linux hostname kent machine x86_64 user matthieu UseRobust 0 Loading ./tmp.mri_nu_correct.mni.4297/ones.mgz Loading ./tmp.mri_nu_correct.mni.4297/nu1.mnc Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 16777216 16777216.000 Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.4297/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.4297/nu1.mnc ./tmp.mri_nu_correct.mni.4297/nu1.mnc mul 1.00412921196784903365 Saving result to './tmp.mri_nu_correct.mni.4297/nu1.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.4297/nu1.mnc nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.4297/nu1.mnc nu.mgz --like orig.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from ./tmp.mri_nu_correct.mni.4297/nu1.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -2.98023e-08, 3.53903e-08) j_ras = (1.80677e-07, 5.42495e-08, -1) k_ras = (2.98023e-08, 1, -2.84053e-08) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 0 minutes and 14 seconds. mapping ( 0, 83) to ( 3, 110) Mon Dec 7 15:59:12 CET 2015 mri_nu_correct.mni done mri_add_xform_to_header -c /NAS/tupac/matthieu/FS5.3/M0_2013-02-19/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Mon Dec 7 15:59:14 CET 2015 /NAS/tupac/matthieu/FS5.3/M0_2013-02-19/mri mri_normalize -g 1 nu.mgz T1.mgz using max gradient = 1.000 reading from nu.mgz... normalizing image... talairach transform 1.051 0.169 -0.035 2.737; -0.106 0.949 0.568 -6.402; 0.109 -0.515 1.024 -9.653; 0.000 0.000 0.000 1.000; processing without aseg, no1d=0 MRInormInit(): INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRInormalize(): MRIsplineNormalize(): npeaks = 1 ERROR: number of peaks must be > 1 for spline 1d normalization failed - trying no1d... building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 111 white matter peak found at 93 gm peak at 46 (44), valley at 35 (33) csf peak at 22, setting threshold to 38 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 111 white matter peak found at 110 gm peak at 82 (80), valley at 71 (69) csf peak at 40, setting threshold to 68 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 3 minutes and 13 seconds. #-------------------------------------------- #@# Skull Stripping Mon Dec 7 16:02:28 CET 2015 /NAS/tupac/matthieu/FS5.3/M0_2013-02-19/mri mri_em_register -skull nu.mgz /home/global//freesurfer5.3//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 '/home/global//freesurfer5.3//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=7.0 skull bounding box = (47, 22, 24) --> (208, 255, 234) using (101, 100, 129) as brain centroid... mean wm in atlas = 126, using box (81,71,103) --> (120, 128,154) to find MRI wm before smoothing, mri peak at 94 after smoothing, mri peak at 93, scaling input intensities by 1.355 scaling channel 0 by 1.35484 initial log_p = -4.8 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.859966 @ (9.091, -45.455, -27.273) max log p = -4.842788 @ (-4.545, -4.545, -4.545) max log p = -4.835035 @ (2.273, 2.273, 2.273) max log p = -4.824720 @ (1.136, -1.136, -1.136) max log p = -4.799149 @ (-0.568, -0.568, -0.568) max log p = -4.799149 @ (0.000, 0.000, 0.000) Found translation: (7.4, -49.4, -31.3): log p = -4.799 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.6, old_max_log_p =-4.8 (thresh=-4.8) 1.051 -0.006 -0.652 86.745; -0.057 1.231 -0.104 -85.587; 0.649 0.119 1.045 -140.955; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.6, old_max_log_p =-4.6 (thresh=-4.6) 0.866 -0.334 -1.214 254.160; 0.226 1.491 -0.249 -144.083; 1.239 -0.038 0.894 -155.646; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.5, old_max_log_p =-4.6 (thresh=-4.5) 1.517 -0.576 -0.675 147.764; 0.620 1.645 -0.010 -266.358; 0.511 -0.184 1.305 -86.973; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 3 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.5, old_max_log_p =-4.5 (thresh=-4.5) 1.517 -0.576 -0.675 147.764; 0.620 1.645 -0.010 -266.358; 0.511 -0.184 1.305 -86.973; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.5, old_max_log_p =-4.5 (thresh=-4.5) 1.546 -0.527 -0.732 142.303; 0.564 1.699 -0.030 -267.727; 0.591 -0.152 1.305 -104.432; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 5 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.5, old_max_log_p =-4.5 (thresh=-4.5) 1.476 -0.839 -0.831 223.468; 0.805 1.688 -0.261 -261.792; 0.712 -0.074 1.226 -127.097; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 6 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.5, old_max_log_p =-4.5 (thresh=-4.5) 1.502 -0.783 -0.839 210.887; 0.770 1.747 -0.238 -273.894; 0.699 -0.072 1.203 -120.851; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.5, old_max_log_p =-4.5 (thresh=-4.5) 1.461 -0.822 -0.860 225.917; 0.794 1.726 -0.278 -268.233; 0.750 -0.063 1.180 -126.652; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 8 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.5, old_max_log_p =-4.5 (thresh=-4.5) 1.461 -0.822 -0.860 225.917; 0.792 1.722 -0.278 -267.321; 0.752 -0.063 1.183 -127.198; 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 1.46129 -0.82246 -0.85967 225.91666; 0.79195 1.72212 -0.27765 -267.32092; 0.75190 -0.06292 1.18307 -127.19754; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.46129 -0.82246 -0.85967 225.91666; 0.79195 1.72212 -0.27765 -267.32092; 0.75190 -0.06292 1.18307 -127.19754; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 011: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.461 -0.822 -0.860 225.917; 0.792 1.722 -0.278 -267.321; 0.752 -0.063 1.183 -127.198; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -4.5 (old=-4.8) transform before final EM align: 1.461 -0.822 -0.860 225.917; 0.792 1.722 -0.278 -267.321; 0.752 -0.063 1.183 -127.198; 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 1.46129 -0.82246 -0.85967 225.91666; 0.79195 1.72212 -0.27765 -267.32092; 0.75190 -0.06292 1.18307 -127.19754; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.46129 -0.82246 -0.85967 225.91666; 0.79195 1.72212 -0.27765 -267.32092; 0.75190 -0.06292 1.18307 -127.19754; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 013: -log(p) = 4.7 tol 0.000000 final transform: 1.461 -0.822 -0.860 225.917; 0.792 1.722 -0.278 -267.321; 0.752 -0.063 1.183 -127.198; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull.lta... registration took 40 minutes and 19 seconds. mri_watershed -T1 -brain_atlas /home/global//freesurfer5.3//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 Weighting the input with atlas information before watershed *************************WATERSHED************************** Sorting... first estimation of the COG coord: x=151 y=155 z=145 r=79 first estimation of the main basin volume: 2089450 voxels Looking for seedpoints 2 found in the cerebellum 1 found in the rest of the brain global maximum in x=172, y=148, z=174, Imax=255 CSF=13, 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=3334549142 voxels, voxel volume =1.000 = 3334549142 mmm3 = 3334549.248 cm3 done. PostAnalyze...Basin Prior 86 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=168,y=206, z=171, r=103161 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=0, CSF_intensity=4, CSF_MAX=8 , nb = 35328 RIGHT_CER CSF_MIN=0, CSF_intensity=4, CSF_MAX=8 , nb = 0 LEFT_CER CSF_MIN=0, CSF_intensity=4, CSF_MAX=8 , nb = 0 RIGHT_BRAIN CSF_MIN=3, CSF_intensity=15, CSF_MAX=57 , nb = 5400 LEFT_BRAIN CSF_MIN=3, CSF_intensity=32, CSF_MAX=52 , nb = 5328 OTHER CSF_MIN=0, CSF_intensity=4, CSF_MAX=8 , nb = 19902 Problem with the least square interpolation in GM_MIN calculation. Problem with the least square interpolation in GM_MIN calculation. CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 8, 15, 62, 88 after analyzing : 8, 46, 62, 56 RIGHT_CER before analyzing : 8, 15, 62, 88 after analyzing : 8, 46, 62, 56 LEFT_CER before analyzing : 8, 15, 62, 88 after analyzing : 8, 46, 62, 56 RIGHT_BRAIN before analyzing : 57, 60, 62, 88 after analyzing : 57, 61, 62, 67 LEFT_BRAIN before analyzing : 52, 56, 62, 88 after analyzing : 52, 60, 62, 67 OTHER before analyzing : 8, 4, 2, 4 after analyzing : 4, 18, 25, 19 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...111 iterations *********************VALIDATION********************* curvature mean = 0.005, std = 0.083 curvature mean = 32.186, std = 9.044 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 40.64, sigma = 94.92 after rotation: sse = 40.64, sigma = 94.92 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 53.86, its var is 76.34 before Erosion-Dilatation 51.93% of inacurate vertices after Erosion-Dilatation 71.60% of inacurate vertices 54.96% of 'positive' inacurate vertices 45.04% of 'negative' inacurate vertices The surface validation has detected a possible Error If the final segmentation is not valid, try using the option '-atlas' Scaling of atlas fields onto current surface fields ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...102 iterations mri_strip_skull: done peeling brain Brain Size = 2305045 voxels, voxel volume = 1.000 mm3 = 2305045 mmm3 = 2305.045 cm3 ****************************** Saving brainmask.auto.mgz done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Mon Dec 7 16:43:40 CET 2015 /NAS/tupac/matthieu/FS5.3/M0_2013-02-19/mri mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /home/global//freesurfer5.3//average/RB_all_2008-03-26.gca transforms/talairach.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 3 using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading '/home/global//freesurfer5.3//average/RB_all_2008-03-26.gca'... average std = 6.9 using min determinant for regularization = 4.7 0 singular and 1812 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 14.9 or > 790.2 total sample mean = 84.4 (994 zeros) ************************************************ spacing=8, using 2772 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2772, passno 0, spacing 8 resetting wm mean[0]: 102 --> 107 resetting gm mean[0]: 64 --> 64 input volume #1 is the most T1-like using real data threshold=13.0 skull bounding box = (85, 152, 105) --> (195, 255, 229) using (122, 186, 167) as brain centroid... mean wm in atlas = 107, using box (109,173,152) --> (135, 198,182) to find MRI wm before smoothing, mri peak at 59 after smoothing, mri peak at 59, scaling input intensities by 1.814 scaling channel 0 by 1.81356 initial log_p = -4.8 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.805512 @ (-45.455, 27.273, -9.091) max log p = -4.805512 @ (0.000, 0.000, 0.000) max log p = -4.805295 @ (20.455, -11.364, 2.273) max log p = -4.805270 @ (1.136, -1.136, 1.136) max log p = -4.805246 @ (-1.705, 1.705, -0.568) max log p = -4.805246 @ (0.000, 0.000, 0.000) Found translation: (-25.6, 16.5, -6.3): log p = -4.805 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.8, old_max_log_p =-4.8 (thresh=-4.8) 0.704 0.697 0.184 -58.457; -0.511 0.385 0.831 58.515; 0.547 -0.735 0.584 49.627; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 1 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.8, old_max_log_p =-4.8 (thresh=-4.8) 0.763 0.664 0.142 -56.298; -0.403 0.343 0.944 36.823; 0.561 -0.772 0.448 71.530; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 