‫جمعه ۲۳ دسامبر ۱۶، ساعت ۰۴:۴۵:۴۸ (IRST)‬ /home/fmri-04/Documents/workshop/subjects/Subject004 /usr/local/freesurfer/bin/recon-all -subjid Subject004 -i /home/fmri-04/Desktop/TEST/T1Img/Subject004/mprage.nii -all subjid Subject004 setenv SUBJECTS_DIR /home/fmri-04/Documents/workshop/subjects FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Linux fmri04 3.19.0-25-generic #26~14.04.1-Ubuntu SMP Fri Jul 24 21:16:20 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 23667 maxlocks unlimited maxsignal 23667 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 6080200 5507880 572320 36 3428 130684 -/+ buffers/cache: 5373768 706432 Swap: 9764860 5370056 4394804 ######################################## 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: 2016/12/23-01:15:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: fmri-04 Machine: fmri04 Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 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: 2016/12/23-01:15:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: fmri-04 Machine: fmri04 Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 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: 2016/12/23-01:15:53-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: fmri-04 Machine: fmri04 Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/23-01:15:54-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: fmri-04 Machine: fmri04 Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/23-01:15:54-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: fmri-04 Machine: fmri04 Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/23-01:15:55-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: fmri-04 Machine: fmri04 Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/23-01:15:55-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: fmri-04 Machine: fmri04 Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/23-01:15:55-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: fmri-04 Machine: fmri04 Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ======= NUMBER OF OPENMP THREADS = 1 ======= ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/23-01:15:56-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: fmri-04 Machine: fmri04 Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/23-01:15:56-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: fmri-04 Machine: fmri04 Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/23-01:15:57-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: fmri-04 Machine: fmri04 Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/23-01:15:57-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: fmri-04 Machine: fmri04 Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/23-01:15:58-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: fmri-04 Machine: fmri04 Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/23-01:15:58-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: fmri-04 Machine: fmri04 Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/23-01:15:59-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: fmri-04 Machine: fmri04 Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/23-01:15:59-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: fmri-04 Machine: fmri04 Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/23-01:16:00-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: fmri-04 Machine: fmri04 Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/23-01:16:00-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: fmri-04 Machine: fmri04 Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/23-01:16:01-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: fmri-04 Machine: fmri04 Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/23-01:16:01-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: fmri-04 Machine: fmri04 Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/23-01:16:02-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: fmri-04 Machine: fmri04 Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/23-01:16:02-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: fmri-04 Machine: fmri04 Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/23-01:16:03-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: fmri-04 Machine: fmri04 Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/23-01:16:03-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: fmri-04 Machine: fmri04 Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/23-01:16:04-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: fmri-04 Machine: fmri04 Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/23-01:16:04-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: fmri-04 Machine: fmri04 Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/23-01:16:05-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: fmri-04 Machine: fmri04 Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/23-01:16:05-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: fmri-04 Machine: fmri04 Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/23-01:16:05-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: fmri-04 Machine: fmri04 Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/23-01:16:06-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: fmri-04 Machine: fmri04 Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/23-01:16:06-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: fmri-04 Machine: fmri04 Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/23-01:16:07-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: fmri-04 Machine: fmri04 Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 $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: 2016/12/23-01:16:07-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: fmri-04 Machine: fmri04 Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 $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: 2016/12/23-01:16:08-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: fmri-04 Machine: fmri04 Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/23-01:16:08-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: fmri-04 Machine: fmri04 Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/23-01:16:08-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: fmri-04 Machine: fmri04 Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/23-01:16:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: fmri-04 Machine: fmri04 Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/23-01:16:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: fmri-04 Machine: fmri04 Platform: Linux PlatformVersion: 3.19.0-25-generic CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /usr/local/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /usr/local/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### /home/fmri-04/Documents/workshop/subjects/Subject004 mri_convert /home/fmri-04/Desktop/TEST/T1Img/Subject004/mprage.nii /home/fmri-04/Documents/workshop/subjects/Subject004/mri/orig/001.mgz mri_convert /home/fmri-04/Desktop/TEST/T1Img/Subject004/mprage.nii /home/fmri-04/Documents/workshop/subjects/Subject004/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/fmri-04/Desktop/TEST/T1Img/Subject004/mprage.nii... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, 1, 0) k_ras = (-0, -0, 1) writing to /home/fmri-04/Documents/workshop/subjects/Subject004/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor ‫جمعه ۲۳ دسامبر ۱۶، ساعت ۰۴:۴۶:۱۵ (IRST)‬ Found 1 runs /home/fmri-04/Documents/workshop/subjects/Subject004/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 /home/fmri-04/Documents/workshop/subjects/Subject004/mri/orig/001.mgz /home/fmri-04/Documents/workshop/subjects/Subject004/mri/rawavg.mgz /home/fmri-04/Documents/workshop/subjects/Subject004 mri_convert /home/fmri-04/Documents/workshop/subjects/Subject004/mri/rawavg.mgz /home/fmri-04/Documents/workshop/subjects/Subject004/mri/orig.mgz --conform mri_convert /home/fmri-04/Documents/workshop/subjects/Subject004/mri/rawavg.mgz /home/fmri-04/Documents/workshop/subjects/Subject004/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/fmri-04/Documents/workshop/subjects/Subject004/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, 1, 0) k_ras = (-0, -0, 1) Original Data has (1.33, 1, 1) mm size and (128, 256, 256) 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 /home/fmri-04/Documents/workshop/subjects/Subject004/mri/orig.mgz... mri_add_xform_to_header -c /home/fmri-04/Documents/workshop/subjects/Subject004/mri/transforms/talairach.xfm /home/fmri-04/Documents/workshop/subjects/Subject004/mri/orig.mgz /home/fmri-04/Documents/workshop/subjects/Subject004/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach ‫جمعه ۲۳ دسامبر ۱۶، ساعت ۰۴:۴۶:۲۴ (IRST)‬ /home/fmri-04/Documents/workshop/subjects/Subject004/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 ‫جمعه ۲۳ دسامبر ۱۶، ساعت ۰۴:۴۸:۴۵ (IRST)‬ /home/fmri-04/Documents/workshop/subjects/Subject004/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.4063, pval=0.0643 >= threshold=0.0050) awk -f /usr/local/freesurfer/bin/extract_talairach_avi_QA.awk /home/fmri-04/Documents/workshop/subjects/Subject004/mri/transforms/talairach_avi.log tal_QC_AZS /home/fmri-04/Documents/workshop/subjects/Subject004/mri/transforms/talairach_avi.log TalAviQA: 0.97490 z-score: 0 #-------------------------------------------- #@# Nu Intensity Correction ‫جمعه ۲۳ دسامبر ۱۶، ساعت ۰۴:۴۸:۴۵ (IRST)‬ mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /home/fmri-04/Documents/workshop/subjects/Subject004/mri /usr/local/freesurfer/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $ Linux fmri04 3.19.0-25-generic #26~14.04.1-Ubuntu SMP Fri Jul 24 21:16:20 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux ‫جمعه ۲۳ دسامبر ۱۶، ساعت ۰۴:۴۸:۴۵ (IRST)‬ 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.27559 /home/fmri-04/Documents/workshop/subjects/Subject004/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.27559/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.27559/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=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.27559/nu0.mnc... -------------------------------------------------------- Iteration 1 ‫جمعه ۲۳ دسامبر ۱۶، ساعت ۰۴:۴۸:۵۰ (IRST)‬ nu_correct -clobber ./tmp.mri_nu_correct.mni.27559/nu0.mnc ./tmp.mri_nu_correct.mni.27559/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.27559/0/ defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 165. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 170. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 211. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1051. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1054. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1449. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1455. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1457. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1481. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1631. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1633. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1635. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1637. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1639. (Maybe you should just omit the defined()?) [fmri-04@fmri04:/home/fmri-04/Documents/workshop/subjects/Subject004/mri/] [2016-12-23 04:48:51] running: /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.27559/0/ ./tmp.mri_nu_correct.mni.27559/nu0.mnc ./tmp.mri_nu_correct.mni.27559/nu1.imp Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Number of iterations: 49 CV of field change: 0.000960388 [fmri-04@fmri04:/home/fmri-04/Documents/workshop/subjects/Subject004/mri/] [2016-12-23 04:49:16] running: /usr/local/freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.27559/nu0.mnc ./tmp.mri_nu_correct.mni.27559/0//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done -------------------------------------------------------- Iteration 2 ‫جمعه ۲۳ دسامبر ۱۶، ساعت ۰۴:۴۹:۲۰ (IRST)‬ nu_correct -clobber ./tmp.mri_nu_correct.mni.27559/nu1.mnc ./tmp.mri_nu_correct.mni.27559/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.27559/1/ defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 165. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 170. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 211. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1051. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1054. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1449. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1455. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1457. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1481. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1631. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1633. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1635. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1637. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1639. (Maybe you should just omit the defined()?) [fmri-04@fmri04:/home/fmri-04/Documents/workshop/subjects/Subject004/mri/] [2016-12-23 04:49:21] running: /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.27559/1/ ./tmp.mri_nu_correct.mni.27559/nu1.mnc ./tmp.mri_nu_correct.mni.27559/nu2.imp Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Number of iterations: 25 CV of field change: 0.00095279 [fmri-04@fmri04:/home/fmri-04/Documents/workshop/subjects/Subject004/mri/] [2016-12-23 04:49:34] running: /usr/local/freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.27559/nu1.mnc ./tmp.mri_nu_correct.mni.27559/1//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done mri_binarize --i ./tmp.mri_nu_correct.mni.27559/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.27559/ones.mgz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /home/fmri-04/Documents/workshop/subjects/Subject004/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.27559/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.27559/ones.mgz sysname Linux hostname fmri04 machine x86_64 user fmri-04 input ./tmp.mri_nu_correct.mni.27559/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.27559/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.27559/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.27559/sum.junk --avgwf ./tmp.mri_nu_correct.mni.27559/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.27559/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.27559/sum.junk --avgwf ./tmp.mri_nu_correct.mni.27559/input.mean.dat sysname Linux hostname fmri04 machine x86_64 user fmri-04 UseRobust 0 Loading ./tmp.mri_nu_correct.mni.27559/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.27559/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.27559/ones.mgz --i ./tmp.mri_nu_correct.mni.27559/nu2.mnc --sum ./tmp.mri_nu_correct.mni.27559/sum.junk --avgwf ./tmp.mri_nu_correct.mni.27559/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.27559/ones.mgz --i ./tmp.mri_nu_correct.mni.27559/nu2.mnc --sum ./tmp.mri_nu_correct.mni.27559/sum.junk --avgwf ./tmp.mri_nu_correct.mni.27559/output.mean.dat sysname Linux hostname fmri04 machine x86_64 user fmri-04 UseRobust 0 Loading ./tmp.mri_nu_correct.mni.27559/ones.mgz Loading ./tmp.mri_nu_correct.mni.27559/nu2.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.27559/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.27559/nu2.mnc ./tmp.mri_nu_correct.mni.27559/nu2.mnc mul .98569886316451989352 Saving result to './tmp.mri_nu_correct.mni.27559/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.27559/nu2.mnc nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.27559/nu2.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.27559/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 0 minutes and 6 seconds. mapping ( 4, 139) to ( 3, 110) ‫جمعه ۲۳ دسامبر ۱۶، ساعت ۰۴:۵۰:۲۶ (IRST)‬ mri_nu_correct.mni done mri_add_xform_to_header -c /home/fmri-04/Documents/workshop/subjects/Subject004/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization ‫جمعه ۲۳ دسامبر ۱۶، ساعت ۰۴:۵۰:۲۷ (IRST)‬ /home/fmri-04/Documents/workshop/subjects/Subject004/mri mri_normalize -g 1 nu.mgz T1.mgz using max gradient = 1.000 reading from nu.mgz... normalizing image... talairach transform 0.969 0.074 -0.058 -8.140; -0.086 1.112 -0.161 -23.158; 0.040 0.158 1.029 -43.199; 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 = 21 Starting OpenSpline(): npoints = 21 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 109 gm peak at 61 (61), valley at 38 (38) csf peak at 30, setting threshold to 50 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 61 (61), valley at 29 (29) csf peak at 30, setting threshold to 50 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 1 minutes and 39 seconds. #-------------------------------------------- #@# Skull Stripping ‫جمعه ۲۳ دسامبر ۱۶، ساعت ۰۴:۵۲:۰۷ (IRST)‬ /home/fmri-04/Documents/workshop/subjects/Subject004/mri mri_em_register -skull nu.mgz /usr/local/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta ======= NUMBER OF OPENMP THREADS = 1 ======= aligning to atlas containing skull, setting unknown_nbr_spacing = 5 reading 1 input volumes... logging results to talairach_with_skull.log reading '/usr/local/freesurfer/average/RB_all_withskull_2008-03-26.gca'... average std = 23.1 using min determinant for regularization = 53.4 0 singular and 5702 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 20.2 or > 943.7 total sample mean = 92.0 (1443 zeros) ************************************************ spacing=8, using 3481 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3481, passno 0, spacing 8 resetting wm mean[0]: 117 --> 126 resetting gm mean[0]: 74 --> 74 input volume #1 is the most T1-like using real data threshold=7.0 skull bounding box = (43, 30, 28) --> (215, 209, 212) using (100, 90, 120) as brain centroid... mean wm in atlas = 126, using box (79,68,97) --> (121, 112,142) to find MRI wm before smoothing, mri peak at 107 after smoothing, mri peak at 107, scaling input intensities by 1.178 scaling channel 0 by 1.17757 initial log_p = -4.4 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.339255 @ (0.000, 0.000, 0.000) max log p = -4.204378 @ (-4.545, 4.545, -4.545) max log p = -4.204378 @ (0.000, 0.000, 0.000) max