2 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.8, old_max_log_p =-4.8 (thresh=-4.8) 0.763 0.664 0.142 -56.298; -0.403 0.343 0.944 36.823; 0.561 -0.772 0.448 71.530; 0.000 0.000 0.000 1.000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 2772 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 0.76298 0.66410 0.14168 -56.29847; -0.40309 0.34297 0.94448 36.82255; 0.56095 -0.77247 0.44802 71.53012; 0.00000 0.00000 0.00000 1.00000; nsamples 2772 Quasinewton: input matrix 0.76298 0.66410 0.14168 -56.29847; -0.40309 0.34297 0.94448 36.82255; 0.56095 -0.77247 0.44802 71.53012; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 4 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 005: -log(p) = -0.0 tol 0.000010 Resulting transform: 0.763 0.664 0.142 -56.298; -0.403 0.343 0.944 36.823; 0.561 -0.772 0.448 71.530; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -4.8 (old=-4.8) transform before final EM align: 0.763 0.664 0.142 -56.298; -0.403 0.343 0.944 36.823; 0.561 -0.772 0.448 71.530; 0.000 0.000 0.000 1.000; ************************************************** EM alignment process ... Computing final MAP estimate using 312841 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 0.76298 0.66410 0.14168 -56.29847; -0.40309 0.34297 0.94448 36.82255; 0.56095 -0.77247 0.44802 71.53012; 0.00000 0.00000 0.00000 1.00000; nsamples 312841 Quasinewton: input matrix 0.76298 0.66410 0.14168 -56.29847; -0.40309 0.34297 0.94448 36.82255; 0.56095 -0.77247 0.44802 71.53012; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 007: -log(p) = 5.0 tol 0.000000 final transform: 0.763 0.664 0.142 -56.298; -0.403 0.343 0.944 36.823; 0.561 -0.772 0.448 71.530; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach.lta... registration took 11 minutes and 35 seconds. #-------------------------------------- #@# CA Normalize Mon Dec 7 16:55:15 CET 2015 /NAS/tupac/matthieu/FS5.3/M0_2013-02-19/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /home/global//freesurfer5.3//average/RB_all_2008-03-26.gca transforms/talairach.lta norm.mgz writing control point volume to ctrl_pts.mgz using MR volume brainmask.mgz to mask input volume... reading 1 input volume reading atlas from '/home/global//freesurfer5.3//average/RB_all_2008-03-26.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 102 --> 107 resetting gm mean[0]: 64 --> 64 input volume #1 is the most T1-like using real data threshold=8.0 skull bounding box = (84, 151, 104) --> (200, 255, 230) using (123, 186, 167) as brain centroid... mean wm in atlas = 107, using box (109,173,152) --> (137, 198,182) to find MRI wm before smoothing, mri peak at 63 after smoothing, mri peak at 60, scaling input intensities by 1.783 scaling channel 0 by 1.78333 using 244171 sample points... INFO: compute sample coordinates transform 0.763 0.664 0.142 -56.298; -0.403 0.343 0.944 36.823; 0.561 -0.772 0.448 71.530; 0.000 0.000 0.000 1.000; INFO: transform used finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (82, 53, 38) --> (194, 179, 165) finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (57, 35, 34) --> (168, 152, 162) finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (89, 126, 100) --> (134, 175, 146) finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (55, 108, 100) --> (106, 151, 144) finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (84, 104, 106) --> (130, 144, 160) skipping region 1 with no control points detected finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (82, 53, 38) --> (194, 179, 165) finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (57, 35, 34) --> (168, 152, 162) finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (89, 126, 100) --> (134, 175, 146) finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (55, 108, 100) --> (106, 151, 144) finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (84, 104, 106) --> (130, 144, 160) skipping region 2 with no control points detected finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (82, 53, 38) --> (194, 179, 165) finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (57, 35, 34) --> (168, 152, 162) finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (89, 126, 100) --> (134, 175, 146) finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (55, 108, 100) --> (106, 151, 144) finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (84, 104, 106) --> (130, 144, 160) skipping region 3 with no control points detected writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 0 minutes and 35 seconds. #-------------------------------------- #@# CA Reg Mon Dec 7 16:55:50 CET 2015 /NAS/tupac/matthieu/FS5.3/M0_2013-02-19/mri mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /home/global//freesurfer5.3//average/RB_all_2008-03-26.gca transforms/talairach.m3z not handling expanded ventricles... using previously computed transform transforms/talairach.lta renormalizing sequences with structure alignment, equivalent to: -renormalize -regularize_mean 0.500 -regularize 0.500 using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading input volume 'norm.mgz'... reading GCA '/home/global//freesurfer5.3//average/RB_all_2008-03-26.gca'... label assignment complete, 0 changed (0.00%) det(m_affine) = 1.16 (predicted orig area = 6.9) label assignment complete, 0 changed (0.00%) freeing gibbs priors...done. average std[0] = 5.0 **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.039 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=2.326, neg=0, invalid=96777 0001: dt=0.000000, rms=2.322 (0.179%), neg=0, invalid=96777 0002: dt=0.000000, rms=2.322 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=2.322, neg=0, invalid=96777 0003: dt=0.000000, rms=2.322 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=2.322, neg=0, invalid=96777 0004: dt=1.620000, rms=2.322 (0.000%), neg=0, invalid=96777 0005: dt=1.620000, rms=2.322 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=2.322, neg=0, invalid=96777 0006: dt=0.000000, rms=2.322 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=2.322, neg=0, invalid=96777 0007: dt=0.000000, rms=2.322 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=2.322, neg=0, invalid=96777 0008: dt=0.000000, rms=2.322 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=2.322, neg=0, invalid=96777 0009: dt=0.000000, rms=2.322 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=2.322, neg=0, invalid=96777 0010: dt=0.000000, rms=2.322 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 5.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=2.322, neg=0, invalid=96777 0011: dt=0.000000, rms=2.322 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=2.322, neg=0, invalid=96777 0012: dt=0.000000, rms=2.322 (0.000%), neg=0, invalid=96777 resetting metric properties... setting smoothness coefficient to 10.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=2.322, neg=0, invalid=96777 0013: dt=0.000375, rms=2.322 (0.000%), neg=0, invalid=96777 0014: dt=0.000375, rms=2.322 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=2.322, neg=0, invalid=96777 0015: dt=0.000000, rms=2.322 (0.000%), neg=0, invalid=96777 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.11725 (24) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.14022 (22) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.24234 (100) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.19192 (97) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.24007 (63) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.29892 (64) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.12541 (104) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.13686 (104) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.11691 (63) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.13270 (63) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.15182 (70) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.14251 (76) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.12116 (60) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.12723 (61) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.22684 (88) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.21067 (87) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.25455 (62) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.39668 (62) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.10129 (93) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.12071 (89) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.13716 (82) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.15214 (84) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.08983 (85) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.11809 (92) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.12914 (94) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.21100 (36) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.13542 (27) uniform distribution in MR - rejecting arbitrary fit gca peak Unknown = 0.94427 ( 0) gca peak Left_Cerebral_White_Matter = 0.13686 (104) gca peak Left_Cerebral_Cortex = 0.11691 (63) gca peak Left_Lateral_Ventricle = 0.11725 (24) gca peak Left_Inf_Lat_Vent = 0.21802 (40) gca peak Left_Cerebellum_White_Matter = 0.22684 (88) gca peak Left_Cerebellum_Cortex = 0.12116 (60) gca peak Left_Thalamus_Proper = 0.10129 (93) gca peak Left_Caudate = 0.14251 (76) gca peak Left_Putamen = 0.13716 (82) gca peak Left_Pallidum = 0.19192 (97) gca peak Third_Ventricle = 0.21100 (36) gca peak Fourth_Ventricle = 0.13542 (27) gca peak Brain_Stem = 0.08983 (85) gca peak Left_Hippocampus = 0.29892 (64) gca peak Left_Amygdala = 0.25455 (62) gca peak CSF = 0.17123 (45) gca peak Left_Accumbens_area = 0.25875 (69) gca peak Left_VentralDC = 0.12914 (94) gca peak Left_undetermined = 0.96240 (36) gca peak Left_vessel = 0.33262 (65) gca peak Left_choroid_plexus = 0.09846 (46) gca peak Right_Cerebral_White_Matter = 0.12541 (104) gca peak Right_Cerebral_Cortex = 0.13270 (63) gca peak Right_Lateral_Ventricle = 0.14022 (22) gca peak Right_Inf_Lat_Vent = 0.28113 (34) gca peak Right_Cerebellum_White_Matter = 0.21067 (87) gca peak Right_Cerebellum_Cortex = 0.12723 (61) gca peak Right_Thalamus_Proper = 0.12071 (89) gca peak Right_Caudate = 0.15182 (70) gca peak Right_Putamen = 0.15214 (84) gca peak Right_Pallidum = 0.24234 (100) gca peak Right_Hippocampus = 0.24007 (63) gca peak Right_Amygdala = 0.39668 (62) gca peak Right_Accumbens_area = 0.27120 (72) gca peak Right_VentralDC = 0.11809 (92) gca peak Right_vessel = 0.61915 (60) gca peak Right_choroid_plexus = 0.12775 (51) gca peak Fifth_Ventricle = 0.45329 (44) gca peak WM_hypointensities = 0.11729 (81) gca peak non_WM_hypointensities = 0.10912 (56) gca peak Optic_Chiasm = 0.33287 (75) label assignment complete, 0 changed (0.00%) not using caudate to estimate GM means estimating mean gm scale to be 1.00 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.00 x + 0.0 setting left cbm cortex = 1.00 x + 0.00 setting right cbm cortex = 1.00 x + 0.00 saving intensity scales to talairach.label_intensities.txt **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=2.322, neg=0, invalid=96777 0016: dt=0.000000, rms=2.322 