log p = -4.166054 @ (-1.136, -3.409, -3.409) max log p = -4.148460 @ (0.568, -0.568, -5.114) max log p = -4.148460 @ (0.000, 0.000, 0.000) Found translation: (-5.1, 0.6, -13.1): log p = -4.148 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.9, old_max_log_p =-4.1 (thresh=-4.1) 1.000 0.000 0.000 -5.114; 0.000 1.140 -0.150 9.051; 0.000 0.150 1.140 -47.856; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.000 0.000 0.000 -5.114; 0.000 1.194 -0.320 23.270; 0.000 0.298 1.111 -61.166; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.8, old_max_log_p =-3.9 (thresh=-3.9) 0.978 -0.048 -0.068 11.395; 0.031 1.154 -0.165 3.342; 0.064 0.136 1.119 -52.174; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.8, old_max_log_p =-3.8 (thresh=-3.8) 0.958 -0.084 -0.061 19.255; 0.062 1.130 -0.164 0.066; 0.065 0.139 1.140 -55.140; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.8, old_max_log_p =-3.8 (thresh=-3.8) 0.958 -0.084 -0.061 19.255; 0.062 1.130 -0.164 0.066; 0.065 0.139 1.140 -55.140; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.8, old_max_log_p =-3.8 (thresh=-3.8) 0.959 -0.059 -0.084 18.355; 0.039 1.132 -0.153 2.936; 0.081 0.129 1.140 -56.411; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.8, old_max_log_p =-3.8 (thresh=-3.8) 0.959 -0.059 -0.084 18.355; 0.039 1.132 -0.153 2.936; 0.081 0.129 1.140 -56.411; 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 0.95924 -0.05872 -0.08379 18.35540; 0.03857 1.13167 -0.15265 2.93639; 0.08072 0.12855 1.14032 -56.41076; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 0.95924 -0.05872 -0.08379 18.35540; 0.03857 1.13167 -0.15265 2.93639; 0.08072 0.12855 1.14032 -56.41076; 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: 009: -log(p) = -0.0 tol 0.000010 Resulting transform: 0.959 -0.059 -0.084 18.355; 0.039 1.132 -0.153 2.936; 0.081 0.129 1.140 -56.411; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -3.8 (old=-4.4) transform before final EM align: 0.959 -0.059 -0.084 18.355; 0.039 1.132 -0.153 2.936; 0.081 0.129 1.140 -56.411; 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 0.95924 -0.05872 -0.08379 18.35540; 0.03857 1.13167 -0.15265 2.93639; 0.08072 0.12855 1.14032 -56.41076; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 0.95924 -0.05872 -0.08379 18.35540; 0.03857 1.13167 -0.15265 2.93639; 0.08072 0.12855 1.14032 -56.41076; 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) = 4.2 tol 0.000000 final transform: 0.959 -0.059 -0.084 18.355; 0.039 1.132 -0.153 2.936; 0.081 0.129 1.140 -56.411; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull.lta... registration took 26 minutes and 39 seconds. mri_watershed -T1 -brain_atlas /usr/local/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details) ********************************************************* The input file is T1.mgz The output file is brainmask.auto.mgz Weighting the input with atlas information before watershed *************************WATERSHED************************** Sorting... first estimation of the COG coord: x=129 y=112 z=124 r=80 first estimation of the main basin volume: 2149812 voxels Looking for seedpoints 2 found in the cerebellum 17 found in the rest of the brain global maximum in x=164, y=110, z=90, 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=21643836606 voxels, voxel volume =1.000 = 21643836606 mmm3 = 21643837.440 cm3 done. PostAnalyze...Basin Prior 32 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=129,y=114, z=117, r=8947 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=0, CSF_intensity=9, CSF_MAX=38 , nb = 44252 RIGHT_CER CSF_MIN=0, CSF_intensity=9, CSF_MAX=28 , nb = -1060241824 LEFT_CER CSF_MIN=0, CSF_intensity=9, CSF_MAX=28 , nb = 1084206437 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=38 , nb = 1094296038 LEFT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=39 , nb = 1074063844 OTHER CSF_MIN=0, CSF_intensity=14, CSF_MAX=35 , nb = 1075413804 Problem with the least square interpolation in GM_MIN calculation. (2) Problem with the least square interpolation in GM_MIN calculation. CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 38, 39, 41, 57 after analyzing : 38, 40, 41, 44 RIGHT_CER before analyzing : 28, 35, 42, 60 after analyzing : 28, 39, 42, 44 LEFT_CER before analyzing : 28, 35, 42, 60 after analyzing : 28, 39, 42, 44 RIGHT_BRAIN before analyzing : 38, 39, 41, 57 after analyzing : 38, 40, 41, 44 LEFT_BRAIN before analyzing : 39, 40, 41, 57 after analyzing : 39, 40, 41, 44 OTHER before analyzing : 35, 34, 33, 58 after analyzing : 25, 34, 34, 40 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...60 iterations *********************VALIDATION********************* curvature mean = -0.013, std = 0.010 curvature mean = 71.984, std = 6.328 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 9.60, sigma = 15.92 after rotation: sse = 9.60, sigma = 15.92 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 11.10, its var is 15.24 before Erosion-Dilatation 13.55% of inacurate vertices after Erosion-Dilatation 19.29% of inacurate vertices Validation of the shape of the surface done. Scaling of atlas fields onto current surface fields ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...43 iterations mri_strip_skull: done peeling brain Brain Size = 1834249 voxels, voxel volume = 1.000 mm3 = 1834249 mmm3 = 1834.249 cm3 ****************************** Saving brainmask.auto.mgz done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration ‫جمعه ۲۳ دسامبر ۱۶، ساعت ۰۵:۱۹:۲۱ (IRST)‬ /home/fmri-04/Documents/workshop/subjects/Subject004/mri mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /usr/local/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.lta ======= NUMBER OF OPENMP THREADS = 1 ======= 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 '/usr/local/freesurfer/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=26.9 skull bounding box = (54, 47, 43) --> (202, 158, 202) using (103, 84, 123) as brain centroid... mean wm in atlas = 107, using box (85,70,103) --> (121, 97,142) to find MRI wm before smoothing, mri peak at 105 after smoothing, mri peak at 106, scaling input intensities by 1.009 scaling channel 0 by 1.00943 initial log_p = -4.2 ************************************************ First Search limited to translation only. ************************************************ max log p = -3.822523 @ (-9.091, 9.091, -9.091) max log p = -3.702406 @ (4.545, -4.545, -4.545) max log p = -3.702406 @ (0.000, 0.000, 0.000) max log p = -3.702110 @ (-1.136, 1.136, 5.682) max log p = -3.685815 @ (-0.568, 1.705, -0.568) max log p = -3.670552 @ (-0.852, -2.557, 0.284) Found translation: (-7.1, 4.8, -8.2): log p = -3.671 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.5, old_max_log_p =-3.7 (thresh=-3.7) 0.925 0.000 0.000 2.941; 0.000 1.066 -0.140 13.261; 0.000 0.140 1.066 -39.212; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.5, old_max_log_p =-3.5 (thresh=-3.5) 0.994 0.000 0.000 -6.349; 0.000 1.066 -0.140 13.261; 0.000 0.130 0.986 -28.372; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.5, old_max_log_p =-3.5 (thresh=-3.5) 0.994 0.000 0.000 -6.349; 0.000 1.066 -0.140 13.261; 0.000 0.130 0.986 -28.372; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.3, old_max_log_p =-3.5 (thresh=-3.5) 0.952 -0.048 -0.092 19.525; 0.033 1.088 -0.113 3.293; 0.099 0.098 1.022 -38.424; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.3, old_max_log_p =-3.3 (thresh=-3.3) 0.952 -0.048 -0.092 19.525; 0.029 1.084 -0.146 9.933; 0.100 0.133 1.018 -42.128; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 5 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.3, old_max_log_p =-3.3 (thresh=-3.3) 0.952 -0.048 -0.092 19.525; 0.029 1.084 -0.146 9.933; 0.100 0.133 1.018 -42.128; 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=-3.3, old_max_log_p =-3.3 (thresh=-3.3) 0.954 -0.063 -0.065 16.748; 0.047 1.081 -0.130 5.216; 0.076 0.117 1.026 -39.098; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.3, old_max_log_p =-3.3 (thresh=-3.3) 0.955 -0.063 -0.065 16.619; 0.046 1.080 -0.130 5.350; 0.076 0.117 1.026 -39.098; 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 0.95548 -0.06273 -0.06479 16.61881; 0.04650 1.08010 -0.13032 5.34967; 0.07606 0.11728 1.02583 -39.09846; 0.00000 0.00000 0.00000 1.00000; nsamples 2772 Quasinewton: input matrix 0.95548 -0.06273 -0.06479 16.61881; 0.04650 1.08010 -0.13032 5.34967; 0.07606 0.11728 1.02583 -39.09846; 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: 010: -log(p) = -0.0 tol 0.000010 Resulting transform: 0.955 -0.063 -0.065 16.619; 0.046 1.080 -0.130 5.350; 0.076 0.117 1.026 -39.098; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -3.3 (old=-4.2) transform before final EM align: 0.955 -0.063 -0.065 16.619; 0.046 1.080 -0.130 5.350; 0.076 0.117 1.026 -39.098; 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 0.95548 -0.06273 -0.06479 16.61881; 0.04650 1.08010 -0.13032 5.34967; 0.07606 0.11728 1.02583 -39.09846; 0.00000 0.00000 0.00000 1.00000; nsamples 312841 Quasinewton: input matrix 0.95548 -0.06273 -0.06479 16.61881; 0.04650 1.08010 -0.13032 5.34967; 0.07606 0.11728 1.02583 -39.09846; 0.00000 0.00000 0.00000 1.00000; dfp_em_step_func: 011: -log(p) = 3.7 after pass:transform: ( 0.96, -0.06, -0.06, 16.62) ( 0.05, 1.08, -0.13, 5.35) ( 0.08, 0.12, 1.03, -39.10) 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 TOLERANCESpass 2 through quasi-newton minimization... 