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=2.322, neg=0, invalid=96777 0017: dt=0.000000, rms=2.322 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=2.322, neg=0, invalid=96777 0018: dt=5.184000, rms=2.322 (0.000%), neg=0, invalid=96777 0019: dt=0.000051, rms=2.322 (0.000%), neg=0, invalid=96777 0020: dt=0.000051, rms=2.322 (0.000%), neg=0, invalid=96777 0021: dt=0.000051, rms=2.322 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=2.322, neg=0, invalid=96777 0022: dt=0.000000, rms=2.322 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=2.322, neg=0, invalid=96777 0023: dt=0.000000, rms=2.322 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=2.322, neg=0, invalid=96777 0024: dt=0.000000, rms=2.322 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=2.322, neg=0, invalid=96777 0025: dt=0.000000, rms=2.322 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=2.322, neg=0, invalid=96777 0026: dt=0.000000, rms=2.322 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=2.322, neg=0, invalid=96777 0027: dt=0.000000, rms=2.322 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=2.322, neg=0, invalid=96777 0028: dt=0.000000, rms=2.322 (0.000%), neg=0, invalid=96777 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=2.322, neg=0, invalid=96777 0029: dt=0.001750, rms=2.322 (0.000%), neg=0, invalid=96777 0030: dt=0.001750, rms=2.322 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=2.322, neg=0, invalid=96777 0031: dt=0.001000, rms=2.322 (0.000%), neg=0, invalid=96777 0032: dt=0.001000, rms=2.322 (-0.000%), neg=0, invalid=96777 label assignment complete, 0 changed (0.00%) ********************************************************************************************* ********************************************************************************************* ********************************************************************************************* ********************* ALLOWING NEGATIVE NODES IN DEFORMATION ******************************** ********************************************************************************************* ********************************************************************************************* ********************************************************************************************* **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=2.322, neg=0, invalid=96777 0033: dt=0.007902, rms=2.322 (0.000%), neg=0, invalid=96777 0034: dt=0.007902, rms=2.322 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=2.322, neg=0, invalid=96777 0035: dt=0.000000, rms=2.322 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=2.322, neg=0, invalid=96777 0036: dt=1.296000, rms=2.322 (0.000%), neg=0, invalid=96777 0037: dt=1.296000, rms=2.322 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=2.322, neg=0, invalid=96777 0038: dt=0.000000, rms=2.322 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=2.322, neg=0, invalid=96777 0039: dt=0.000586, rms=2.322 (0.000%), neg=0, invalid=96777 0040: dt=0.000586, rms=2.322 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=2.322, neg=0, invalid=96777 0041: dt=0.000000, rms=2.322 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=2.322, neg=0, invalid=96777 0042: dt=0.000000, rms=2.322 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=2.322, neg=0, invalid=96777 0043: dt=0.000000, rms=2.322 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=2.322, neg=0, invalid=96777 0044: dt=0.000000, rms=2.322 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=2.322, neg=0, invalid=96777 0045: dt=0.000000, rms=2.322 (0.000%), neg=0, invalid=96777 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=2.322, neg=0, invalid=96777 0046: dt=0.001750, rms=2.322 (0.000%), neg=0, invalid=96777 0047: dt=0.001750, rms=2.322 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=2.322, neg=0, invalid=96777 0048: dt=0.001000, rms=2.322 (0.000%), neg=0, invalid=96777 0049: dt=0.001000, rms=2.322 (-0.000%), neg=0, invalid=96777 label assignment complete, 0 changed (0.00%) label assignment complete, 0 changed (0.00%) ***************** morphing with label term set to 0 ******************************* **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=2.322, neg=0, invalid=96777 0050: dt=18.496000, rms=2.326 (-0.189%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=2.326, neg=0, invalid=96777 0051: dt=129.472000, rms=2.326 (0.000%), neg=0, invalid=96777 0052: dt=129.472000, rms=2.326 (-0.000%), neg=0, invalid=96777 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=2.326, neg=0, invalid=96777 0053: dt=0.324000, rms=2.326 (0.000%), neg=0, invalid=96777 0054: dt=0.324000, rms=2.326 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=2.326, neg=0, invalid=96777 0055: dt=0.001582, rms=2.326 (0.000%), neg=0, invalid=96777 0056: dt=0.001582, rms=2.326 (-0.000%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=2.326, neg=0, invalid=96777 0057: dt=0.120370, rms=2.326 (0.000%), neg=0, invalid=96777 0058: dt=0.120370, rms=2.326 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=2.326, neg=0, invalid=96777 0059: dt=2.800000, rms=2.326 (0.000%), neg=0, invalid=96777 0060: dt=2.800000, rms=2.326 (-0.000%), neg=0, invalid=96777 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=2.326, neg=0, invalid=96777 0061: dt=0.063000, rms=2.326 (0.000%), neg=0, invalid=96777 0062: dt=0.063000, rms=2.326 (0.000%), neg=0, invalid=96777 0063: dt=0.063000, rms=2.326 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=2.326, neg=0, invalid=96777 0064: dt=1.728000, rms=2.326 (0.000%), neg=0, invalid=96777 0065: dt=1.728000, rms=2.326 (-0.000%), neg=0, invalid=96777 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=2.326, neg=0, invalid=96777 0066: dt=0.448000, rms=2.326 (0.000%), neg=0, invalid=96777 0067: dt=0.112000, rms=2.326 (0.000%), neg=0, invalid=96777 0068: dt=0.112000, rms=2.326 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=2.326, neg=0, invalid=96777 0069: dt=4.096000, rms=2.326 (0.000%), neg=0, invalid=96777 0070: dt=4.096000, rms=2.326 (0.000%), neg=0, invalid=96777 0071: dt=4.096000, rms=2.326 (-0.000%), neg=0, invalid=96777 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=2.326, neg=0, invalid=96777 0072: dt=0.321429, rms=2.326 (0.000%), neg=0, invalid=96777 0073: dt=0.000000, rms=2.326 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=2.326, neg=0, invalid=96777 0074: dt=0.448000, rms=2.326 (0.000%), neg=0, invalid=96777 0075: dt=0.000023, rms=2.326 (0.000%), neg=0, invalid=96777 0076: dt=0.000023, rms=2.326 (0.000%), neg=0, invalid=96777 0077: dt=0.000023, rms=2.326 (-0.000%), neg=0, invalid=96777 writing output transformation to transforms/talairach.m3z... GCAMwrite registration took 1 hours, 16 minutes and 14 seconds. #-------------------------------------- #@# CA Reg Inv Mon Dec 7 18:12:04 CET 2015 /NAS/tupac/matthieu/FS5.3/M0_2013-02-19/mri mri_ca_register -invert-and-save transforms/talairach.m3z Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z Inverting GCAM Saving inverse #-------------------------------------- #@# Remove Neck Mon Dec 7 18:13:53 CET 2015 mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z /home/global//freesurfer5.3//average/RB_all_2008-03-26.gca nu_noneck.mgz erasing everything more than 25 mm from possible brain reading atlas '/home/global//freesurfer5.3//average/RB_all_2008-03-26.gca'... reading input volume 'nu.mgz'... reading transform 'transforms/talairach.m3z'... removing structures at least 25 mm from brain... 10824359 nonbrain voxels erased writing output to nu_noneck.mgz... nonbrain removal took 1 minutes and 59 seconds. #-------------------------------------- #@# SkullLTA Mon Dec 7 18:15:53 CET 2015 mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz /home/global//freesurfer5.3//average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull_2.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 5 using previously computed transform transforms/talairach.lta reading 1 input volumes... logging results to talairach_with_skull_2.log reading '/home/global//freesurfer5.3//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_noneck.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 = (43, 23, 21) --> (205, 215, 199) using (97, 87, 110) as brain centroid... mean wm in atlas = 126, using box (77,63,88) --> (116, 110,131) to find MRI wm before smoothing, mri peak at 94 after smoothing, mri peak at 94, scaling input intensities by 1.340 scaling channel 0 by 1.34043 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.6, old_max_log_p =-4.7 (thresh=-4.7) 1.222 0.049 -0.272 2.353; 0.125 0.937 0.373 -29.974; 0.279 -0.473 1.155 -2.838; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.5, old_max_log_p =-4.6 (thresh=-4.5) 1.222 0.049 -0.272 2.353; 0.173 0.933 0.560 -55.193; 0.241 -0.547 1.014 24.430; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.5, old_max_log_p =-4.5 (thresh=-4.5) 1.150 -0.021 -0.127 -4.767; 0.199 1.072 0.644 -81.639; 0.079 -0.548 1.041 41.236; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 3 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.5, old_max_log_p =-4.5 (thresh=-4.5) 1.150 -0.021 -0.127 -4.767; 0.199 1.072 0.644 -81.639; 0.079 -0.548 1.041 41.236; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.5, old_max_log_p =-4.5 (thresh=-4.5) 1.089 -0.083 -0.281 29.428; 0.296 1.084 0.537 -83.635; 0.206 -0.475 1.064 15.011; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 5 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.5, old_max_log_p =-4.5 (thresh=-4.5) 1.089 -0.083 -0.281 29.428; 0.296 1.084 0.537 -83.635; 0.206 -0.475 1.064 15.011; 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=-4.4, old_max_log_p =-4.5 (thresh=-4.5) 1.091 -0.032 -0.299 25.498; 0.260 1.093 0.540 -80.463; 0.245 -0.469 1.060 8.696; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.4, old_max_log_p =-4.4 (thresh=-4.4) 1.091 -0.032 -0.299 25.967; 0.260 1.094 0.540 -80.699; 0.245 -0.469 1.061 8.582; 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 1.09083 -0.03247 -0.29855 25.96711; 0.26036 1.09412 0.54045 -80.69916; 0.24501 -0.46923 1.06085 8.58190; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.09083 -0.03247 -0.29855 25.96711; 0.26036 1.09412 0.54045 -80.69916; 0.24501 -0.46923 1.06085 8.58190; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 4 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.091 -0.032 -0.299 25.967; 0.260 1.094 0.540 -80.699; 0.245 -0.469 1.061 8.582; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -4.4 (old=-4.7) transform before final EM align: 1.091 -0.032 -0.299 25.967; 0.260 1.094 0.540 -80.699; 0.245 -0.469 1.061 8.582; 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 1.09083 -0.03247 -0.29855 25.96711; 0.26036 1.09412 0.54045 -80.69916; 0.24501 -0.46923 1.06085 8.58190; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.09083 -0.03247 -0.29855 25.96711; 0.26036 1.09412 0.54045 -80.69916; 0.24501 -0.46923 1.06085 8.58190; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 011: -log(p) = 4.8 tol 0.000000 final transform: 1.091 -0.032 -0.299 25.967; 0.260 1.094 0.540 -80.699; 0.245 -0.469 1.061 8.582; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull_2.lta... registration took 36 minutes and 35 seconds. #-------------------------------------- #@# SubCort Seg Mon Dec 7 18:52:28 CET 2015 mri_ca_label -align norm.mgz transforms/talairach.m3z /home/global//freesurfer5.3//average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz sysname Linux hostname kent machine x86_64 setenv SUBJECTS_DIR /NAS/tupac/matthieu/FS5.3 cd /NAS/tupac/matthieu/FS5.3/M0_2013-02-19/mri mri_ca_label -align norm.mgz transforms/talairach.m3z /home/global//freesurfer5.3//average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz renormalizing sequences with structure alignment, equivalent to: -renormalize -renormalize_mean 0.500 -regularize 0.500 reading 1 input volumes... reading classifier array from /home/global//freesurfer5.3//average/RB_all_2008-03-26.gca... reading input volume from norm.mgz... average std[0] = 6.9 reading transform from transforms/talairach.m3z... Atlas used for the 3D morph was /home/global//freesurfer5.3//average/RB_all_2008-03-26.gca average std = 6.9 using min determinant for regularization = 4.7 0 singular and 0 ill-conditioned covariance matrices regularized labeling volume... renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.15151 (27) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.14982 (20) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.28003 (97) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.18160 (96) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.27536 (62) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.32745 (63) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.08597 (105) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.09209 (106) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.07826 (63) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.08598 (64) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.24164 (71) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.18227 (75) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.10629 (62) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.11668 (59) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.17849 (88) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.16819 (86) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.41688 (64) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.42394 (62) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.10041 (96) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.13978 (88) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.08514 (81) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.09624 (82) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.07543 (88) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.12757 (95) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.17004 (92) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.21361 (36) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.26069 (23) uniform distribution in MR - rejecting arbitrary fit gca peak Unknown = 0.94427 ( 0) gca peak Left_Cerebral_White_Matter = 0.09209 (106) gca peak Left_Cerebral_Cortex = 0.07826 (63) gca peak Left_Lateral_Ventricle = 0.15151 (27) gca peak Left_Inf_Lat_Vent = 0.31795 (35) gca peak Left_Cerebellum_White_Matter = 0.17849 (88) gca peak Left_Cerebellum_Cortex = 0.10629 (62) gca peak Left_Thalamus_Proper = 0.10041 (96) gca peak Left_Caudate = 0.18227 (75) gca peak Left_Putamen = 0.08514 (81) gca peak Left_Pallidum = 0.18160 (96) gca peak Third_Ventricle = 0.21361 (36) gca peak Fourth_Ventricle = 0.26069 (23) gca peak Brain_Stem = 0.07543 (88) gca peak Left_Hippocampus = 0.32745 (63) gca peak Left_Amygdala = 0.41688 (64) gca peak CSF = 0.14367 (38) gca peak Left_Accumbens_area = 0.57033 (70) gca peak Left_VentralDC = 0.17004 (92) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.65201 (62) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Cerebral_White_Matter = 0.08597 (105) gca peak Right_Cerebral_Cortex = 0.08598 (64) gca peak Right_Lateral_Ventricle = 0.14982 (20) gca peak Right_Inf_Lat_Vent = 0.31129 (32) gca peak Right_Cerebellum_White_Matter = 0.16819 (86) gca peak Right_Cerebellum_Cortex = 0.11668 (59) gca peak Right_Thalamus_Proper = 0.13978 (88) gca peak Right_Caudate = 0.24164 (71) gca peak Right_Putamen = 0.09624 (82) gca peak Right_Pallidum = 0.28003 (97) gca peak Right_Hippocampus = 0.27536 (62) gca peak Right_Amygdala = 0.42394 (62) gca peak Right_Accumbens_area = 0.30219 (72) gca peak Right_VentralDC = 0.12757 (95) gca peak Right_vessel = 0.83418 (60) gca peak Right_choroid_plexus = 0.10189 (48) gca peak Fifth_Ventricle = 0.72939 (42) gca peak WM_hypointensities = 0.14821 (82) gca peak non_WM_hypointensities = 0.10354 (53) gca peak Optic_Chiasm = 0.34849 (76) not using caudate to estimate GM means estimating mean gm scale to be 1.00 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.00 x + 0.0 setting left cbm cortex = 1.00 x + 0.00 setting right cbm cortex = 1.00 x + 0.00 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.15151 (27) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.14982 (20) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.28003 (97) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.18160 (96) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.27536 (62) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.32745 (63) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.08597 (105) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.09209 (106) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.07826 (63) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.08598 (64) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.24164 (71) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.18227 (75) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.10629 (62) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.11668 (59) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.17849 (88) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.16819 (86) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.41688 (64) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.42394 (62) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.10041 (96) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.13978 (88) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.08514 (81) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.09624 (82) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.07543 (88) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.12757 (95) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.17004 (92) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.21361 (36) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.26069 (23) uniform distribution in MR - rejecting arbitrary fit gca peak Unknown = 0.94427 ( 0) gca peak Left_Cerebral_White_Matter = 0.09209 (106) gca peak Left_Cerebral_Cortex = 0.07826 (63) gca peak Left_Lateral_Ventricle = 0.15151 (27) gca peak Left_Inf_Lat_Vent = 0.31795 (35) gca peak Left_Cerebellum_White_Matter = 0.17849 (88) gca peak Left_Cerebellum_Cortex = 0.10629 (62) gca peak Left_Thalamus_Proper = 0.10041 (96) gca peak Left_Caudate = 0.18227 (75) gca peak Left_Putamen = 0.08514 (81) gca peak Left_Pallidum = 0.18160 (96) gca peak Third_Ventricle = 0.21361 (36) gca peak Fourth_Ventricle = 0.26069 (23) gca peak Brain_Stem = 0.07543 (88) gca peak Left_Hippocampus = 0.32745 (63) gca peak Left_Amygdala = 0.41688 (64) gca peak CSF = 0.14367 (38) gca peak Left_Accumbens_area = 0.57033 (70) gca peak Left_VentralDC = 0.17004 (92) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.65201 (62) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Cerebral_White_Matter = 0.08597 (105) gca peak Right_Cerebral_Cortex = 0.08598 (64) gca peak Right_Lateral_Ventricle = 0.14982 (20) gca peak Right_Inf_Lat_Vent = 0.31129 (32) gca peak Right_Cerebellum_White_Matter = 0.16819 (86) gca peak Right_Cerebellum_Cortex = 0.11668 (59) gca peak Right_Thalamus_Proper = 0.13978 (88) gca peak Right_Caudate = 0.24164 (71) gca peak Right_Putamen = 0.09624 (82) gca peak Right_Pallidum = 0.28003 (97) gca peak Right_Hippocampus = 0.27536 (62) gca peak Right_Amygdala = 0.42394 (62) gca peak Right_Accumbens_area = 0.30219 (72) gca peak Right_VentralDC = 0.12757 (95) gca peak Right_vessel = 0.83418 (60) gca peak Right_choroid_plexus = 0.10189 (48) gca peak Fifth_Ventricle = 0.72939 (42) gca peak WM_hypointensities = 0.14821 (82) gca peak non_WM_hypointensities = 0.10354 (53) gca peak Optic_Chiasm = 0.34849 (76) not using caudate to estimate GM means estimating mean gm scale to be 1.00 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.00 x + 0.0 setting left cbm cortex = 1.00 x + 0.00 setting right cbm cortex = 1.00 x + 0.00 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 140 gm and wm labels changed (%100 to gray, % 0 to white out of all changed labels) 308 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 25825 changed. image ll: -15.791, PF=1.000 pass 2: 5123 changed. pass 3: 1919 changed. writing labeled volume to aseg.auto_noCCseg.mgz... auto-labeling took 26 minutes and 49 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /NAS/tupac/matthieu/FS5.3/M0_2013-02-19/mri/transforms/cc_up.lta M0_2013-02-19 will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /NAS/tupac/matthieu/FS5.3/M0_2013-02-19/mri/transforms/cc_up.lta reading aseg from /NAS/tupac/matthieu/FS5.3/M0_2013-02-19/mri/aseg.auto_noCCseg.mgz reading norm from /NAS/tupac/matthieu/FS5.3/M0_2013-02-19/mri/norm.mgz 134733 voxels in left wm, 147119 in right wm, xrange [84, 171] searching rotation angles z=[-47 -33], y=[ 4 18] searching scale 1 Z rot -47.4 searching scale 1 Z rot -47.1 searching scale 1 Z rot -46.9 searching scale 1 Z rot -46.6 searching scale 1 Z rot -46.4 searching scale 1 Z rot -46.1 searching scale 1 Z rot -45.9 searching scale 1 Z rot -45.6 searching scale 1 Z rot -45.4 searching scale 1 Z rot -45.1 searching scale 1 Z rot -44.9 searching scale 1 Z rot -44.6 searching scale 1 Z rot -44.4 searching scale 1 Z rot -44.1 searching scale 1 Z rot -43.9 searching scale 1 Z rot -43.6 searching scale 1 Z rot -43.4 searching scale 1 Z rot -43.1 searching scale 1 Z rot -42.9 searching scale 1 Z rot -42.6 searching scale 1 Z rot -42.4 searching scale 1 Z rot -42.1 searching scale 1 Z rot -41.9 searching scale 1 Z rot -41.6 searching scale 1 Z rot -41.4 searching scale 1 Z rot -41.1 searching scale 1 Z rot -40.9 searching scale 1 Z rot -40.6 searching scale 1 Z rot -40.4 searching scale 1 Z rot -40.1 searching scale 1 Z rot -39.9 searching scale 1 Z rot -39.6 searching scale 1 Z rot -39.4 searching scale 1 Z rot -39.1 searching scale 1 Z rot -38.9 searching scale 1 Z rot -38.6 searching scale 1 Z rot -38.4 searching scale 1 Z rot -38.1 searching scale 1 Z rot -37.9 searching scale 1 Z rot -37.6 searching scale 1 Z rot -37.4 searching scale 1 Z rot -37.1 global minimum found at slice 143.0, rotations (14.05, -44.15) final transformation (x=143.0, yr=14.053, zr=-44.146): 0.696 0.696 0.174 -51.477; -0.676 0.718 -0.169 183.750; -0.243 0.000 0.970 47.285; 0.000 0.000 0.000 1.000;