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: 013: -log(p) = 3.7 tol 0.000000 final transform: 0.955 -0.063 -0.065 16.619; 0.046 1.080 -0.130 5.350; 0.076 0.117 1.026 -39.098; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach.lta... registration took 21 minutes and 13 seconds. #-------------------------------------- #@# CA Normalize ‫جمعه ۲۳ دسامبر ۱۶، ساعت ۰۵:۴۰:۳۵ (IRST)‬ /home/fmri-04/Documents/workshop/subjects/Subject004/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /usr/local/freesurfer/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 '/usr/local/freesurfer/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=26.9 skull bounding box = (54, 47, 43) --> (202, 158, 202) using (103, 84, 123) as brain centroid... mean wm in atlas = 107, using box (85,70,103) --> (121, 97,142) to find MRI wm before smoothing, mri peak at 105 after smoothing, mri peak at 106, scaling input intensities by 1.009 scaling channel 0 by 1.00943 using 244171 sample points... INFO: compute sample coordinates transform 0.955 -0.063 -0.065 16.619; 0.046 1.080 -0.130 5.350; 0.076 0.117 1.026 -39.098; 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 (123, 50, 39) --> (199, 162, 202) Left_Cerebral_White_Matter: limiting intensities to 94.0 --> 183.0 0 of 54 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (61, 52, 43) --> (134, 165, 204) Right_Cerebral_White_Matter: limiting intensities to 97.0 --> 183.0 0 of 62 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (130, 124, 57) --> (182, 164, 110) Left_Cerebellum_White_Matter: limiting intensities to 93.0 --> 183.0 0 of 15 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (82, 124, 57) --> (130, 167, 112) Right_Cerebellum_White_Matter: limiting intensities to 95.0 --> 183.0 0 of 18 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (114, 123, 88) --> (149, 184, 123) Brain_Stem: limiting intensities to 95.0 --> 183.0 0 of 10 (0.0%) samples deleted using 159 total control points for intensity normalization... bias field = 0.971 +- 0.084 0 of 159 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (123, 50, 39) --> (199, 162, 202) Left_Cerebral_White_Matter: limiting intensities to 92.0 --> 170.0 0 of 104 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (61, 52, 43) --> (134, 165, 204) Right_Cerebral_White_Matter: limiting intensities to 89.0 --> 170.0 0 of 112 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (130, 124, 57) --> (182, 164, 110) Left_Cerebellum_White_Matter: limiting intensities to 85.0 --> 170.0 0 of 41 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (82, 124, 57) --> (130, 167, 112) Right_Cerebellum_White_Matter: limiting intensities to 86.0 --> 170.0 0 of 57 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (114, 123, 88) --> (149, 184, 123) Brain_Stem: limiting intensities to 83.0 --> 170.0 0 of 68 (0.0%) samples deleted using 382 total control points for intensity normalization... bias field = 0.969 +- 0.062 0 of 382 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (123, 50, 39) --> (199, 162, 202) Left_Cerebral_White_Matter: limiting intensities to 104.0 --> 164.0 42 of 183 (23.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (61, 52, 43) --> (134, 165, 204) Right_Cerebral_White_Matter: limiting intensities to 86.0 --> 164.0 2 of 183 (1.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (130, 124, 57) --> (182, 164, 110) Left_Cerebellum_White_Matter: limiting intensities to 82.0 --> 164.0 0 of 75 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (82, 124, 57) --> (130, 167, 112) Right_Cerebellum_White_Matter: limiting intensities to 79.0 --> 164.0 0 of 92 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (114, 123, 88) --> (149, 184, 123) Brain_Stem: limiting intensities to 76.0 --> 164.0 0 of 97 (0.0%) samples deleted using 630 total control points for intensity normalization... bias field = 0.990 +- 0.047 3 of 586 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 16 seconds. #-------------------------------------- #@# CA Reg ‫جمعه ۲۳ دسامبر ۱۶، ساعت ۰۵:۴۱:۵۲ (IRST)‬ /home/fmri-04/Documents/workshop/subjects/Subject004/mri mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /usr/local/freesurfer/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 ======= NUMBER OF OPENMP THREADS = 1 ======= reading input volume 'norm.mgz'... reading GCA '/usr/local/freesurfer/average/RB_all_2008-03-26.gca'... label assignment complete, 0 changed (0.00%) det(m_affine) = 1.08 (predicted orig area = 7.4) 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=0.816, neg=0, invalid=96777 0001: dt=129.472000, rms=0.735 (9.892%), neg=0, invalid=96777 0002: dt=221.952000, rms=0.699 (4.976%), neg=0, invalid=96777 0003: dt=129.472000, rms=0.695 (0.505%), neg=0, invalid=96777 0004: dt=295.936000, rms=0.683 (1.754%), neg=0, invalid=96777 0005: dt=73.984000, rms=0.681 (0.344%), neg=0, invalid=96777 0006: dt=517.888000, rms=0.676 (0.676%), neg=0, invalid=96777 0007: dt=129.472000, rms=0.669 (1.005%), neg=0, invalid=96777 0008: dt=55.488000, rms=0.669 (0.046%), neg=0, invalid=96777 0009: dt=55.488000, rms=0.669 (0.058%), neg=0, invalid=96777 0010: dt=55.488000, rms=0.668 (0.112%), neg=0, invalid=96777 0011: dt=55.488000, rms=0.667 (0.206%), neg=0, invalid=96777 0012: dt=55.488000, rms=0.665 (0.282%), neg=0, invalid=96777 0013: dt=55.488000, rms=0.662 (0.335%), neg=0, invalid=96777 0014: dt=55.488000, rms=0.660 (0.318%), neg=0, invalid=96777 0015: dt=55.488000, rms=0.658 (0.311%), neg=0, invalid=96777 0016: dt=55.488000, rms=0.656 (0.284%), neg=0, invalid=96777 0017: dt=55.488000, rms=0.655 (0.253%), neg=0, invalid=96777 0018: dt=55.488000, rms=0.653 (0.252%), neg=0, invalid=96777 0019: dt=55.488000, rms=0.651 (0.251%), neg=0, invalid=96777 0020: dt=55.488000, rms=0.650 (0.257%), neg=0, invalid=96777 0021: dt=55.488000, rms=0.648 (0.222%), neg=0, invalid=96777 0022: dt=55.488000, rms=0.647 (0.180%), neg=0, invalid=96777 0023: dt=55.488000, rms=0.646 (0.164%), neg=0, invalid=96777 0024: dt=55.488000, rms=0.645 (0.162%), neg=0, invalid=96777 0025: dt=55.488000, rms=0.644 (0.162%), neg=0, invalid=96777 0026: dt=55.488000, rms=0.643 (0.142%), neg=0, invalid=96777 0027: dt=55.488000, rms=0.642 (0.119%), neg=0, invalid=96777 0028: dt=55.488000, rms=0.642 (0.120%), neg=0, invalid=96777 0029: dt=55.488000, rms=0.641 (0.123%), neg=0, invalid=96777 0030: dt=55.488000, rms=0.640 (0.099%), neg=0, invalid=96777 0031: dt=32.368000, rms=0.640 (0.004%), neg=0, invalid=96777 0032: dt=32.368000, rms=0.640 (0.018%), neg=0, invalid=96777 0033: dt=32.368000, rms=0.640 (0.042%), neg=0, invalid=96777 0034: dt=32.368000, rms=0.640 (0.027%), neg=0, invalid=96777 0035: dt=32.368000, rms=0.639 (0.031%), neg=0, invalid=96777 0036: dt=32.368000, rms=0.639 (0.016%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.639, neg=0, invalid=96777 0037: dt=129.472000, rms=0.639 (0.052%), neg=0, invalid=96777 0038: dt=517.888000, rms=0.638 (0.135%), neg=0, invalid=96777 0039: dt=110.976000, rms=0.638 (0.018%), neg=0, invalid=96777 0040: dt=110.976000, rms=0.638 (0.036%), neg=0, invalid=96777 0041: dt=110.976000, rms=0.638 (0.013%), neg=0, invalid=96777 0042: dt=110.976000, rms=0.638 (0.017%), neg=0, invalid=96777 0043: dt=110.976000, rms=0.638 (0.001%), neg=0, invalid=96777 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.643, neg=0, invalid=96777 0044: dt=145.152000, rms=0.629 (2.176%), neg=0, invalid=96777 0045: dt=20.736000, rms=0.628 (0.106%), neg=0, invalid=96777 0046: dt=20.736000, rms=0.626 (0.286%), neg=0, invalid=96777 0047: dt=20.736000, rms=0.624 (0.421%), neg=0, invalid=96777 0048: dt=20.736000, rms=0.620 (0.541%), neg=0, invalid=96777 0049: dt=20.736000, rms=0.616 (0.635%), neg=0, invalid=96777 0050: dt=20.736000, rms=0.612 (0.660%), neg=0, invalid=96777 0051: dt=20.736000, rms=0.608 (0.657%), neg=0, invalid=96777 0052: dt=20.736000, rms=0.604 (0.613%), neg=0, invalid=96777 0053: dt=20.736000, rms=0.601 (0.554%), neg=0, invalid=96777 0054: dt=20.736000, rms=0.598 (0.529%), neg=0, invalid=96777 0055: dt=20.736000, rms=0.595 (0.473%), neg=0, invalid=96777 0056: dt=20.736000, rms=0.593 (0.426%), neg=0, invalid=96777 0057: dt=20.736000, rms=0.590 (0.392%), neg=0, invalid=96777 0058: dt=20.736000, rms=0.588 (0.381%), neg=0, invalid=96777 0059: dt=20.736000, rms=0.586 (0.331%), neg=0, invalid=96777 0060: dt=20.736000, rms=0.584 (0.304%), neg=0, invalid=96777 0061: dt=20.736000, rms=0.583 (0.257%), neg=0, invalid=96777 0062: dt=20.736000, rms=0.581 (0.238%), neg=0, invalid=96777 0063: dt=20.736000, rms=0.580 (0.202%), neg=0, invalid=96777 0064: dt=20.736000, rms=0.579 (0.160%), neg=0, invalid=96777 0065: dt=20.736000, rms=0.578 (0.148%), neg=0, invalid=96777 0066: dt=20.736000, rms=0.578 (0.136%), neg=0, invalid=96777 0067: dt=20.736000, rms=0.577 (0.128%), neg=0, invalid=96777 0068: dt=20.736000, rms=0.576 (0.123%), neg=0, invalid=96777 0069: dt=20.736000, rms=0.576 (0.108%), neg=0, invalid=96777 0070: dt=103.680000, rms=0.575 (0.045%), neg=0, invalid=96777 0071: dt=103.680000, rms=0.575 (0.015%), neg=0, invalid=96777 0072: dt=103.680000, rms=0.574 (0.157%), neg=0, invalid=96777 0073: dt=103.680000, rms=0.574 (-0.145%), neg=0, invalid=96777 0074: dt=15.552000, rms=0.574 (0.009%), neg=0, invalid=96777 0075: dt=31.104000, rms=0.574 (0.014%), neg=0, invalid=96777 0076: dt=124.416000, rms=0.574 (0.038%), neg=0, invalid=96777 0077: dt=20.736000, rms=0.574 (0.011%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.574, neg=0, invalid=96777 0078: dt=36.288000, rms=0.574 (0.038%), neg=0, invalid=96777 0079: dt=36.288000, rms=0.574 (0.021%), neg=0, invalid=96777 0080: dt=36.288000, rms=0.574 (-0.008%), neg=0, invalid=96777 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.600, neg=0, invalid=96777 0081: dt=6.978723, rms=0.600 (0.083%), neg=0, invalid=96777 0082: dt=2.800000, rms=0.600 (0.006%), neg=0, invalid=96777 0083: dt=2.800000, rms=0.600 (-0.005%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.600, neg=0, invalid=96777 0084: dt=0.000000, rms=0.600 (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=0.670, neg=0, invalid=96777 0085: dt=5.831579, rms=0.651 (2.789%), neg=0, invalid=96777 0086: dt=3.456000, rms=0.650 (0.152%), neg=0, invalid=96777 0087: dt=3.456000, rms=0.650 (0.009%), neg=0, invalid=96777 0088: dt=3.456000, rms=0.650 (-0.335%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.650, neg=0, invalid=96777 0089: dt=0.000000, rms=0.650 (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=0.709, neg=0, invalid=96777 0090: dt=0.448000, rms=0.708 (0.076%), neg=0, invalid=96777 0091: dt=0.573529, rms=0.707 (0.097%), neg=0, invalid=96777 0092: dt=1.397849, rms=0.706 (0.200%), neg=0, invalid=96777 0093: dt=2.400000, rms=0.704 (0.341%), neg=0, invalid=96777 0094: dt=0.500000, rms=0.703 (0.054%), neg=0, invalid=96777 0095: dt=0.500000, rms=0.703 (0.018%), neg=0, invalid=96777 0096: dt=0.500000, rms=0.703 (0.042%), neg=0, invalid=96777 0097: dt=0.500000, rms=0.703 (0.042%), neg=0, invalid=96777 0098: dt=0.500000, rms=0.703 (0.012%), neg=0, invalid=96777 0099: dt=1.792000, rms=0.702 (0.050%), neg=0, invalid=96777 0100: dt=0.448000, rms=0.702 (0.005%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.702, neg=0, invalid=96777 0101: dt=1.024000, rms=0.701 (0.090%), neg=0, invalid=96777 0102: dt=0.000000, rms=0.701 (-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=0.665, neg=0, invalid=96777 0103: dt=0.320000, rms=0.654 (1.665%), neg=0, invalid=96777 0104: dt=0.000000, rms=0.654 (0.007%), neg=0, invalid=96777 0105: dt=0.050000, rms=0.654 (-0.193%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.654, neg=0, invalid=96777 0106: dt=0.000000, rms=0.654 (0.000%), neg=0, invalid=96777 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.11725 (24) mri peak = 0.11809 (12) Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (1456 voxels, overlap=0.201) Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (1456 voxels, peak = 9), gca=9.6 gca peak = 0.14022 (22) mri peak = 0.13629 (12) Right_Lateral_Ventricle (43): linear fit = 0.50 x + 0.0 (1305 voxels, overlap=0.007) Right_Lateral_Ventricle (43): linear fit = 0.50 x + 0.0 (1305 voxels, peak = 11), gca=10.9 gca peak = 0.24234 (100) mri peak = 0.06021 (92) Right_Pallidum (52): linear fit = 0.93 x + 0.0 (486 voxels, overlap=0.686) Right_Pallidum (52): linear fit = 0.93 x + 0.0 (486 voxels, peak = 92), gca=92.5 gca peak = 0.19192 (97) mri peak = 0.12041 (75) Left_Pallidum (13): linear fit = 0.77 x + 0.0 (521 voxels, overlap=0.034) Left_Pallidum (13): linear fit = 0.77 x + 0.0 (521 voxels, peak = 75), gca=75.2 gca peak = 0.24007 (63) mri peak = 0.07762 (63) Right_Hippocampus (53): linear fit = 0.95 x + 0.0 (864 voxels, overlap=0.961) Right_Hippocampus (53): linear fit = 0.95 x + 0.0 (864 voxels, peak = 60), gca=60.2 gca peak = 0.29892 (64) mri peak = 0.10201 (61) Left_Hippocampus (17): linear fit = 0.94 x + 0.0 (1058 voxels, overlap=0.928) Left_Hippocampus (17): linear fit = 0.94 x + 0.0 (1058 voxels, peak = 60), gca=59.8 gca peak = 0.12541 (104) mri peak = 0.07097 (109) Right_Cerebral_White_Matter (41): linear fit = 1.04 x + 0.0 (78756 voxels, overlap=0.760) Right_Cerebral_White_Matter (41): linear fit = 1.04 x + 0.0 (78756 voxels, peak = 109), gca=108.7 gca peak = 0.13686 (104) mri peak = 0.07830 (107) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (80678 voxels, overlap=0.824) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (80678 voxels, peak = 107), gca=106.6 gca peak = 0.11691 (63) mri peak = 0.04888 (58) Left_Cerebral_Cortex (3): linear fit = 0.88 x + 0.0 (37044 voxels, overlap=0.611) Left_Cerebral_Cortex (3): linear fit = 0.88 x + 0.0 (37044 voxels, peak = 56), gca=55.8 gca peak = 0.13270 (63) mri peak = 0.04848 (56) Right_Cerebral_Cortex (42): linear fit = 0.90 x + 0.0 (39252 voxels, overlap=0.839) Right_Cerebral_Cortex (42): linear fit = 0.90 x + 0.0 (39252 voxels, peak = 57), gca=57.0 gca peak = 0.15182 (70) mri peak = 0.12069 (71) Right_Caudate (50): linear fit = 0.99 x + 0.0 (454 voxels, overlap=0.934) Right_Caudate (50): linear fit = 0.99 x + 0.0 (454 voxels, peak = 69), gca=69.0 gca peak = 0.14251 (76) mri peak = 0.08579 (77) Left_Caudate (11): linear fit = 0.94 x + 0.0 (783 voxels, overlap=0.839) Left_Caudate (11): linear fit = 0.94 x + 0.0 (783 voxels, peak = 72), gca=71.8 gca peak = 0.12116 (60) mri peak = 0.04373 (59) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (25632 voxels, overlap=0.967) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (25632 voxels, peak = 62), gca=61.5 gca peak = 0.12723 (61) mri peak = 0.04511 (63) Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (25937 voxels, overlap=0.959) Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (25937 voxels, peak = 63), gca=62.5 gca peak = 0.22684 (88) mri peak = 0.08361 (91) Left_Cerebellum_White_Matter (7): linear fit = 1.04 x + 0.0 (8392 voxels, overlap=0.582) Left_Cerebellum_White_Matter (7): linear fit = 1.04 x + 0.0 (8392 voxels, peak = 92), gca=92.0 gca peak = 0.21067 (87) mri peak = 0.08201 (89) Right_Cerebellum_White_Matter (46): linear fit = 1.04 x + 0.0 (7394 voxels, overlap=0.731) Right_Cerebellum_White_Matter (46): linear fit = 1.04 x + 0.0 (7394 voxels, peak = 91), gca=90.9 gca peak = 0.25455 (62) mri peak = 0.07517 (63) Left_Amygdala (18): linear fit = 0.99 x + 0.0 (372 voxels, overlap=1.005) Left_Amygdala (18): linear fit = 0.99 x + 0.0 (372 voxels, peak = 61), gca=61.1 gca peak = 0.39668 (62) mri peak = 0.12163 (57) Right_Amygdala (54): linear fit = 0.90 x + 0.0 (178 voxels, overlap=0.433) Right_Amygdala (54): linear fit = 0.90 x + 0.0 (178 voxels, peak = 56), gca=56.1 gca peak = 0.10129 (93) mri peak = 0.05138 (106) Left_Thalamus_Proper (10): linear fit = 1.12 x + 0.0 (6316 voxels, overlap=0.614) Left_Thalamus_Proper (10): linear fit = 1.12 x + 0.0 (6316 voxels, peak = 105), gca=104.6 gca peak = 0.12071 (89) mri peak = 0.04941 (93) Right_Thalamus_Proper (49): linear fit = 1.10 x + 0.0 (4982 voxels, overlap=0.672) Right_Thalamus_Proper (49): linear fit = 1.10 x + 0.0 (4982 voxels, peak = 97), gca=97.5 gca peak = 0.13716 (82) mri peak = 0.05671 (82) Left_Putamen (12): linear fit = 0.99 x + 0.0 (2833 voxels, overlap=0.999) Left_Putamen (12): linear fit = 0.99 x + 0.0 (2833 voxels, peak = 81), gca=80.8 gca peak = 0.15214 (84) mri peak = 0.06010 (81) Right_Putamen (51): linear fit = 0.99 x + 0.0 (2885 voxels, overlap=0.982) Right_Putamen (51): linear fit = 0.99 x + 0.0 (2885 voxels, peak = 83), gca=82.7 gca peak = 0.08983 (85) mri peak = 0.06198 (92) Brain_Stem (16): linear fit = 1.09 x + 0.0 (12090 voxels, overlap=0.592) Brain_Stem (16): linear fit = 1.09 x + 0.0 (12090 voxels, peak = 92), gca=92.2 gca peak = 0.11809 (92) mri peak = 0.05231 (91) Right_VentralDC (60): linear fit = 1.08 x + 0.0 (862 voxels, overlap=0.811) Right_VentralDC (60): linear fit = 1.08 x + 0.0 (862 voxels, peak = 99), gca=98.9 gca peak = 0.12914 (94) mri peak = 0.06376 (106) Left_VentralDC (28): linear fit = 1.12 x + 0.0 (1062 voxels, overlap=0.528) Left_VentralDC (28): linear fit = 1.12 x + 0.0 (1062 voxels, peak = 106), gca=105.8 gca peak = 0.21100 (36) mri peak = 0.11255 (52) Third_Ventricle (14): linear fit = 1.40 x + 0.0 (101 voxels, overlap=0.076) Third_Ventricle (14): linear fit = 1.40 x + 0.0 (101 voxels, peak = 51), gca=50.6 gca peak = 0.13542 (27) mri peak = 0.13274 (15) Fourth_Ventricle (15): linear fit = 0.41 x + 0.0 (627 voxels, overlap=0.031) Fourth_Ventricle (15): linear fit = 0.41 x + 0.0 (627 voxels, peak = 11), gca=10.9 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.21802 (40) gca peak Fourth_Ventricle = 0.13542 (27) gca peak CSF = 0.17123 (45) gca peak Left_Accumbens_area = 0.25875 (69) 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_Inf_Lat_Vent = 0.28113 (34) gca peak Right_Accumbens_area = 0.27120 (72) 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 0.93 x + 0.0 estimating mean wm scale to be 1.03 x + 0.0 estimating mean csf scale to be 0.77 x + 0.0 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=0.696, neg=0, invalid=96777 0107: dt=8.092000, rms=0.695 (0.148%), neg=0, invalid=96777 0108: dt=8.092000, rms=0.694 (0.136%), neg=0, invalid=96777 0109: dt=4.000000, rms=0.694 (0.066%), neg=0, invalid=96777 0110: dt=0.031609, rms=0.694 (-0.001%), neg=0, invalid=96777 0111: dt=0.031609, rms=0.694 (0.000%), neg=0, invalid=96777 0112: dt=0.000988, rms=0.694 (0.000%), neg=0, invalid=96777 0113: dt=0.000247, rms=0.694 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.694, neg=0, invalid=96777 0114: dt=0.000000, rms=0.694 (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=0.694, neg=0, invalid=96777 0115: dt=82.944000, rms=0.665 (4.180%), neg=0, invalid=96777 0116: dt=36.288000, rms=0.654 (1.601%), neg=0, invalid=96777 0117: dt=145.152000, rms=0.639 (2.243%), neg=0, invalid=96777 0118: dt=36.288000, rms=0.633 (0.898%), neg=0, invalid=96777 0119: dt=31.104000, rms=0.632 (0.276%), neg=0, invalid=96777 0120: dt=145.152000, rms=0.625 (1.034%), neg=0, invalid=96777 0121: dt=9.072000, rms=0.623 (0.310%), neg=0, invalid=96777 0122: dt=9.072000, rms=0.622 (0.196%), neg=0, invalid=96777 0123: dt=2.268000, rms=0.622 (0.043%), neg=0, invalid=96777 0124: dt=0.283500, rms=0.622 (0.008%), neg=0, invalid=96777 0125: dt=0.141750, rms=0.622 (0.001%), neg=0, invalid=96777 0126: dt=0.070875, rms=0.622 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.622, neg=0, invalid=96777 0127: dt=0.035437, rms=0.622 (0.000%), neg=0, invalid=96777 0128: dt=0.035437, rms=0.622 (0.001%), neg=0, invalid=96777 0129: dt=0.008859, rms=0.622 (-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=0.623, neg=0, invalid=96777 0130: dt=0.001750, rms=0.623 (0.000%), neg=0, invalid=96777 0131: dt=0.000000, rms=0.623 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.623, neg=0, invalid=96777 0132: dt=0.000000, rms=0.623 (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=0.628, neg=0, invalid=96777 0133: dt=0.000000, rms=0.628 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.628, neg=0, invalid=96777 0134: dt=0.000000, rms=0.628 (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=0.638, neg=0, invalid=96777 0135: dt=0.448000, rms=0.632 (0.931%), neg=0, invalid=96777 0136: dt=1.280000, rms=0.618 (2.298%), neg=0, invalid=96777 0137: dt=1.280000, rms=0.609 (1.491%), neg=0, invalid=96777 0138: dt=1.792000, rms=0.600 (1.355%), neg=0, invalid=96777 0139: dt=1.792000, rms=0.596 (0.761%), neg=0, invalid=96777 0140: dt=1.792000, rms=0.593 (0.435%), neg=0, invalid=96777 0141: dt=1.792000, rms=0.592 (0.277%), neg=0, invalid=96777 0142: dt=1.792000, rms=0.591 (0.176%), neg=0, invalid=96777 0143: dt=6.144000, rms=0.588 (0.364%), neg=0, invalid=96777 0144: dt=1.024000, rms=0.588 (0.002%), neg=0, invalid=96777 0145: dt=1.024000, rms=0.588 (0.002%), neg=0, invalid=96777 0146: dt=1.024000, rms=0.588 (-0.011%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.588, neg=0, invalid=96777 0147: dt=1.792000, rms=0.587 (0.297%), neg=0, invalid=96777 0148: dt=1.792000, rms=0.586 (0.119%), neg=0, invalid=96777 0149: dt=2.750000, rms=0.586 (0.068%), neg=0, invalid=96777 0150: dt=4.096000, rms=0.585 (0.021%), neg=0, invalid=96777 0151: dt=2.048000, rms=0.585 (-0.010%), 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=0.572, neg=0, invalid=96777 0152: dt=0.158874, rms=0.565 (1.113%), neg=0, invalid=96777 0153: dt=0.007000, rms=0.565 (0.039%), neg=0, invalid=96777 0154: dt=0.007000, rms=0.565 (0.036%), neg=0, invalid=96777 0155: dt=0.007000, rms=0.565 (0.067%), neg=0, invalid=96777 0156: dt=0.007000, rms=0.564 (0.096%), neg=0, invalid=96777 0157: dt=0.007000, rms=0.563 (0.119%), neg=0, invalid=96777 0158: dt=0.007000, rms=0.563 (0.139%), neg=0, invalid=96777 0159: dt=0.007000, rms=0.562 (0.154%), neg=0, invalid=96777 0160: dt=0.007000, rms=0.561 (0.167%), neg=0, invalid=96777 0161: dt=0.007000, rms=0.560 (0.178%), neg=0, invalid=96777 0162: dt=0.007000, rms=0.559 (0.185%), neg=0, invalid=96777 0163: dt=0.007000, rms=0.558 (0.189%), neg=0, invalid=96777 0164: dt=0.007000, rms=0.557 (0.189%), neg=0, invalid=96777 0165: dt=0.007000, rms=0.556 (0.190%), neg=0, invalid=96777 0166: dt=0.007000, rms=0.555 (0.187%), neg=0, invalid=96777 0167: dt=0.007000, rms=0.554 (0.185%), neg=0, invalid=96777 0168: dt=0.007000, rms=0.553 (0.177%), neg=0, invalid=96777 0169: dt=0.007000, rms=0.552 (0.173%), neg=0, invalid=96777 0170: dt=0.007000, rms=0.551 (0.160%), neg=0, invalid=96777 0171: dt=0.007000, rms=0.550 (0.158%), neg=0, invalid=96777 0172: dt=0.007000, rms=0.549 (0.146%), neg=0, invalid=96777 0173: dt=0.007000, rms=0.548 (0.138%), neg=0, invalid=96777 0174: dt=0.007000, rms=0.548 (0.130%), neg=0, invalid=96777 0175: dt=0.007000, rms=0.547 (0.119%), neg=0, invalid=96777 0176: dt=0.007000, rms=0.546 (0.111%), neg=0, invalid=96777 0177: dt=0.007000, rms=0.546 (0.099%), neg=0, invalid=96777 0178: dt=0.007000, rms=0.545 (0.092%), neg=0, invalid=96777 0179: dt=0.007000, rms=0.545 (0.083%), neg=0, invalid=96777 0180: dt=0.007000, rms=0.544 (0.076%), neg=0, invalid=96777 0181: dt=0.007000, rms=0.544 (0.069%), neg=0, invalid=96777 0182: dt=0.007000, rms=0.544 (0.062%), neg=0, invalid=96777 0183: dt=0.007000, rms=0.543 (0.052%), neg=0, invalid=96777 0184: dt=0.007000, rms=0.543 (0.048%), neg=0, invalid=96777 0185: dt=0.007000, rms=0.543 (0.043%), neg=0, invalid=96777 0186: dt=0.007000, rms=0.543 (0.038%), neg=0, invalid=96777 0187: dt=0.007000, rms=0.543 (0.033%), neg=0, invalid=96777 0188: dt=0.007000, rms=0.542 (0.030%), neg=0, invalid=96777 0189: dt=0.007000, rms=0.542 (0.028%), neg=0, invalid=96777 0190: dt=0.007000, rms=0.542 (0.024%), neg=0, invalid=96777 0191: dt=0.007000, rms=0.542 (0.023%), neg=0, invalid=96777 0192: dt=0.112000, rms=0.542 (0.005%), neg=0, invalid=96777 0193: dt=0.112000, rms=0.542 (0.014%), neg=0, invalid=96777 0194: dt=0.056000, rms=0.542 (0.007%), neg=0, invalid=96777 0195: dt=0.056000, rms=0.542 (0.011%), neg=0, invalid=96777 0196: dt=0.056000, rms=0.542 (0.017%), neg=0, invalid=96777 0197: dt=0.056000, rms=0.542 (0.028%), neg=0, invalid=96777 0198: dt=0.056000, rms=0.541 (0.014%), neg=0, invalid=96777 0199: dt=0.056000, rms=0.541 (0.025%), neg=0, invalid=96777 0200: dt=0.056000, rms=0.541 (0.035%), neg=0, invalid=96777 0201: dt=0.056000, rms=0.541 (0.045%), neg=0, invalid=96777 0202: dt=0.056000, rms=0.541 (0.054%), neg=0, invalid=96777 0203: dt=0.056000, rms=0.540 (0.064%), neg=0, invalid=96777 0204: dt=0.056000, rms=0.540 (0.012%), neg=0, invalid=96777 0205: dt=0.056000, rms=0.540 (0.028%), neg=0, invalid=96777 0206: dt=0.056000, rms=0.540 (0.013%), neg=0, invalid=96777 0207: dt=0.056000, rms=0.540 (0.023%), neg=0, invalid=96777 0208: dt=0.056000, rms=0.540 (0.032%), neg=0, invalid=96777 0209: dt=0.056000, rms=0.540 (0.012%), neg=0, invalid=96777 0210: dt=0.056000, rms=0.540 (0.022%), neg=0, invalid=96777 0211: dt=0.056000, rms=0.539 (0.031%), neg=0, invalid=96777 0212: dt=0.056000, rms=0.539 (0.038%), neg=0, invalid=96777 0213: dt=0.056000, rms=0.539 (0.040%), neg=0, invalid=96777 0214: dt=0.056000, rms=0.539 (0.048%), neg=0, invalid=96777 0215: dt=0.056000, rms=0.538 (0.052%), neg=0, invalid=96777 0216: dt=0.056000, rms=0.538 (0.049%), neg=0, invalid=96777 0217: dt=0.056000, rms=0.538 (0.055%), neg=0, invalid=96777 0218: dt=0.056000, rms=0.538 (0.052%), neg=0, invalid=96777 0219: dt=0.056000, rms=0.537 (0.049%), neg=0, invalid=96777 0220: dt=0.056000, rms=0.537 (0.052%), neg=0, invalid=96777 0221: dt=0.056000, rms=0.537 (0.052%), neg=0, invalid=96777 0222: dt=0.056000, rms=0.536 (0.047%), neg=0, invalid=96777 0223: dt=0.056000, rms=0.536 (0.046%), neg=0, invalid=96777 0224: dt=0.056000, rms=0.536 (0.040%), neg=0, invalid=96777 0225: dt=0.056000, rms=0.536 (0.002%), neg=0, invalid=96777 0226: dt=0.056000, rms=0.536 (0.002%), neg=0, invalid=96777 0227: dt=0.056000, rms=0.536 (0.007%), neg=0, invalid=96777 0228: dt=0.056000, rms=0.536 (0.009%), neg=0, invalid=96777 0229: dt=0.056000, rms=0.536 (0.004%), neg=0, invalid=96777 0230: dt=0.112000, rms=0.536 (0.004%), neg=0, invalid=96777 0231: dt=0.112000, rms=0.536 (0.004%), neg=0, invalid=96777 0232: dt=0.112000, rms=0.536 (0.005%), neg=0, invalid=96777 0233: dt=0.112000, rms=0.536 (0.005%), neg=0, invalid=96777 0234: dt=0.112000, rms=0.536 (0.004%), neg=0, invalid=96777 0235: dt=0.112000, rms=0.536 (0.005%), neg=0, invalid=96777 0236: dt=0.014000, rms=0.536 (0.003%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.536, neg=0, invalid=96777 0237: dt=0.112000, rms=0.534 (0.251%), neg=0, invalid=96777 0238: dt=0.384000, rms=0.531 (0.604%), neg=0, invalid=96777 0239: dt=0.028000, rms=0.531 (0.004%), neg=0, invalid=96777 0240: dt=0.028000, rms=0.531 (0.008%), neg=0, invalid=96777 0241: dt=0.028000, rms=0.531 (0.012%), neg=0, invalid=96777 0242: dt=0.028000, rms=0.531 (0.015%), neg=0, invalid=96777 0243: dt=0.028000, rms=0.531 (0.017%), neg=0, invalid=96777 0244: dt=0.028000, rms=0.531 (0.020%), neg=0, invalid=96777 0245: dt=0.028000, rms=0.531 (0.001%), neg=0, invalid=96777 0246: dt=0.028000, rms=0.531 (0.002%), neg=0, invalid=96777 0247: dt=0.028000, rms=0.531 (0.002%), neg=0, invalid=96777 0248: dt=0.112000, rms=0.531 (0.004%), neg=0, invalid=96777 0249: dt=0.320000, rms=0.531 (0.004%), 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=0.527, neg=0, invalid=96777 0250: dt=8.092000, rms=0.527 (-0.001%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.527, neg=0, invalid=96777 0251: dt=129.472000, rms=0.527 (0.072%), neg=0, invalid=96777 0252: dt=129.472000, rms=0.527 (0.088%), neg=0, invalid=96777 0253: dt=32.368000, rms=0.526 (0.017%), neg=0, invalid=96777 0254: dt=32.368000, rms=0.526 (-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=0.527, neg=0, invalid=96777 0255: dt=36.288000, rms=0.525 (0.200%), neg=0, invalid=96777 0256: dt=103.680000, rms=0.523 (0.434%), neg=0, invalid=96777 0257: dt=25.920000, rms=0.523 (0.101%), neg=0, invalid=96777 0258: dt=25.920000, rms=0.522 (0.121%), neg=0, invalid=96777 0259: dt=25.920000, rms=0.521 (0.148%), neg=0, invalid=96777 0260: dt=25.920000, rms=0.521 (0.141%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0261: dt=25.920000, rms=0.520 (0.095%), neg=0, invalid=96777 0262: dt=25.920000, rms=0.520 (0.072%), neg=0, invalid=96777 0263: dt=124.416000, rms=0.519 (0.116%), neg=0, invalid=96777 0264: dt=15.552000, rms=0.519 (0.049%), neg=0, invalid=96777 0265: dt=15.552000, rms=0.519 (0.030%), neg=0, invalid=96777 0266: dt=15.552000, rms=0.518 (0.032%), neg=0, invalid=96777 0267: dt=15.552000, rms=0.518 (0.043%), neg=0, invalid=96777 0268: dt=15.552000, rms=0.518 (0.043%), neg=0, invalid=96777 0269: dt=15.552000, rms=0.518 (0.050%), neg=0, invalid=96777 0270: dt=15.552000, rms=0.518 (0.054%), neg=0, invalid=96777 0271: dt=15.552000, rms=0.517 (0.043%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.517, neg=0, invalid=96777 0272: dt=36.288000, rms=0.515 (0.409%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0273: dt=145.152000, rms=0.513 (0.487%), neg=0, invalid=96777 0274: dt=36.288000, rms=0.512 (0.132%), neg=0, invalid=96777 0275: dt=36.288000, rms=0.512 (0.073%), neg=0, invalid=96777 0276: dt=36.288000, rms=0.511 (0.082%), neg=0, invalid=96777 0277: dt=36.288000, rms=0.511 (0.102%), neg=0, invalid=96777 0278: dt=36.288000, rms=0.510 (0.118%), neg=0, invalid=96777 0279: dt=36.288000, rms=0.509 (0.165%), neg=0, invalid=96777 0280: dt=36.288000, rms=0.509 (0.122%), neg=0, invalid=96777 0281: dt=36.288000, rms=0.508 (0.091%), neg=0, invalid=96777 0282: dt=82.944000, rms=0.508 (0.061%), neg=0, invalid=96777 0283: dt=82.944000, rms=0.508 (-0.158%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.509, neg=0, invalid=96777 0284: dt=25.600000, rms=0.506 (0.468%), neg=0, invalid=96777 iter 0, gcam->neg = 4 after 6 iterations, nbhd size=1, neg = 0 0285: dt=32.000000, rms=0.503 (0.711%), neg=0, invalid=96777 0286: dt=7.719745, rms=0.501 (0.368%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0287: dt=38.400000, rms=0.499 (0.467%), neg=0, invalid=96777 0288: dt=7.515152, rms=0.497 (0.314%), neg=0, invalid=96777 0289: dt=38.400000, rms=0.495 (0.447%), neg=0, invalid=96777 0290: dt=6.744526, rms=0.494 (0.268%), neg=0, invalid=96777 0291: dt=44.800000, rms=0.492 (0.368%), neg=0, invalid=96777 0292: dt=7.565891, rms=0.491 (0.171%), neg=0, invalid=96777 0293: dt=7.565891, rms=0.490 (0.135%), neg=0, invalid=96777 0294: dt=7.565891, rms=0.490 (0.144%), neg=0, invalid=96777 0295: dt=7.565891, rms=0.489 (0.190%), neg=0, invalid=96777 0296: dt=7.565891, rms=0.488 (0.204%), neg=0, invalid=96777 0297: dt=7.565891, rms=0.486 (0.235%), neg=0, invalid=96777 0298: dt=7.565891, rms=0.485 (0.259%), neg=0, invalid=96777 0299: dt=7.565891, rms=0.484 (0.249%), neg=0, invalid=96777 0300: dt=7.565891, rms=0.483 (0.251%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0301: dt=7.565891, rms=0.482 (0.248%), neg=0, invalid=96777 0302: dt=7.565891, rms=0.480 (0.259%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0303: dt=7.565891, rms=0.479 (0.253%), neg=0, invalid=96777 0304: dt=7.565891, rms=0.478 (0.221%), neg=0, invalid=96777 0305: dt=7.565891, rms=0.477 (0.201%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0306: dt=7.565891, rms=0.476 (0.166%), neg=0, invalid=96777 0307: dt=7.565891, rms=0.476 (0.158%), neg=0, invalid=96777 0308: dt=7.565891, rms=0.475 (0.154%), neg=0, invalid=96777 0309: dt=7.565891, rms=0.474 (0.134%), neg=0, invalid=96777 0310: dt=7.565891, rms=0.474 (0.125%), neg=0, invalid=96777 0311: dt=7.565891, rms=0.473 (0.107%), neg=0, invalid=96777 0312: dt=19.200000, rms=0.473 (0.041%), neg=0, invalid=96777 0313: dt=19.200000, rms=0.473 (-0.026%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.473, neg=0, invalid=96777 iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0314: dt=25.600000, rms=0.471 (0.435%), neg=0, invalid=96777 0315: dt=11.200000, rms=0.470 (0.153%), neg=0, invalid=96777 0316: dt=11.200000, rms=0.470 (0.072%), neg=0, invalid=96777 0317: dt=11.200000, rms=0.469 (0.095%), neg=0, invalid=96777 0318: dt=11.200000, rms=0.469 (0.127%), neg=0, invalid=96777 0319: dt=11.200000, rms=0.468 (0.071%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0320: dt=11.200000, rms=0.468 (0.047%), neg=0, invalid=96777 0321: dt=11.200000, rms=0.468 (0.029%), neg=0, invalid=96777 0322: dt=11.200000, rms=0.468 (0.024%), neg=0, invalid=96777 0323: dt=11.200000, rms=0.468 (0.013%), neg=0, invalid=96777 0324: dt=11.200000, rms=0.468 (0.031%), neg=0, invalid=96777 0325: dt=11.200000, rms=0.468 (0.031%), neg=0, invalid=96777 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.479, neg=0, invalid=96777 0326: dt=0.000000, rms=0.479 (0.002%), neg=0, invalid=96777 0327: dt=0.000000, rms=0.479 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.479, neg=0, invalid=96777 0328: dt=1.008000, rms=0.479 (0.013%), neg=0, invalid=96777 0329: dt=1.008000, rms=0.479 (0.006%), neg=0, invalid=96777 0330: dt=1.008000, rms=0.479 (0.002%), neg=0, invalid=96777 0331: dt=1.008000, rms=0.479 (-0.029%), neg=0, invalid=96777 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.501, neg=0, invalid=96777 0332: dt=1.302682, rms=0.499 (0.344%), neg=0, invalid=96777 0333: dt=0.384000, rms=0.499 (0.012%), neg=0, invalid=96777 0334: dt=0.384000, rms=0.499 (-0.005%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.499, neg=0, invalid=96777 0335: dt=1.348148, rms=0.498 (0.192%), neg=0, invalid=96777 0336: dt=0.448000, rms=0.498 (0.012%), neg=0, invalid=96777 0337: dt=0.448000, rms=0.498 (0.001%), neg=0, invalid=96777 0338: dt=0.448000, rms=0.498 (-0.045%), 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=0.479, neg=0, invalid=96777 iter 0, gcam->neg = 628 after 11 iterations, nbhd size=1, neg = 0 0339: dt=2.138903, rms=0.441 (8.014%), neg=0, invalid=96777 0340: dt=0.000750, rms=0.441 (0.004%), neg=0, invalid=96777 0341: dt=0.000750, rms=0.441 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.441, neg=0, invalid=96777 0342: dt=0.007000, rms=0.441 (0.005%), neg=0, invalid=96777 0343: dt=0.007000, rms=0.441 (0.003%), neg=0, invalid=96777 0344: dt=0.007000, rms=0.441 (-0.001%), 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=0.421, neg=0, invalid=96777 0345: dt=0.000000, rms=0.422 (-0.251%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.422, neg=0, invalid=96777 0346: dt=55.488000, rms=0.422 (0.018%), neg=0, invalid=96777 0347: dt=92.480000, rms=0.422 (0.005%), neg=0, invalid=96777 0348: dt=92.480000, rms=0.422 (0.006%), neg=0, invalid=96777 0349: dt=92.480000, rms=0.422 (0.006%), neg=0, invalid=96777 0350: dt=92.480000, rms=0.422 (0.002%), neg=0, invalid=96777 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.422, neg=0, invalid=96777 0351: dt=7.776000, rms=0.422 (0.007%), neg=0, invalid=96777 0352: dt=1.944000, rms=0.422 (0.000%), neg=0, invalid=96777 0353: dt=1.944000, rms=0.422 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.422, neg=0, invalid=96777 0354: dt=145.152000, rms=0.421 (0.167%), neg=0, invalid=96777 0355: dt=36.288000, rms=0.421 (0.108%), neg=0, invalid=96777 0356: dt=36.288000, rms=0.421 (0.037%), neg=0, invalid=96777 0357: dt=36.288000, rms=0.420 (0.059%), neg=0, invalid=96777 0358: dt=36.288000, rms=0.420 (0.070%), neg=0, invalid=96777 0359: dt=36.288000, rms=0.420 (0.071%), neg=0, invalid=96777 0360: dt=36.288000, rms=0.419 (0.065%), neg=0, invalid=96777 0361: dt=36.288000, rms=0.419 (0.060%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.420, neg=0, invalid=96777 0362: dt=11.200000, rms=0.419 (0.157%), neg=0, invalid=96777 0363: dt=11.200000, rms=0.419 (0.090%), neg=0, invalid=96777 0364: dt=11.200000, rms=0.419 (0.080%), neg=0, invalid=96777 0365: dt=11.200000, rms=0.418 (0.083%), neg=0, invalid=96777 iter 0, gcam->neg = 4 after 6 iterations, nbhd size=1, neg = 0 0366: dt=11.200000, rms=0.418 (0.049%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 5 iterations, nbhd size=1, neg = 0 0367: dt=11.200000, rms=0.418 (0.046%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.418, neg=0, invalid=96777 0368: dt=38.400000, rms=0.413 (1.104%), neg=0, invalid=96777 0369: dt=19.200000, rms=0.412 (0.336%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0370: dt=44.800000, rms=0.411 (0.340%), neg=0, invalid=96777 0371: dt=19.200000, rms=0.410 (0.100%), neg=0, invalid=96777 0372: dt=19.200000, rms=0.410 (0.102%), neg=0, invalid=96777 0373: dt=19.200000, rms=0.409 (0.151%), neg=0, invalid=96777 0374: dt=19.200000, rms=0.408 (0.179%), neg=0, invalid=96777 0375: dt=19.200000, rms=0.408 (0.182%), neg=0, invalid=96777 0376: dt=19.200000, rms=0.407 (0.198%), neg=0, invalid=96777 0377: dt=19.200000, rms=0.406 (0.201%), neg=0, invalid=96777 0378: dt=19.200000, rms=0.405 (0.180%), neg=0, invalid=96777 0379: dt=19.200000, rms=0.405 (0.160%), neg=0, invalid=96777 0380: dt=19.200000, rms=0.404 (0.139%), neg=0, invalid=96777 0381: dt=19.200000, rms=0.404 (0.141%), neg=0, invalid=96777 0382: dt=19.200000, rms=0.403 (0.136%), neg=0, invalid=96777 0383: dt=19.200000, rms=0.402 (0.117%), neg=0, invalid=96777 0384: dt=19.200000, rms=0.402 (0.098%), neg=0, invalid=96777 0385: dt=44.800000, rms=0.402 (0.012%), neg=0, invalid=96777 0386: dt=44.800000, rms=0.402 (-0.001%), neg=0, invalid=96777 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.408, neg=0, invalid=96777 0387: dt=0.000000, rms=0.408 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.408, neg=0, invalid=96777 0388: dt=0.000000, rms=0.408 (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=0.422, neg=0, invalid=96777 0389: dt=0.000000, rms=0.422 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.422, neg=0, invalid=96777 0390: dt=0.007000, rms=0.422 (0.000%), neg=0, invalid=96777 0391: dt=0.007000, rms=0.422 (0.000%), neg=0, invalid=96777 0392: dt=0.007000, rms=0.422 (0.000%), neg=0, invalid=96777 0393: dt=0.007000, rms=0.422 (-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=0.399, neg=0, invalid=96777 iter 0, gcam->neg = 480 after 10 iterations, nbhd size=1, neg = 0 0394: dt=0.935886, rms=0.387 (3.115%), neg=0, invalid=96777 0395: dt=0.000188, rms=0.387 (0.002%), neg=0, invalid=96777 0396: dt=0.000188, rms=0.387 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.387, neg=0, invalid=96777 0397: dt=0.000438, rms=0.387 (0.000%), neg=0, invalid=96777 0398: dt=0.000250, rms=0.387 (0.000%), neg=0, invalid=96777 0399: dt=0.000250, rms=0.387 (-0.000%), neg=0, invalid=96777 writing output transformation to transforms/talairach.m3z... GCAMwrite registration took 2 hours, 11 minutes and 56 seconds. #-------------------------------------- #@# CA Reg Inv ‫جمعه ۲۳ دسامبر ۱۶، ساعت ۰۷:۵۳:۵۳ (IRST)‬ /home/fmri-04/Documents/workshop/subjects/Subject004/mri mri_ca_register -invert-and-save transforms/talairach.m3z Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z Inverting GCAM Saving inverse #-------------------------------------- #@# Remove Neck ‫جمعه ۲۳ دسامبر ۱۶، ساعت ۰۷:۵۴:۲۸ (IRST)‬ mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2008-03-26.gca nu_noneck.mgz erasing everything more than 25 mm from possible brain reading atlas '/usr/local/freesurfer/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... 10723887 nonbrain voxels erased writing output to nu_noneck.mgz... nonbrain removal took 1 minutes and 13 seconds. #-------------------------------------- #@# SkullLTA ‫جمعه ۲۳ دسامبر ۱۶، ساعت ۰۷:۵۵:۴۲ (IRST)‬ mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz /usr/local/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull_2.lta ======= NUMBER OF OPENMP THREADS = 1 ======= 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 '/usr/local/freesurfer/average/RB_all_withskull_2008-03-26.gca'... average std = 23.1 using min determinant for regularization = 53.4 0 singular and 5702 ill-conditioned covariance matrices regularized reading 'nu_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=6.0 skull bounding box = (42, 30, 29) --> (215, 202, 217) using (100, 87, 123) as brain centroid... mean wm in atlas = 126, using box (79,66,100) --> (121, 108,146) to find MRI wm before smoothing, mri peak at 105 after smoothing, mri peak at 106, scaling input intensities by 1.189 scaling channel 0 by 1.18868 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.9, old_max_log_p =-4.0 (thresh=-4.0) 0.955 -0.063 -0.065 16.619; 0.046 1.080 -0.130 5.350; 0.087 0.135 1.180 -60.869; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 0.955 -0.063 -0.065 16.619; 0.046 1.080 -0.130 5.350; 0.087 0.135 1.180 -60.869; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.8, old_max_log_p =-3.9 (thresh=-3.9) 0.976 -0.024 -0.034 5.757; 0.015 1.101 -0.132 7.126; 0.051 0.129 1.116 -47.878; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.8, old_max_log_p =-3.8 (thresh=-3.8) 0.976 -0.024 -0.034 5.757; 0.015 1.101 -0.132 7.126; 0.051 0.129 1.116 -47.878; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.8, old_max_log_p =-3.8 (thresh=-3.8) 0.975 -0.026 -0.052 7.857; 0.014 1.095 -0.149 10.055; 0.067 0.148 1.117 -53.158; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.8, old_max_log_p =-3.8 (thresh=-3.8) 0.977 -0.026 -0.052 7.581; 0.015 1.095 -0.140 8.888; 0.067 0.139 1.118 -51.776; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.8, old_max_log_p =-3.8 (thresh=-3.8) 0.977 -0.026 -0.052 7.581; 0.015 1.093 -0.140 9.020; 0.067 0.139 1.119 -51.960; 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 0.97725 -0.02617 -0.05213 7.58106; 0.01500 1.09344 -0.13988 9.01994; 0.06714 0.13871 1.11914 -51.96045; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 0.97725 -0.02617 -0.05213 7.58106; 0.01500 1.09344 -0.13988 9.01994; 0.06714 0.13871 1.11914 -51.96045; 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: 008: -log(p) = -0.0 tol 0.000010 Resulting transform: 0.977 -0.026 -0.052 7.581; 0.015 1.093 -0.140 9.020; 0.067 0.139 1.119 -51.960; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -3.8 (old=-4.0) transform before final EM align: 0.977 -0.026 -0.052 7.581; 0.015 1.093 -0.140 9.020; 0.067 0.139 1.119 -51.960; 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 0.97725 -0.02617 -0.05213 7.58106; 0.01500 1.09344 -0.13988 9.01994; 0.06714 0.13871 1.11914 -51.96045; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 0.97725 -0.02617 -0.05213 7.58106; 0.01500 1.09344 -0.13988 9.01994; 0.06714 0.13871 1.11914 -51.96045; 0.00000 0.00000 0.00000 1.00000; dfp_em_step_func: 009: -log(p) = 4.2 after pass:transform: ( 0.98, -0.03, -0.05, 7.58) ( 0.02, 1.09, -0.14, 9.02) ( 0.07, 0.14, 1.12, -51.96) 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 TOLERANCESpass 2 through quasi-newton minimization... 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) = 4.2 tol 0.000000 final transform: 0.977 -0.026 -0.052 7.581; 0.015 1.093 -0.140 9.020; 0.067 0.139 1.119 -51.960; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull_2.lta... registration took 22 minutes and 13 seconds. #-------------------------------------- #@# SubCort Seg ‫جمعه ۲۳ دسامبر ۱۶، ساعت ۰۸:۱۷:۵۶ (IRST)‬ mri_ca_label -align norm.mgz transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz sysname Linux hostname fmri04 machine x86_64 setenv SUBJECTS_DIR /home/fmri-04/Documents/workshop/subjects cd /home/fmri-04/Documents/workshop/subjects/Subject004/mri mri_ca_label -align norm.mgz transforms/talairach.m3z /usr/local/freesurfer/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 /usr/local/freesurfer/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 /usr/local/freesurfer/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) mri peak = 0.16125 (12) Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (348 voxels, overlap=0.007) Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (348 voxels, peak = 11), gca=10.8 gca peak = 0.14982 (20) mri peak = 0.15422 (12) Right_Lateral_Ventricle (43): linear fit = 0.50 x + 0.0 (615 voxels, overlap=0.007) Right_Lateral_Ventricle (43): linear fit = 0.50 x + 0.0 (615 voxels, peak = 10), gca=9.9 gca peak = 0.28003 (97) mri peak = 0.11594 (99) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (483 voxels, overlap=0.901) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (483 voxels, peak = 97), gca=97.5 gca peak = 0.18160 (96) mri peak = 0.11459 (86) Left_Pallidum (13): linear fit = 0.85 x + 0.0 (179 voxels, overlap=0.054) Left_Pallidum (13): linear fit = 0.85 x + 0.0 (179 voxels, peak = 81), gca=81.1 gca peak = 0.27536 (62) mri peak = 0.09379 (62) Right_Hippocampus (53): linear fit = 0.96 x + 0.0 (858 voxels, overlap=0.944) Right_Hippocampus (53): linear fit = 0.96 x + 0.0 (858 voxels, peak = 60), gca=59.8 gca peak = 0.32745 (63) mri peak = 0.09688 (61) Left_Hippocampus (17): linear fit = 0.94 x + 0.0 (923 voxels, overlap=1.013) Left_Hippocampus (17): linear fit = 0.94 x + 0.0 (923 voxels, peak = 60), gca=59.5 gca peak = 0.08597 (105) mri peak = 0.07899 (109) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (42081 voxels, overlap=0.701) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (42081 voxels, peak = 109), gca=108.7 gca peak = 0.09209 (106) mri peak = 0.08303 (107) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (42821 voxels, overlap=0.750) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (42821 voxels, peak = 108), gca=107.6 Killed Linux fmri04 3.19.0-25-generic #26~14.04.1-Ubuntu SMP Fri Jul 24 21:16:20 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux recon-all -s Subject004 exited with ERRORS at ‫جمعه ۲۳ دسامبر ۱۶، ساعت ۰۸:۲۱:۱۵ (IRST)‬ To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting