Wed Mar 30 11:22:24 EDT 2016 /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435 /usr/local/freesurfer//bin/recon-all -long MS0435090516 MS0435 -all -mail erm2021@med.cornell.edu subjid MS0435090516.long.MS0435 setenv SUBJECTS_DIR /mnt/fourtb/SAG_3D_BRAVO FREESURFER_HOME /usr/local/freesurfer/ Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Linux umeshu 3.2.0-70-generic #105-Ubuntu SMP Wed Sep 24 19:49:16 UTC 2014 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 95971 maxlocks unlimited maxsignal 95971 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 12301940 5652280 6649660 0 51184 1163620 -/+ buffers/cache: 4437476 7864464 Swap: 12578812 2327156 10251656 ######################################## program versions used $Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/03/30-15:22:24-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ User: ms Machine: umeshu Platform: Linux PlatformVersion: 3.2.0-70-generic CompilerName: GCC CompilerVersion: 30400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/03/30-15:22:25-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: ms Machine: umeshu Platform: Linux PlatformVersion: 3.2.0-70-generic CompilerName: GCC CompilerVersion: 30400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/03/30-15:22:26-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: ms Machine: umeshu Platform: Linux PlatformVersion: 3.2.0-70-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/03/30-15:22:26-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_normalize.c,v 1.73 2011/03/11 20:55:38 fischl Exp $ User: ms Machine: umeshu Platform: Linux PlatformVersion: 3.2.0-70-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/03/30-15:22:26-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_watershed.cpp,v 1.96 2011/03/16 21:23:49 nicks Exp $ User: ms Machine: umeshu Platform: Linux PlatformVersion: 3.2.0-70-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/03/30-15:22:26-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: ms Machine: umeshu Platform: Linux PlatformVersion: 3.2.0-70-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/03/30-15:22:26-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: ms Machine: umeshu Platform: Linux PlatformVersion: 3.2.0-70-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/03/30-15:22:26-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_label2label.c,v 1.40.2.1 2011/05/19 17:21:56 greve Exp $ User: ms Machine: umeshu Platform: Linux PlatformVersion: 3.2.0-70-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/03/30-15:22:26-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_em_register.c,v 1.84 2011/03/16 21:23:48 nicks Exp $ User: ms Machine: umeshu Platform: Linux PlatformVersion: 3.2.0-70-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/03/30-15:22:26-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_normalize.c,v 1.52 2011/03/02 00:04:14 nicks Exp $ User: ms Machine: umeshu Platform: Linux PlatformVersion: 3.2.0-70-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/03/30-15:22:27-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_register.c,v 1.78 2011/03/02 14:27:40 fischl Exp $ User: ms Machine: umeshu Platform: Linux PlatformVersion: 3.2.0-70-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/03/30-15:22:27-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_label.c,v 1.96 2011/03/02 00:04:13 nicks Exp $ User: ms Machine: umeshu Platform: Linux PlatformVersion: 3.2.0-70-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/03/30-15:22:27-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: ms Machine: umeshu Platform: Linux PlatformVersion: 3.2.0-70-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/03/30-15:22:27-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: ms Machine: umeshu Platform: Linux PlatformVersion: 3.2.0-70-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/03/30-15:22:27-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: ms Machine: umeshu Platform: Linux PlatformVersion: 3.2.0-70-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/03/30-15:22:27-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: ms Machine: umeshu Platform: Linux PlatformVersion: 3.2.0-70-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/03/30-15:22:27-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: ms Machine: umeshu Platform: Linux PlatformVersion: 3.2.0-70-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/03/30-15:22:28-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: ms Machine: umeshu Platform: Linux PlatformVersion: 3.2.0-70-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/03/30-15:22:28-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: ms Machine: umeshu Platform: Linux PlatformVersion: 3.2.0-70-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/03/30-15:22:28-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: ms Machine: umeshu Platform: Linux PlatformVersion: 3.2.0-70-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/03/30-15:22:28-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: ms Machine: umeshu Platform: Linux PlatformVersion: 3.2.0-70-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/03/30-15:22:28-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: ms Machine: umeshu Platform: Linux PlatformVersion: 3.2.0-70-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/03/30-15:22:28-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: ms Machine: umeshu Platform: Linux PlatformVersion: 3.2.0-70-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/03/30-15:22:28-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: ms Machine: umeshu Platform: Linux PlatformVersion: 3.2.0-70-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/03/30-15:22:28-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_euler_number.c,v 1.8 2011/03/02 00:04:32 nicks Exp $ User: ms Machine: umeshu Platform: Linux PlatformVersion: 3.2.0-70-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/03/30-15:22:29-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks Exp $ User: ms Machine: umeshu Platform: Linux PlatformVersion: 3.2.0-70-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/03/30-15:22:29-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: ms Machine: umeshu Platform: Linux PlatformVersion: 3.2.0-70-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/03/30-15:22:29-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: ms Machine: umeshu Platform: Linux PlatformVersion: 3.2.0-70-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/03/30-15:22:29-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: ms Machine: umeshu Platform: Linux PlatformVersion: 3.2.0-70-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/03/30-15:22:29-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: ms Machine: umeshu Platform: Linux PlatformVersion: 3.2.0-70-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/03/30-15:22:29-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: ms Machine: umeshu Platform: Linux PlatformVersion: 3.2.0-70-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/03/30-15:22:29-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_calc.c,v 1.37.2.4 2011/04/04 00:53:08 nicks Exp $ User: ms Machine: umeshu Platform: Linux PlatformVersion: 3.2.0-70-generic CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_register.cpp,v 1.52 2011/03/16 21:23:49 nicks Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/03/30-15:22:29-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_robust_register.cpp,v 1.52 2011/03/16 21:23:49 nicks Exp $ User: ms Machine: umeshu Platform: Linux PlatformVersion: 3.2.0-70-generic CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/03/30-15:22:30-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ User: ms Machine: umeshu Platform: Linux PlatformVersion: 3.2.0-70-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/03/30-15:22:30-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: ms Machine: umeshu Platform: Linux PlatformVersion: 3.2.0-70-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/03/30-15:22:30-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: ms Machine: umeshu Platform: Linux PlatformVersion: 3.2.0-70-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/03/30-15:22:30-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: ms Machine: umeshu Platform: Linux PlatformVersion: 3.2.0-70-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/03/30-15:22:30-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ User: ms Machine: umeshu Platform: Linux PlatformVersion: 3.2.0-70-generic CompilerName: GCC CompilerVersion: 30400 ####################################### 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 ####################################### mkdir -p /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/tmp mri_map_cpdat -in /mnt/fourtb/SAG_3D_BRAVO/MS0435090516/tmp/control.dat -out /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/tmp/control.dat -lta /mnt/fourtb/SAG_3D_BRAVO/MS0435/mri/transforms/MS0435090516_to_MS0435.lta --in: Using /mnt/fourtb/SAG_3D_BRAVO/MS0435090516/tmp/control.dat as input file. --out: Using /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/tmp/control.dat as output file. --lta: Using /mnt/fourtb/SAG_3D_BRAVO/MS0435/mri/transforms/MS0435090516_to_MS0435.lta as transform. Reading 39 control points... Reading LTA Mapping control points... Writing control points... #-------------------------------------------- #@# MotionCor Wed Mar 30 11:22:30 EDT 2016 mri_convert -at /mnt/fourtb/SAG_3D_BRAVO/MS0435/mri/transforms/MS0435090516_to_MS0435.lta -odt uchar /mnt/fourtb/SAG_3D_BRAVO/MS0435090516/mri/orig/001.mgz /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/mri/orig.mgz mri_convert -at /mnt/fourtb/SAG_3D_BRAVO/MS0435/mri/transforms/MS0435090516_to_MS0435.lta -odt uchar /mnt/fourtb/SAG_3D_BRAVO/MS0435090516/mri/orig/001.mgz /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/mri/orig.mgz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /mnt/fourtb/SAG_3D_BRAVO/MS0435090516/mri/orig/001.mgz... TR=8.76, TE=3.43, TI=450.00, flip angle=15.00 i_ras = (0.0427869, -0.999084, 0) j_ras = (0, 0, -1) k_ras = (0.999096, 0.0425006, 0) INFO: Applying transformation from file /mnt/fourtb/SAG_3D_BRAVO/MS0435/mri/transforms/MS0435090516_to_MS0435.lta... Reading transform with LTAreadEx() INFO: Applying transformation from file /mnt/fourtb/SAG_3D_BRAVO/MS0435/mri/transforms/MS0435090516_to_MS0435.lta... --------------------------------- INFO: Transform Matrix (linear_ras_to_ras) 0.999 0.006 0.052 -5.387; 0.000 0.994 -0.110 23.061; -0.052 0.110 0.993 -34.704; 0.000 0.000 0.000 1.000; --------------------------------- Applying LTAtransformInterp (resample_type 1) changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram writing to /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/mri/orig.mgz... mri_add_xform_to_header -c /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/mri/transforms/talairach.xfm /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/mri/orig.mgz /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Wed Mar 30 11:22:40 EDT 2016 /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/mri cp /mnt/fourtb/SAG_3D_BRAVO/MS0435/mri/transforms/talairach.xfm /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/mri/transforms/talairach.auto.xfm cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Wed Mar 30 11:22:41 EDT 2016 /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.6412, pval=0.3663 >= threshold=0.0050) #-------------------------------------------- #@# Nu Intensity Correction Wed Mar 30 11:22:41 EDT 2016 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/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 2011/03/02 20:16:39 nicks Exp $ Linux umeshu 3.2.0-70-generic #105-Ubuntu SMP Wed Sep 24 19:49:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux Wed Mar 30 11:22:41 EDT 2016 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.17701 /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.17701/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.17701/nu0.mnc -odt float $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from orig.mgz... TR=8.76, TE=3.43, TI=450.00, flip angle=15.00 i_ras = (-1, 1.28522e-07, -7.07805e-08) j_ras = (1.2666e-07, -5.58792e-09, -1) k_ras = (-7.63685e-08, 1, 3.25963e-09) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.17701/nu0.mnc... -------------------------------------------------------- Iteration 1 Wed Mar 30 11:22:43 EDT 2016 nu_correct -clobber ./tmp.mri_nu_correct.mni.17701/nu0.mnc ./tmp.mri_nu_correct.mni.17701/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.17701/0/ [ms@umeshu:/mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/mri/] [2016-03-30 11:22:43] 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.17701/0/ ./tmp.mri_nu_correct.mni.17701/nu0.mnc ./tmp.mri_nu_correct.mni.17701/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 Number of iterations: 32 CV of field change: 0.00099552 [ms@umeshu:/mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/mri/] [2016-03-30 11:23:07] running: /usr/local/freesurfer//mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.17701/nu0.mnc ./tmp.mri_nu_correct.mni.17701/0//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done -------------------------------------------------------- Iteration 2 Wed Mar 30 11:23:09 EDT 2016 nu_correct -clobber ./tmp.mri_nu_correct.mni.17701/nu1.mnc ./tmp.mri_nu_correct.mni.17701/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.17701/1/ [ms@umeshu:/mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/mri/] [2016-03-30 11:23:09] 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.17701/1/ ./tmp.mri_nu_correct.mni.17701/nu1.mnc ./tmp.mri_nu_correct.mni.17701/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 Number of iterations: 17 CV of field change: 0.000996909 [ms@umeshu:/mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/mri/] [2016-03-30 11:23:24] running: /usr/local/freesurfer//mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.17701/nu1.mnc ./tmp.mri_nu_correct.mni.17701/1//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done mri_binarize --i ./tmp.mri_nu_correct.mni.17701/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.17701/ones.mgz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.17701/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.17701/ones.mgz sysname Linux hostname umeshu machine x86_64 user ms input ./tmp.mri_nu_correct.mni.17701/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.17701/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.17701/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.17701/sum.junk --avgwf ./tmp.mri_nu_correct.mni.17701/input.mean.dat $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.17701/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.17701/sum.junk --avgwf ./tmp.mri_nu_correct.mni.17701/input.mean.dat sysname Linux hostname umeshu machine x86_64 user ms Loading ./tmp.mri_nu_correct.mni.17701/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 1.67772e+07 Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.17701/input.mean.dat mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.17701/ones.mgz --i ./tmp.mri_nu_correct.mni.17701/nu2.mnc --sum ./tmp.mri_nu_correct.mni.17701/sum.junk --avgwf ./tmp.mri_nu_correct.mni.17701/output.mean.dat $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.17701/ones.mgz --i ./tmp.mri_nu_correct.mni.17701/nu2.mnc --sum ./tmp.mri_nu_correct.mni.17701/sum.junk --avgwf ./tmp.mri_nu_correct.mni.17701/output.mean.dat sysname Linux hostname umeshu machine x86_64 user ms Loading ./tmp.mri_nu_correct.mni.17701/ones.mgz Loading ./tmp.mri_nu_correct.mni.17701/nu2.mnc Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 16777216 1.67772e+07 Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.17701/output.mean.dat mris_calc -o ./tmp.mri_nu_correct.mni.17701/nu2.mnc ./tmp.mri_nu_correct.mni.17701/nu2.mnc mul 1.03526967707607921690 Saving result to './tmp.mri_nu_correct.mni.17701/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.17701/nu2.mnc nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.17701/nu2.mnc nu.mgz --like orig.mgz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from ./tmp.mri_nu_correct.mni.17701/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 1.28522e-07, -7.07805e-08) j_ras = (1.2666e-07, -5.58792e-09, -1) k_ras = (-7.63685e-08, 1, 3.25963e-09) 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 8 seconds. mapping (16, 132) to ( 3, 110) Wed Mar 30 11:24:05 EDT 2016 mri_nu_correct.mni done #-------------------------------------------- #@# Intensity Normalization Wed Mar 30 11:24:05 EDT 2016 /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/mri mri_normalize -g 1 nu.mgz T1.mgz using max gradient = 1.000 reading from nu.mgz... normalizing image... talairach transform 0.961 0.013 -0.078 -1.193; -0.021 0.940 0.176 -72.756; 0.073 -0.094 1.036 17.146; 0.000 0.000 0.000 1.000; INFO: Modifying talairach volume c_(r,a,s) based on average_305 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 1 of 2 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 2 of 2 building Voronoi diagram... performing soap bubble smoothing... writing output to T1.mgz 3D bias adjustment took 2 minutes and 13 seconds. MRIsplineNormalize(): npeaks = 7 Starting OpenSpline(): npoints = 7 white matter peak found at 111 white matter peak found at 110 gm peak at 84 (84), valley at 73 (73) csf peak at 42, setting threshold to 70 white matter peak found at 111 white matter peak found at 110 gm peak at 84 (84), valley at 58 (58) csf peak at 42, setting threshold to 70 #-------------------------------------------- #@# Skull Stripping Wed Mar 30 11:26:18 EDT 2016 /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/mri cp -vf /mnt/fourtb/SAG_3D_BRAVO/MS0435/mri/brainmask.mgz ./brainmask_MS0435.mgz `/mnt/fourtb/SAG_3D_BRAVO/MS0435/mri/brainmask.mgz' -> `./brainmask_MS0435.mgz' mri_mask -keep_mask_deletion_edits T1.mgz brainmask_MS0435.mgz brainmask.auto.mgz Transferring mask edits ('1' voxels) to dst vol DoAbs = 0 Found 16777216 voxels in mask Writing masked volume to brainmask.auto.mgz...done. mri_mask -transfer 255 -keep_mask_deletion_edits brainmask.auto.mgz brainmask_MS0435.mgz brainmask.auto.mgz transfer mask voxels=255 to dst vol Transferring mask edits ('1' voxels) to dst vol DoAbs = 0 Found 16777216 voxels in mask Writing masked volume to brainmask.auto.mgz...done. cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Wed Mar 30 11:26:23 EDT 2016 /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/mri cp -vf /mnt/fourtb/SAG_3D_BRAVO/MS0435/mri/transforms/talairach.lta transforms/talairach.lta `/mnt/fourtb/SAG_3D_BRAVO/MS0435/mri/transforms/talairach.lta' -> `transforms/talairach.lta' #-------------------------------------- #@# CA Normalize Wed Mar 30 11:26:23 EDT 2016 /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/mri cp -vf /mnt/fourtb/SAG_3D_BRAVO/MS0435/mri/aseg.mgz aseg_MS0435.mgz `/mnt/fourtb/SAG_3D_BRAVO/MS0435/mri/aseg.mgz' -> `aseg_MS0435.mgz' mri_ca_normalize -long aseg_MS0435.mgz -mask brainmask.mgz nu.mgz /usr/local/freesurfer//average/RB_all_2008-03-26.gca transforms/talairach.lta norm.mgz using longitudinal segmentation volume aseg_MS0435.mgz to generate control points... using MR volume brainmask.mgz to mask input volume... reading 1 input volumes reading atlas from '/usr/local/freesurfer//average/RB_all_2008-03-26.gca'... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 102 --> 104 resetting gm mean[0]: 63 --> 63 input volume #1 is the most T1-like using real data threshold=23.0 skull bounding box = (53, 60, 39) --> (199, 226, 223) using (102, 115, 131) as brain centroid... mean wm in atlas = 104, using box (84,95,108) --> (119, 135,153) to find MRI wm before smoothing, mri peak at 101 after smoothing, mri peak at 101, scaling input intensities by 1.030 scaling channel 0 by 1.0297 using 244171 sample points... INFO: compute sample coordinates transform 0.947 -0.057 -0.027 15.595; 0.071 1.066 0.110 -39.952; 0.028 -0.113 0.933 -1.607; 0.000 0.000 0.000 1.000; INFO: transform used using 167515 total control points for intensity normalization... bias field = 0.918 +- 0.101 57 of 167515 control points discarded using 167515 total control points for intensity normalization... bias field = 1.098 +- 0.094 58 of 167515 control points discarded using 167515 total control points for intensity normalization... bias field = 1.080 +- 0.082 64 of 167515 control points discarded writing normalized volume to norm.mgz... freeing GCA...done. normalization took 1 minutes and 32 seconds. #-------------------------------------- #@# CA Reg Wed Mar 30 11:27:54 EDT 2016 /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/mri mri_ca_register -nobigventricles -levels 2 -A 1 -l /mnt/fourtb/SAG_3D_BRAVO/MS0435/mri/transforms/talairach.m3z identity.nofile -align-after -mask brainmask.mgz norm.mgz /usr/local/freesurfer//average/RB_all_2008-03-26.gca transforms/talairach.m3z not handling expanded ventricles... levels = 2 smoothing gradient with 1 averages... reading previously computed atlas xform /mnt/fourtb/SAG_3D_BRAVO/MS0435/mri/transforms/talairach.m3z and applying inverse registration identity.nofile renormalizing sequences with structure alignment, equivalent to: -renormalize -regularize_mean 0.500 -regularize 0.500 using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading input volume 'norm.mgz'... reading GCA '/usr/local/freesurfer//average/RB_all_2008-03-26.gca'... MatrixAsciiReadFrom: could not scanf parms gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 freeing gibbs priors...done. average std[0] = 5.0 zcat /mnt/fourtb/SAG_3D_BRAVO/MS0435/mri/transforms/talairach.m3z Segmentation fault (core dumped) #-------------------------------------- #@# CA Reg Inv Wed Mar 30 11:27:59 EDT 2016 /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/mri mri_ca_register -invert-and-save transforms/talairach.m3z Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z ERROR: cannot find or read transforms/talairach.m3z #-------------------------------------- #@# Remove Neck Wed Mar 30 11:27:59 EDT 2016 INFO: transforms/talairach.m3z not found, using talairach.lta instead mri_remove_neck -radius 25 nu.mgz transforms/talairach.lta /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'... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 reading input volume 'nu.mgz'... reading transform 'transforms/talairach.lta'... removing structures at least 25 mm from brain... 10117673 nonbrain voxels erased writing output to nu_noneck.mgz... nonbrain removal took 0 minutes and 18 seconds. #-------------------------------------- #@# SkullLTA Wed Mar 30 11:28:16 EDT 2016 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.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 5 using previously computed transform transforms/talairach.lta reading 1 input volumes... logging results to talairach_with_skull.log reading '/usr/local/freesurfer//average/RB_all_withskull_2008-03-26.gca'... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 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=20.0 skull bounding box = (48, 47, 26) --> (208, 229, 221) using (101, 108, 124) as brain centroid... mean wm in atlas = 126, using box (81,86,100) --> (120, 130,148) to find MRI wm before smoothing, mri peak at 103 after smoothing, mri peak at 102, scaling input intensities by 1.235 scaling channel 0 by 1.23529 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-10349.0, old_max_log_p =-10381.3 (thresh=-10370.9) 1.001 0.271 -0.105 -16.357; -0.183 1.160 -0.259 27.335; 0.055 0.325 0.901 -50.050; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-10345.2, old_max_log_p =-10349.0 (thresh=-10338.7) 1.076 0.292 -0.113 -27.016; -0.150 1.114 -0.016 -7.544; 0.093 0.013 0.867 -10.973; 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=-10339.8, old_max_log_p =-10345.2 (thresh=-10334.9) 1.112 0.149 -0.201 -0.097; -0.007 1.122 -0.039 -20.847; 0.206 0.040 0.884 -31.891; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 3 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-10335.1, old_max_log_p =-10339.8 (thresh=-10329.4) 1.110 0.149 -0.201 0.198; -0.007 1.120 -0.039 -20.680; 0.206 0.040 0.886 -32.215; 0.000 0.000 0.000 1.000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 3481 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.10977 0.14873 -0.20070 0.19781; -0.00738 1.12034 -0.03911 -20.68010; 0.20601 0.04019 0.88610 -32.21457; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.10977 0.14873 -0.20070 0.19781; -0.00738 1.12034 -0.03911 -20.68010; 0.20601 0.04019 0.88610 -32.21457; 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: 005: -log(p) = 10335.1 tol 0.000010 Resulting transform: 1.110 0.149 -0.201 0.198; -0.007 1.120 -0.039 -20.680; 0.206 0.040 0.886 -32.215; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -10335.1 (old=-10381.3) transform before final EM align: 1.110 0.149 -0.201 0.198; -0.007 1.120 -0.039 -20.680; 0.206 0.040 0.886 -32.215; 0.000 0.000 0.000 1.000; ************************************************** EM alignment process ... Computing final MAP estimate using 382743 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.10977 0.14873 -0.20070 0.19781; -0.00738 1.12034 -0.03911 -20.68010; 0.20601 0.04019 0.88610 -32.21457; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.10977 0.14873 -0.20070 0.19781; -0.00738 1.12034 -0.03911 -20.68010; 0.20601 0.04019 0.88610 -32.21457; 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: 007: -log(p) = 1146130.0 tol 0.000000 final transform: 1.110 0.149 -0.201 0.198; -0.007 1.120 -0.039 -20.680; 0.206 0.040 0.886 -32.215; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull.lta... registration took 17 minutes and 43 seconds. #-------------------------------------- #@# SubCort Seg Wed Mar 30 11:45:59 EDT 2016 /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/mri cp -vf /mnt/fourtb/SAG_3D_BRAVO/MS0435/mri/transforms/MS0435090516_to_MS0435.lta /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/mri/transforms/MS0435090516_to_MS0435090516.long.MS0435.lta `/mnt/fourtb/SAG_3D_BRAVO/MS0435/mri/transforms/MS0435090516_to_MS0435.lta' -> `/mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/mri/transforms/MS0435090516_to_MS0435090516.long.MS0435.lta' cp -vf /mnt/fourtb/SAG_3D_BRAVO/MS0435/mri/transforms/MS0435100504_to_MS0435.lta /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/mri/transforms/MS0435100504_to_MS0435090516.long.MS0435.lta `/mnt/fourtb/SAG_3D_BRAVO/MS0435/mri/transforms/MS0435100504_to_MS0435.lta' -> `/mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/mri/transforms/MS0435100504_to_MS0435090516.long.MS0435.lta' cp -vf /mnt/fourtb/SAG_3D_BRAVO/MS0435/mri/transforms/MS0435110513_to_MS0435.lta /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/mri/transforms/MS0435110513_to_MS0435090516.long.MS0435.lta `/mnt/fourtb/SAG_3D_BRAVO/MS0435/mri/transforms/MS0435110513_to_MS0435.lta' -> `/mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/mri/transforms/MS0435110513_to_MS0435090516.long.MS0435.lta' cp -vf /mnt/fourtb/SAG_3D_BRAVO/MS0435/mri/transforms/MS0435120511_to_MS0435.lta /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/mri/transforms/MS0435120511_to_MS0435090516.long.MS0435.lta `/mnt/fourtb/SAG_3D_BRAVO/MS0435/mri/transforms/MS0435120511_to_MS0435.lta' -> `/mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/mri/transforms/MS0435120511_to_MS0435090516.long.MS0435.lta' mri_fuse_segmentations -a aseg.mgz -c aseg.auto_noCCseg.mgz -n norm.mgz MS0435090516.long.MS0435 MS0435090516 MS0435100504 MS0435110513 MS0435120511 aseg.fused.mgz fusing took 0 minutes and 34 seconds. using aseg.mgz as aseg volume using aseg.auto_noCCseg.mgz as aseg no-CC-label volume using norm.mgz as norm volume reading /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/mri/norm.mgz and processing 4 timepoints, writing to aseg.fused.mgz loading data for subject MS0435090516 ... loading data for subject MS0435100504 ... loading data for subject MS0435110513 ... loading data for subject MS0435120511 ... fusing... relabeled 14759 CC labels writing fused segmentation to aseg.fused.mgz mri_ca_label -align -nobigventricles -r /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/mri/aseg.fused.mgz -ri /mnt/fourtb/SAG_3D_BRAVO/MS0435/mri/aseg.auto_noCCseg.label_intensities.txt norm.mgz transforms/talairach.m3z /usr/local/freesurfer//average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz transforms/talairach.m3z: could not open transform renormalizing sequences with structure alignment, equivalent to: -renormalize -renormalize_mean 0.500 -regularize 0.500 not handling expanded ventricles... reading previously labeled volume from /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/mri/aseg.fused.mgz... reading intensity scaling from /mnt/fourtb/SAG_3D_BRAVO/MS0435/mri/aseg.auto_noCCseg.label_intensities.txt... reading 1 input volumes... reading classifier array from /usr/local/freesurfer//average/RB_all_2008-03-26.gca... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 reading input volume from norm.mgz... average std[0] = 6.9 reading transform from transforms/talairach.m3z... ERROR: cannot find or read transforms/talairach.m3z No such file or directory mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/mri/transforms/cc_up.lta MS0435090516.long.MS0435 will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/mri/transforms/cc_up.lta mghRead(/mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/mri/aseg.auto_noCCseg.mgz, -1): could not open file reading aseg from /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/mri/aseg.auto_noCCseg.mgz mri_cc: could not read aseg volume from /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/mri/aseg.auto_noCCseg.mgz #-------------------------------------- #@# Merge ASeg Wed Mar 30 11:46:53 EDT 2016 cp aseg.auto.mgz aseg.mgz cp: cannot stat `aseg.auto.mgz': No such file or directory #-------------------------------------------- #@# Intensity Normalization2 Wed Mar 30 11:46:53 EDT 2016 /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/mri mri_normalize -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz using segmentation for initial intensity normalization reading from norm.mgz... mghRead(/mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/mri/aseg.mgz, -1): could not open file using MR volume brainmask.mgz to mask input volume... mri_normalize: could not read aseg from file aseg.mgz #-------------------------------------------- #@# Mask BFS Wed Mar 30 11:46:54 EDT 2016 /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 mghRead(/mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/mri/brain.mgz, -1): could not open file mri_mask: could not read source volume brain.mgz #-------------------------------------------- #@# WM Segmentation Wed Mar 30 11:46:55 EDT 2016 mri_segment brain.mgz wm.seg.mgz mghRead(/mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/mri/brain.mgz, -1): could not open file mri_segment: could not read source volume from brain.mgz mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.mgz wm.asegedit.mgz preserving editing changes in input volume... mghRead(/mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/mri/wm.seg.mgz, -1): could not open file reading wm segmentation from wm.seg.mgz... mri_edit_wm_with_aseg: could not read wm volume from wm.seg.mgz mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz mghRead(/mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/mri/wm.asegedit.mgz, -1): could not open file mri_pretess: could not open wm.asegedit.mgz mri_mask -transfer 255 -keep_mask_deletion_edits -xform /mnt/fourtb/SAG_3D_BRAVO/MS0435/mri/transforms/MS0435090516_to_MS0435.lta wm.mgz /mnt/fourtb/SAG_3D_BRAVO/MS0435090516/mri/wm.mgz wm.mgz transfer mask voxels=255 to dst vol Transferring mask edits ('1' voxels) to dst vol transform file name is /mnt/fourtb/SAG_3D_BRAVO/MS0435/mri/transforms/MS0435090516_to_MS0435.lta mghRead(/mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/mri/wm.mgz, -1): could not open file mri_mask: could not read source volume wm.mgz #-------------------------------------------- #@# Fill Wed Mar 30 11:46:55 EDT 2016 /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/mri mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Using transforms/talairach.lta and its offset for Talairach volume ... using segmentation aseg.auto_noCCseg.mgz... reading input volume...mghRead(/mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/mri/wm.mgz, -1): could not open file mri_fill: could not read wm.mgz #-------------------------------------------- #@# Make White Surf lh Wed Mar 30 11:46:55 EDT 2016 cp -vf /mnt/fourtb/SAG_3D_BRAVO/MS0435/surf/lh.white /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/lh.orig `/mnt/fourtb/SAG_3D_BRAVO/MS0435/surf/lh.white' -> `/mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/lh.orig' cp -vf /mnt/fourtb/SAG_3D_BRAVO/MS0435/surf/lh.white /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/lh.orig_white `/mnt/fourtb/SAG_3D_BRAVO/MS0435/surf/lh.white' -> `/mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/lh.orig_white' cp -vf /mnt/fourtb/SAG_3D_BRAVO/MS0435/surf/lh.pial /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/lh.orig_pial `/mnt/fourtb/SAG_3D_BRAVO/MS0435/surf/lh.pial' -> `/mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/lh.orig_pial' /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/scripts mris_make_surfaces -orig_white orig_white -orig orig_white -long -max 3.5 -noaparc -whiteonly -mgz -T1 brain.finalsurfs MS0435090516.long.MS0435 lh reading original vertex positions from orig_white only generating white matter surface using orig_white starting white location... Using longitudinal scheme using max_thickness = 3.5 not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading volume /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/mri/filled.mgz... mghRead(/mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/mri/filled.mgz, -1): could not open file mris_make_surfaces: could not read input volume /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/mri/filled.mgz #-------------------------------------------- #@# Smooth2 lh Wed Mar 30 11:46:55 EDT 2016 mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/scripts smoothing for 3 iterations setting seed for random number generator to 1234 MRISread(../surf/lh.white): could not open file No such file or directory mris_smooth: could not read surface file ../surf/lh.white No such file or directory #-------------------------------------------- #@# Inflation2 lh Wed Mar 30 11:46:55 EDT 2016 /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated MRISread(../surf/lh.smoothwm): could not open file No such file or directory mris_inflate: could not read surface file ../surf/lh.smoothwm No such file or directory mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/lh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm MRISread(../surf/lh.inflated): could not open file thresholding curvature at 99.90% level No such file or directory mris_curvature: could not read surface file ../surf/lh.inflated No such file or directory #----------------------------------------- #@# Curvature Stats lh Wed Mar 30 11:46:55 EDT 2016 /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm MS0435090516.long.MS0435 lh curv sulc Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/lh.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ MS0435090516.long.MS0435/lh.smoothwm ] Reading surface...MRISread(/mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/lh.smoothwm): could not open file No such file or directory [ ok ] mris_curvature_stats: could not read surface file /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/lh.smoothwm No such file or directory #-------------------------------------------- #@# Sphere lh Wed Mar 30 11:46:55 EDT 2016 /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/scripts cp /mnt/fourtb/SAG_3D_BRAVO/MS0435/surf/lh.sphere /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/lh.sphere #-------------------------------------------- #@# Surf Reg lh Wed Mar 30 11:46:55 EDT 2016 /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/scripts mris_register -curv -nosulc -norot /mnt/fourtb/SAG_3D_BRAVO/MS0435/surf/lh.sphere.reg /usr/local/freesurfer//average/lh.average.curvature.filled.buckner40.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment disabling initial sulc alignment... disabling initial rigid alignment... $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading surface from /mnt/fourtb/SAG_3D_BRAVO/MS0435/surf/lh.sphere.reg... reading template parameterization from /usr/local/freesurfer//average/lh.average.curvature.filled.buckner40.tif... will not use the sulcal depth map will not rigidly align the surface writing registered surface to ../surf/lh.sphere.reg... curvature mean = -0.028, std = 0.284 curvature mean = 0.001, std = 0.066 curvature mean = 0.042, std = 0.348 curvature mean = 0.002, std = 0.078 curvature mean = 0.023, std = 0.504 curvature mean = 0.002, std = 0.084 curvature mean = 0.012, std = 0.633 curvature mean = 0.002, std = 0.086 curvature mean = 0.004, std = 0.726 #-------------------------------------------- #@# Jacobian white lh Wed Mar 30 12:00:56 EDT 2016 mris_jacobian ../surf/lh.white ../surf/lh.sphere.reg ../surf/lh.jacobian_white reading surface from ../surf/lh.white... MRISread(../surf/lh.white): could not open file No such file or directory mris_jacobian: could not read surface file ../surf/lh.white No such file or directory #-------------------------------------------- #@# AvgCurv lh Wed Mar 30 12:00:56 EDT 2016 /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/scripts mrisp_paint -a 5 /usr/local/freesurfer//average/lh.average.curvature.filled.buckner40.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/lh.sphere.reg... reading template parameterization from /usr/local/freesurfer//average/lh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/lh.avg_curv... #----------------------------------------- #@# Cortical Parc lh Wed Mar 30 12:00:59 EDT 2016 /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 -long -R /mnt/fourtb/SAG_3D_BRAVO/MS0435/label/lh.aparc.annot MS0435090516.long.MS0435 lh ../surf/lh.sphere.reg /usr/local/freesurfer//average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/lh.aparc.annot No such file or directory mris_ca_label: could not open label file ../label/lh.cortex.label Invalid argument Invalid argument #-------------------------------------------- #@# Make Pial Surf lh Wed Mar 30 12:00:59 EDT 2016 /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/scripts mris_make_surfaces -orig orig_white -orig_white orig_white -orig_pial orig_pial -long -max 3.5 -white NOWRITE -mgz -T1 brain.finalsurfs MS0435090516.long.MS0435 lh reading original vertex positions from orig_white -white NOWRITE indicates that white, curv, area, and cortex.label files will not be written... using orig_white starting white location... using orig_pial starting pial locations... Using longitudinal scheme using max_thickness = 3.5 INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading volume /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/mri/filled.mgz... mghRead(/mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/mri/filled.mgz, -1): could not open file mris_make_surfaces: could not read input volume /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/mri/filled.mgz #-------------------------------------------- #@# Surf Volume lh Wed Mar 30 12:00:59 EDT 2016 /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf mris_calc -o lh.area.mid lh.area add lh.area.pial mris_calc: Sorry, but I seem to have encountered an error. While accessing file 'lh.area', I was unable to identify this file type. Does it exist? mris_calc -o lh.area.mid lh.area.mid div 2 mris_calc: Sorry, but I seem to have encountered an error. While accessing file 'lh.area.mid', I was unable to identify this file type. Does it exist? mris_calc -o lh.volume lh.area.mid mul lh.thickness mris_calc: Sorry, but I seem to have encountered an error. While accessing file 'lh.area.mid', I was unable to identify this file type. Does it exist? #----------------------------------------- #@# Parcellation Stats lh Wed Mar 30 12:00:59 EDT 2016 /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/scripts mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab MS0435090516.long.MS0435 lh white No such file or directory mris_anatomical_stats: could not open label file ../label/lh.cortex.label INFO: assuming MGZ format for volumes. Invalid argument Invalid argument #----------------------------------------- #@# Cortical Parc 2 lh Wed Mar 30 12:00:59 EDT 2016 /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 -long -R /mnt/fourtb/SAG_3D_BRAVO/MS0435/label/lh.aparc.a2009s.annot MS0435090516.long.MS0435 lh ../surf/lh.sphere.reg /usr/local/freesurfer//average/lh.destrieux.simple.2009-07-29.gcs ../label/lh.aparc.a2009s.annot No such file or directory mris_ca_label: could not open label file ../label/lh.cortex.label Invalid argument Invalid argument #----------------------------------------- #@# Parcellation Stats 2 lh Wed Mar 30 12:01:00 EDT 2016 /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/scripts mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.a2009s.stats -b -a ../label/lh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab MS0435090516.long.MS0435 lh white No such file or directory mris_anatomical_stats: could not open label file ../label/lh.cortex.label INFO: assuming MGZ format for volumes. Invalid argument Invalid argument #-------------------------------------------- #@# Make White Surf rh Wed Mar 30 12:01:00 EDT 2016 cp -vf /mnt/fourtb/SAG_3D_BRAVO/MS0435/surf/rh.white /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/rh.orig `/mnt/fourtb/SAG_3D_BRAVO/MS0435/surf/rh.white' -> `/mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/rh.orig' cp -vf /mnt/fourtb/SAG_3D_BRAVO/MS0435/surf/rh.white /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/rh.orig_white `/mnt/fourtb/SAG_3D_BRAVO/MS0435/surf/rh.white' -> `/mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/rh.orig_white' cp -vf /mnt/fourtb/SAG_3D_BRAVO/MS0435/surf/rh.pial /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/rh.orig_pial `/mnt/fourtb/SAG_3D_BRAVO/MS0435/surf/rh.pial' -> `/mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/rh.orig_pial' /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/scripts mris_make_surfaces -orig_white orig_white -orig orig_white -long -max 3.5 -noaparc -whiteonly -mgz -T1 brain.finalsurfs MS0435090516.long.MS0435 rh reading original vertex positions from orig_white only generating white matter surface using orig_white starting white location... Using longitudinal scheme using max_thickness = 3.5 not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading volume /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/mri/filled.mgz... mghRead(/mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/mri/filled.mgz, -1): could not open file mris_make_surfaces: could not read input volume /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/mri/filled.mgz #-------------------------------------------- #@# Smooth2 rh Wed Mar 30 12:01:00 EDT 2016 mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white ../surf/rh.smoothwm /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/scripts smoothing for 3 iterations setting seed for random number generator to 1234 MRISread(../surf/rh.white): could not open file No such file or directory mris_smooth: could not read surface file ../surf/rh.white No such file or directory #-------------------------------------------- #@# Inflation2 rh Wed Mar 30 12:01:00 EDT 2016 /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/scripts mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated MRISread(../surf/rh.smoothwm): could not open file No such file or directory mris_inflate: could not read surface file ../surf/rh.smoothwm No such file or directory mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/rh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm MRISread(../surf/rh.inflated): could not open file thresholding curvature at 99.90% level No such file or directory mris_curvature: could not read surface file ../surf/rh.inflated No such file or directory #----------------------------------------- #@# Curvature Stats rh Wed Mar 30 12:01:00 EDT 2016 /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm MS0435090516.long.MS0435 rh curv sulc Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/rh.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ MS0435090516.long.MS0435/rh.smoothwm ] Reading surface...MRISread(/mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/rh.smoothwm): could not open file No such file or directory [ ok ] mris_curvature_stats: could not read surface file /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/rh.smoothwm No such file or directory #-------------------------------------------- #@# Sphere rh Wed Mar 30 12:01:00 EDT 2016 /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/scripts cp /mnt/fourtb/SAG_3D_BRAVO/MS0435/surf/rh.sphere /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/rh.sphere #-------------------------------------------- #@# Surf Reg rh Wed Mar 30 12:01:00 EDT 2016 /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/scripts mris_register -curv -nosulc -norot /mnt/fourtb/SAG_3D_BRAVO/MS0435/surf/rh.sphere.reg /usr/local/freesurfer//average/rh.average.curvature.filled.buckner40.tif ../surf/rh.sphere.reg using smoothwm curvature for final alignment disabling initial sulc alignment... disabling initial rigid alignment... $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading surface from /mnt/fourtb/SAG_3D_BRAVO/MS0435/surf/rh.sphere.reg... reading template parameterization from /usr/local/freesurfer//average/rh.average.curvature.filled.buckner40.tif... will not use the sulcal depth map will not rigidly align the surface writing registered surface to ../surf/rh.sphere.reg... curvature mean = -0.028, std = 0.294 curvature mean = 0.004, std = 0.069 curvature mean = 0.036, std = 0.344 curvature mean = 0.004, std = 0.082 curvature mean = 0.022, std = 0.484 curvature mean = 0.004, std = 0.088 curvature mean = 0.012, std = 0.606 curvature mean = 0.004, std = 0.090 curvature mean = 0.004, std = 0.694 expanding nbhd size to 1 #-------------------------------------------- #@# Jacobian white rh Wed Mar 30 12:19:33 EDT 2016 mris_jacobian ../surf/rh.white ../surf/rh.sphere.reg ../surf/rh.jacobian_white reading surface from ../surf/rh.white... MRISread(../surf/rh.white): could not open file No such file or directory mris_jacobian: could not read surface file ../surf/rh.white No such file or directory #-------------------------------------------- #@# AvgCurv rh Wed Mar 30 12:19:33 EDT 2016 /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/scripts mrisp_paint -a 5 /usr/local/freesurfer//average/rh.average.curvature.filled.buckner40.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/rh.sphere.reg... reading template parameterization from /usr/local/freesurfer//average/rh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/rh.avg_curv... #----------------------------------------- #@# Cortical Parc rh Wed Mar 30 12:19:36 EDT 2016 /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 -long -R /mnt/fourtb/SAG_3D_BRAVO/MS0435/label/rh.aparc.annot MS0435090516.long.MS0435 rh ../surf/rh.sphere.reg /usr/local/freesurfer//average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/rh.aparc.annot No such file or directory mris_ca_label: could not open label file ../label/rh.cortex.label Invalid argument Invalid argument #-------------------------------------------- #@# Make Pial Surf rh Wed Mar 30 12:19:36 EDT 2016 /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/scripts mris_make_surfaces -orig orig_white -orig_white orig_white -orig_pial orig_pial -long -max 3.5 -white NOWRITE -mgz -T1 brain.finalsurfs MS0435090516.long.MS0435 rh reading original vertex positions from orig_white -white NOWRITE indicates that white, curv, area, and cortex.label files will not be written... using orig_white starting white location... using orig_pial starting pial locations... Using longitudinal scheme using max_thickness = 3.5 INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading volume /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/mri/filled.mgz... mghRead(/mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/mri/filled.mgz, -1): could not open file mris_make_surfaces: could not read input volume /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/mri/filled.mgz #-------------------------------------------- #@# Surf Volume rh Wed Mar 30 12:19:36 EDT 2016 /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf mris_calc -o rh.area.mid rh.area add rh.area.pial mris_calc: Sorry, but I seem to have encountered an error. While accessing file 'rh.area', I was unable to identify this file type. Does it exist? mris_calc -o rh.area.mid rh.area.mid div 2 mris_calc: Sorry, but I seem to have encountered an error. While accessing file 'rh.area.mid', I was unable to identify this file type. Does it exist? mris_calc -o rh.volume rh.area.mid mul rh.thickness mris_calc: Sorry, but I seem to have encountered an error. While accessing file 'rh.area.mid', I was unable to identify this file type. Does it exist? #----------------------------------------- #@# Parcellation Stats rh Wed Mar 30 12:19:36 EDT 2016 /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/scripts mris_anatomical_stats -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab MS0435090516.long.MS0435 rh white No such file or directory mris_anatomical_stats: could not open label file ../label/rh.cortex.label INFO: assuming MGZ format for volumes. Invalid argument Invalid argument #----------------------------------------- #@# Cortical Parc 2 rh Wed Mar 30 12:19:37 EDT 2016 /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 -long -R /mnt/fourtb/SAG_3D_BRAVO/MS0435/label/rh.aparc.a2009s.annot MS0435090516.long.MS0435 rh ../surf/rh.sphere.reg /usr/local/freesurfer//average/rh.destrieux.simple.2009-07-29.gcs ../label/rh.aparc.a2009s.annot No such file or directory mris_ca_label: could not open label file ../label/rh.cortex.label Invalid argument Invalid argument #----------------------------------------- #@# Parcellation Stats 2 rh Wed Mar 30 12:19:37 EDT 2016 /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/scripts mris_anatomical_stats -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.a2009s.stats -b -a ../label/rh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab MS0435090516.long.MS0435 rh white No such file or directory mris_anatomical_stats: could not open label file ../label/rh.cortex.label INFO: assuming MGZ format for volumes. Invalid argument Invalid argument #-------------------------------------------- #@# Cortical ribbon mask Wed Mar 30 12:19:37 EDT 2016 /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/mri mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon MS0435090516.long.MS0435 SUBJECTS_DIR is /mnt/fourtb/SAG_3D_BRAVO MRISread(/mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/lh.white): could not open file loading input data... No such file or directory Exception caught while processing input files std::exception #-------------------------------------------- #@# ASeg Stats Wed Mar 30 12:19:37 EDT 2016 INFO: mri_segstats will not calculate Supratentorial due to missing ribbon.mgz file INFO: ?h.white surfaces not available to mri_segstats. /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435 mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --ctab /usr/local/freesurfer//ASegStatsLUT.txt --subject MS0435090516.long.MS0435 mghRead(mri/aseg.mgz, -1): could not open file $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ cwd cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --ctab /usr/local/freesurfer//ASegStatsLUT.txt --subject MS0435090516.long.MS0435 sysname Linux hostname umeshu machine x86_64 user ms atlas_icv (eTIV) = 2033447 mm^3 (det: 0.958031 ) Loading mri/aseg.mgz ERROR: loading mri/aseg.mgz #----------------------------------------- #@# AParc-to-ASeg Wed Mar 30 12:19:37 EDT 2016 /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435 mri_aparc2aseg --s MS0435090516.long.MS0435 --volmask MRISread(/mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/lh.white): could not open file SUBJECTS_DIR /mnt/fourtb/SAG_3D_BRAVO subject MS0435090516.long.MS0435 outvol /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/lh.white No such file or directory ERROR: could not read /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/lh.white INFO: skipping a2009s aparc2aseg #----------------------------------------- #@# WMParc Wed Mar 30 12:19:37 EDT 2016 /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435 mri_aparc2aseg --s MS0435090516.long.MS0435 --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz ERROR: cannot find aparc+aseg.mgz or /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/mri/aparc+aseg.mgz /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435 mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject MS0435090516.long.MS0435 --surf-wm-vol --ctab /usr/local/freesurfer//WMParcStatsLUT.txt --etiv mghRead(mri/wmparc.mgz, -1): could not open file $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ cwd cmdline mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject MS0435090516.long.MS0435 --surf-wm-vol --ctab /usr/local/freesurfer//WMParcStatsLUT.txt --etiv sysname Linux hostname umeshu machine x86_64 user ms atlas_icv (eTIV) = 2033447 mm^3 (det: 0.958031 ) Loading mri/wmparc.mgz ERROR: loading mri/wmparc.mgz /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/label #-------------------------------------------- #@# BA Labels lh Wed Mar 30 12:19:37 EDT 2016 mri_label2label --srcsubject fsaverage --srclabel /mnt/fourtb/SAG_3D_BRAVO/fsaverage/label/lh.BA1.label --trgsubject MS0435090516.long.MS0435 --trglabel ./lh.BA1.label --hemi lh --regmethod surface srclabel = /mnt/fourtb/SAG_3D_BRAVO/fsaverage/label/lh.BA1.label srcsubject = fsaverage trgsubject = MS0435090516.long.MS0435 trglabel = ./lh.BA1.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /mnt/fourtb/SAG_3D_BRAVO FREESURFER_HOME /usr/local/freesurfer/ Loading source label. Found 4129 points in source label. MRISread(/mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/lh.white): could not open file Starting surface-based mapping Reading source registration /mnt/fourtb/SAG_3D_BRAVO/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/lh.white No such file or directory ERROR: could not read /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/lh.white mri_label2label --srcsubject fsaverage --srclabel /mnt/fourtb/SAG_3D_BRAVO/fsaverage/label/lh.BA2.label --trgsubject MS0435090516.long.MS0435 --trglabel ./lh.BA2.label --hemi lh --regmethod surface srclabel = /mnt/fourtb/SAG_3D_BRAVO/fsaverage/label/lh.BA2.label srcsubject = fsaverage trgsubject = MS0435090516.long.MS0435 trglabel = ./lh.BA2.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /mnt/fourtb/SAG_3D_BRAVO FREESURFER_HOME /usr/local/freesurfer/ Loading source label. Found 7909 points in source label. MRISread(/mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/lh.white): could not open file Starting surface-based mapping Reading source registration /mnt/fourtb/SAG_3D_BRAVO/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/lh.white No such file or directory ERROR: could not read /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/lh.white mri_label2label --srcsubject fsaverage --srclabel /mnt/fourtb/SAG_3D_BRAVO/fsaverage/label/lh.BA3a.label --trgsubject MS0435090516.long.MS0435 --trglabel ./lh.BA3a.label --hemi lh --regmethod surface srclabel = /mnt/fourtb/SAG_3D_BRAVO/fsaverage/label/lh.BA3a.label srcsubject = fsaverage trgsubject = MS0435090516.long.MS0435 trglabel = ./lh.BA3a.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /mnt/fourtb/SAG_3D_BRAVO FREESURFER_HOME /usr/local/freesurfer/ Loading source label. Found 4077 points in source label. MRISread(/mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/lh.white): could not open file Starting surface-based mapping Reading source registration /mnt/fourtb/SAG_3D_BRAVO/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/lh.white No such file or directory ERROR: could not read /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/lh.white mri_label2label --srcsubject fsaverage --srclabel /mnt/fourtb/SAG_3D_BRAVO/fsaverage/label/lh.BA3b.label --trgsubject MS0435090516.long.MS0435 --trglabel ./lh.BA3b.label --hemi lh --regmethod surface srclabel = /mnt/fourtb/SAG_3D_BRAVO/fsaverage/label/lh.BA3b.label srcsubject = fsaverage trgsubject = MS0435090516.long.MS0435 trglabel = ./lh.BA3b.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /mnt/fourtb/SAG_3D_BRAVO FREESURFER_HOME /usr/local/freesurfer/ Loading source label. Found 5983 points in source label. MRISread(/mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/lh.white): could not open file Starting surface-based mapping Reading source registration /mnt/fourtb/SAG_3D_BRAVO/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/lh.white No such file or directory ERROR: could not read /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/lh.white mri_label2label --srcsubject fsaverage --srclabel /mnt/fourtb/SAG_3D_BRAVO/fsaverage/label/lh.BA4a.label --trgsubject MS0435090516.long.MS0435 --trglabel ./lh.BA4a.label --hemi lh --regmethod surface srclabel = /mnt/fourtb/SAG_3D_BRAVO/fsaverage/label/lh.BA4a.label srcsubject = fsaverage trgsubject = MS0435090516.long.MS0435 trglabel = ./lh.BA4a.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /mnt/fourtb/SAG_3D_BRAVO FREESURFER_HOME /usr/local/freesurfer/ Loading source label. Found 5784 points in source label. MRISread(/mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/lh.white): could not open file Starting surface-based mapping Reading source registration /mnt/fourtb/SAG_3D_BRAVO/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/lh.white No such file or directory ERROR: could not read /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/lh.white mri_label2label --srcsubject fsaverage --srclabel /mnt/fourtb/SAG_3D_BRAVO/fsaverage/label/lh.BA4p.label --trgsubject MS0435090516.long.MS0435 --trglabel ./lh.BA4p.label --hemi lh --regmethod surface srclabel = /mnt/fourtb/SAG_3D_BRAVO/fsaverage/label/lh.BA4p.label srcsubject = fsaverage trgsubject = MS0435090516.long.MS0435 trglabel = ./lh.BA4p.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /mnt/fourtb/SAG_3D_BRAVO FREESURFER_HOME /usr/local/freesurfer/ Loading source label. Found 4070 points in source label. MRISread(/mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/lh.white): could not open file Starting surface-based mapping Reading source registration /mnt/fourtb/SAG_3D_BRAVO/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/lh.white No such file or directory ERROR: could not read /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/lh.white mri_label2label --srcsubject fsaverage --srclabel /mnt/fourtb/SAG_3D_BRAVO/fsaverage/label/lh.BA6.label --trgsubject MS0435090516.long.MS0435 --trglabel ./lh.BA6.label --hemi lh --regmethod surface srclabel = /mnt/fourtb/SAG_3D_BRAVO/fsaverage/label/lh.BA6.label srcsubject = fsaverage trgsubject = MS0435090516.long.MS0435 trglabel = ./lh.BA6.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /mnt/fourtb/SAG_3D_BRAVO FREESURFER_HOME /usr/local/freesurfer/ Loading source label. Found 13589 points in source label. MRISread(/mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/lh.white): could not open file Starting surface-based mapping Reading source registration /mnt/fourtb/SAG_3D_BRAVO/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/lh.white No such file or directory ERROR: could not read /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/lh.white mri_label2label --srcsubject fsaverage --srclabel /mnt/fourtb/SAG_3D_BRAVO/fsaverage/label/lh.BA44.label --trgsubject MS0435090516.long.MS0435 --trglabel ./lh.BA44.label --hemi lh --regmethod surface srclabel = /mnt/fourtb/SAG_3D_BRAVO/fsaverage/label/lh.BA44.label srcsubject = fsaverage trgsubject = MS0435090516.long.MS0435 trglabel = ./lh.BA44.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /mnt/fourtb/SAG_3D_BRAVO FREESURFER_HOME /usr/local/freesurfer/ Loading source label. Found 4181 points in source label. MRISread(/mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/lh.white): could not open file Starting surface-based mapping Reading source registration /mnt/fourtb/SAG_3D_BRAVO/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/lh.white No such file or directory ERROR: could not read /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/lh.white mri_label2label --srcsubject fsaverage --srclabel /mnt/fourtb/SAG_3D_BRAVO/fsaverage/label/lh.BA45.label --trgsubject MS0435090516.long.MS0435 --trglabel ./lh.BA45.label --hemi lh --regmethod surface srclabel = /mnt/fourtb/SAG_3D_BRAVO/fsaverage/label/lh.BA45.label srcsubject = fsaverage trgsubject = MS0435090516.long.MS0435 trglabel = ./lh.BA45.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /mnt/fourtb/SAG_3D_BRAVO FREESURFER_HOME /usr/local/freesurfer/ Loading source label. Found 3422 points in source label. MRISread(/mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/lh.white): could not open file Starting surface-based mapping Reading source registration /mnt/fourtb/SAG_3D_BRAVO/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/lh.white No such file or directory ERROR: could not read /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/lh.white mri_label2label --srcsubject fsaverage --srclabel /mnt/fourtb/SAG_3D_BRAVO/fsaverage/label/lh.V1.label --trgsubject MS0435090516.long.MS0435 --trglabel ./lh.V1.label --hemi lh --regmethod surface srclabel = /mnt/fourtb/SAG_3D_BRAVO/fsaverage/label/lh.V1.label srcsubject = fsaverage trgsubject = MS0435090516.long.MS0435 trglabel = ./lh.V1.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /mnt/fourtb/SAG_3D_BRAVO FREESURFER_HOME /usr/local/freesurfer/ Loading source label. Found 4641 points in source label. MRISread(/mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/lh.white): could not open file Starting surface-based mapping Reading source registration /mnt/fourtb/SAG_3D_BRAVO/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/lh.white No such file or directory ERROR: could not read /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/lh.white mri_label2label --srcsubject fsaverage --srclabel /mnt/fourtb/SAG_3D_BRAVO/fsaverage/label/lh.V2.label --trgsubject MS0435090516.long.MS0435 --trglabel ./lh.V2.label --hemi lh --regmethod surface srclabel = /mnt/fourtb/SAG_3D_BRAVO/fsaverage/label/lh.V2.label srcsubject = fsaverage trgsubject = MS0435090516.long.MS0435 trglabel = ./lh.V2.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /mnt/fourtb/SAG_3D_BRAVO FREESURFER_HOME /usr/local/freesurfer/ Loading source label. Found 8114 points in source label. MRISread(/mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/lh.white): could not open file Starting surface-based mapping Reading source registration /mnt/fourtb/SAG_3D_BRAVO/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/lh.white No such file or directory ERROR: could not read /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/lh.white mri_label2label --srcsubject fsaverage --srclabel /mnt/fourtb/SAG_3D_BRAVO/fsaverage/label/lh.MT.label --trgsubject MS0435090516.long.MS0435 --trglabel ./lh.MT.label --hemi lh --regmethod surface srclabel = /mnt/fourtb/SAG_3D_BRAVO/fsaverage/label/lh.MT.label srcsubject = fsaverage trgsubject = MS0435090516.long.MS0435 trglabel = ./lh.MT.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /mnt/fourtb/SAG_3D_BRAVO FREESURFER_HOME /usr/local/freesurfer/ Loading source label. Found 2018 points in source label. MRISread(/mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/lh.white): could not open file Starting surface-based mapping Reading source registration /mnt/fourtb/SAG_3D_BRAVO/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/lh.white No such file or directory ERROR: could not read /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/lh.white mris_label2annot --s MS0435090516.long.MS0435 --hemi lh --ctab /usr/local/freesurfer//average/colortable_BA.txt --l lh.BA1.label --l lh.BA2.label --l lh.BA3a.label --l lh.BA3b.label --l lh.BA4a.label --l lh.BA4p.label --l lh.BA6.label --l lh.BA44.label --l lh.BA45.label --l lh.V1.label --l lh.V2.label --l lh.MT.label --a BA --maxstatwinner --noverbose ERROR: cannot find or read lh.BA1.label mris_anatomical_stats -mgz -f ../stats/lh.BA.stats -b -a ./lh.BA.annot -c ./BA.ctab MS0435090516.long.MS0435 lh white computing statistics for each annotation in ./lh.BA.annot. reading volume /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/mri/wm.mgz... mghRead(/mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/mri/wm.mgz, -1): could not open file INFO: assuming MGZ format for volumes. mris_anatomical_stats: could not read input volume /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/mri/wm.mgz #-------------------------------------------- #@# BA Labels rh Wed Mar 30 12:20:07 EDT 2016 mri_label2label --srcsubject fsaverage --srclabel /mnt/fourtb/SAG_3D_BRAVO/fsaverage/label/rh.BA1.label --trgsubject MS0435090516.long.MS0435 --trglabel ./rh.BA1.label --hemi rh --regmethod surface srclabel = /mnt/fourtb/SAG_3D_BRAVO/fsaverage/label/rh.BA1.label srcsubject = fsaverage trgsubject = MS0435090516.long.MS0435 trglabel = ./rh.BA1.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /mnt/fourtb/SAG_3D_BRAVO FREESURFER_HOME /usr/local/freesurfer/ Loading source label. Found 3962 points in source label. MRISread(/mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/rh.white): could not open file Starting surface-based mapping Reading source registration /mnt/fourtb/SAG_3D_BRAVO/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/rh.white No such file or directory ERROR: could not read /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/rh.white mri_label2label --srcsubject fsaverage --srclabel /mnt/fourtb/SAG_3D_BRAVO/fsaverage/label/rh.BA2.label --trgsubject MS0435090516.long.MS0435 --trglabel ./rh.BA2.label --hemi rh --regmethod surface srclabel = /mnt/fourtb/SAG_3D_BRAVO/fsaverage/label/rh.BA2.label srcsubject = fsaverage trgsubject = MS0435090516.long.MS0435 trglabel = ./rh.BA2.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /mnt/fourtb/SAG_3D_BRAVO FREESURFER_HOME /usr/local/freesurfer/ Loading source label. Found 6687 points in source label. MRISread(/mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/rh.white): could not open file Starting surface-based mapping Reading source registration /mnt/fourtb/SAG_3D_BRAVO/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/rh.white No such file or directory ERROR: could not read /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/rh.white mri_label2label --srcsubject fsaverage --srclabel /mnt/fourtb/SAG_3D_BRAVO/fsaverage/label/rh.BA3a.label --trgsubject MS0435090516.long.MS0435 --trglabel ./rh.BA3a.label --hemi rh --regmethod surface srclabel = /mnt/fourtb/SAG_3D_BRAVO/fsaverage/label/rh.BA3a.label srcsubject = fsaverage trgsubject = MS0435090516.long.MS0435 trglabel = ./rh.BA3a.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /mnt/fourtb/SAG_3D_BRAVO FREESURFER_HOME /usr/local/freesurfer/ Loading source label. Found 3980 points in source label. MRISread(/mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/rh.white): could not open file Starting surface-based mapping Reading source registration /mnt/fourtb/SAG_3D_BRAVO/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/rh.white No such file or directory ERROR: could not read /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/rh.white mri_label2label --srcsubject fsaverage --srclabel /mnt/fourtb/SAG_3D_BRAVO/fsaverage/label/rh.BA3b.label --trgsubject MS0435090516.long.MS0435 --trglabel ./rh.BA3b.label --hemi rh --regmethod surface srclabel = /mnt/fourtb/SAG_3D_BRAVO/fsaverage/label/rh.BA3b.label srcsubject = fsaverage trgsubject = MS0435090516.long.MS0435 trglabel = ./rh.BA3b.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /mnt/fourtb/SAG_3D_BRAVO FREESURFER_HOME /usr/local/freesurfer/ Loading source label. Found 4522 points in source label. MRISread(/mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/rh.white): could not open file Starting surface-based mapping Reading source registration /mnt/fourtb/SAG_3D_BRAVO/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/rh.white No such file or directory ERROR: could not read /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/rh.white mri_label2label --srcsubject fsaverage --srclabel /mnt/fourtb/SAG_3D_BRAVO/fsaverage/label/rh.BA4a.label --trgsubject MS0435090516.long.MS0435 --trglabel ./rh.BA4a.label --hemi rh --regmethod surface srclabel = /mnt/fourtb/SAG_3D_BRAVO/fsaverage/label/rh.BA4a.label srcsubject = fsaverage trgsubject = MS0435090516.long.MS0435 trglabel = ./rh.BA4a.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /mnt/fourtb/SAG_3D_BRAVO FREESURFER_HOME /usr/local/freesurfer/ Loading source label. Found 5747 points in source label. MRISread(/mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/rh.white): could not open file Starting surface-based mapping Reading source registration /mnt/fourtb/SAG_3D_BRAVO/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/rh.white No such file or directory ERROR: could not read /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/rh.white mri_label2label --srcsubject fsaverage --srclabel /mnt/fourtb/SAG_3D_BRAVO/fsaverage/label/rh.BA4p.label --trgsubject MS0435090516.long.MS0435 --trglabel ./rh.BA4p.label --hemi rh --regmethod surface srclabel = /mnt/fourtb/SAG_3D_BRAVO/fsaverage/label/rh.BA4p.label srcsubject = fsaverage trgsubject = MS0435090516.long.MS0435 trglabel = ./rh.BA4p.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /mnt/fourtb/SAG_3D_BRAVO FREESURFER_HOME /usr/local/freesurfer/ Loading source label. Found 4473 points in source label. MRISread(/mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/rh.white): could not open file Starting surface-based mapping Reading source registration /mnt/fourtb/SAG_3D_BRAVO/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/rh.white No such file or directory ERROR: could not read /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/rh.white mri_label2label --srcsubject fsaverage --srclabel /mnt/fourtb/SAG_3D_BRAVO/fsaverage/label/rh.BA6.label --trgsubject MS0435090516.long.MS0435 --trglabel ./rh.BA6.label --hemi rh --regmethod surface srclabel = /mnt/fourtb/SAG_3D_BRAVO/fsaverage/label/rh.BA6.label srcsubject = fsaverage trgsubject = MS0435090516.long.MS0435 trglabel = ./rh.BA6.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /mnt/fourtb/SAG_3D_BRAVO FREESURFER_HOME /usr/local/freesurfer/ Loading source label. Found 12256 points in source label. MRISread(/mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/rh.white): could not open file Starting surface-based mapping Reading source registration /mnt/fourtb/SAG_3D_BRAVO/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/rh.white No such file or directory ERROR: could not read /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/rh.white mri_label2label --srcsubject fsaverage --srclabel /mnt/fourtb/SAG_3D_BRAVO/fsaverage/label/rh.BA44.label --trgsubject MS0435090516.long.MS0435 --trglabel ./rh.BA44.label --hemi rh --regmethod surface srclabel = /mnt/fourtb/SAG_3D_BRAVO/fsaverage/label/rh.BA44.label srcsubject = fsaverage trgsubject = MS0435090516.long.MS0435 trglabel = ./rh.BA44.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /mnt/fourtb/SAG_3D_BRAVO FREESURFER_HOME /usr/local/freesurfer/ Loading source label. Found 6912 points in source label. MRISread(/mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/rh.white): could not open file Starting surface-based mapping Reading source registration /mnt/fourtb/SAG_3D_BRAVO/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/rh.white No such file or directory ERROR: could not read /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/rh.white mri_label2label --srcsubject fsaverage --srclabel /mnt/fourtb/SAG_3D_BRAVO/fsaverage/label/rh.BA45.label --trgsubject MS0435090516.long.MS0435 --trglabel ./rh.BA45.label --hemi rh --regmethod surface srclabel = /mnt/fourtb/SAG_3D_BRAVO/fsaverage/label/rh.BA45.label srcsubject = fsaverage trgsubject = MS0435090516.long.MS0435 trglabel = ./rh.BA45.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /mnt/fourtb/SAG_3D_BRAVO FREESURFER_HOME /usr/local/freesurfer/ Loading source label. Found 5355 points in source label. MRISread(/mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/rh.white): could not open file Starting surface-based mapping Reading source registration /mnt/fourtb/SAG_3D_BRAVO/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/rh.white No such file or directory ERROR: could not read /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/rh.white mri_label2label --srcsubject fsaverage --srclabel /mnt/fourtb/SAG_3D_BRAVO/fsaverage/label/rh.V1.label --trgsubject MS0435090516.long.MS0435 --trglabel ./rh.V1.label --hemi rh --regmethod surface srclabel = /mnt/fourtb/SAG_3D_BRAVO/fsaverage/label/rh.V1.label srcsubject = fsaverage trgsubject = MS0435090516.long.MS0435 trglabel = ./rh.V1.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /mnt/fourtb/SAG_3D_BRAVO FREESURFER_HOME /usr/local/freesurfer/ Loading source label. Found 4727 points in source label. MRISread(/mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/rh.white): could not open file Starting surface-based mapping Reading source registration /mnt/fourtb/SAG_3D_BRAVO/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/rh.white No such file or directory ERROR: could not read /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/rh.white mri_label2label --srcsubject fsaverage --srclabel /mnt/fourtb/SAG_3D_BRAVO/fsaverage/label/rh.V2.label --trgsubject MS0435090516.long.MS0435 --trglabel ./rh.V2.label --hemi rh --regmethod surface srclabel = /mnt/fourtb/SAG_3D_BRAVO/fsaverage/label/rh.V2.label srcsubject = fsaverage trgsubject = MS0435090516.long.MS0435 trglabel = ./rh.V2.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /mnt/fourtb/SAG_3D_BRAVO FREESURFER_HOME /usr/local/freesurfer/ Loading source label. Found 8016 points in source label. MRISread(/mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/rh.white): could not open file Starting surface-based mapping Reading source registration /mnt/fourtb/SAG_3D_BRAVO/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/rh.white No such file or directory ERROR: could not read /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/rh.white mri_label2label --srcsubject fsaverage --srclabel /mnt/fourtb/SAG_3D_BRAVO/fsaverage/label/rh.MT.label --trgsubject MS0435090516.long.MS0435 --trglabel ./rh.MT.label --hemi rh --regmethod surface srclabel = /mnt/fourtb/SAG_3D_BRAVO/fsaverage/label/rh.MT.label srcsubject = fsaverage trgsubject = MS0435090516.long.MS0435 trglabel = ./rh.MT.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /mnt/fourtb/SAG_3D_BRAVO FREESURFER_HOME /usr/local/freesurfer/ Loading source label. Found 1932 points in source label. MRISread(/mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/rh.white): could not open file Starting surface-based mapping Reading source registration /mnt/fourtb/SAG_3D_BRAVO/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/rh.white No such file or directory ERROR: could not read /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/rh.white mris_label2annot --s MS0435090516.long.MS0435 --hemi rh --ctab /usr/local/freesurfer//average/colortable_BA.txt --l rh.BA1.label --l rh.BA2.label --l rh.BA3a.label --l rh.BA3b.label --l rh.BA4a.label --l rh.BA4p.label --l rh.BA6.label --l rh.BA44.label --l rh.BA45.label --l rh.V1.label --l rh.V2.label --l rh.MT.label --a BA --maxstatwinner --noverbose ERROR: cannot find or read rh.BA1.label mris_anatomical_stats -mgz -f ../stats/rh.BA.stats -b -a ./rh.BA.annot -c ./BA.ctab MS0435090516.long.MS0435 rh white computing statistics for each annotation in ./rh.BA.annot. reading volume /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/mri/wm.mgz... mghRead(/mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/mri/wm.mgz, -1): could not open file INFO: assuming MGZ format for volumes. mris_anatomical_stats: could not read input volume /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/mri/wm.mgz /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/label #-------------------------------------------- #@# Ex-vivo Entorhinal Cortex Label lh Wed Mar 30 12:20:36 EDT 2016 mris_spherical_average -erode 1 -orig white -t 0.4 -o MS0435090516.long.MS0435 label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label painting output onto subject MS0435090516.long.MS0435. processing subject lh.EC_average... reading output surface /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/lh.sphere.reg... MRISreadVertexPosition(white): could not open file /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/lh.white eroding label 1 times before writing thresholding label stat at 0.400 before writing only 1 subject - copying statistics... No such file or directory MRISreadOriginalProperties: could not read surface file white No such file or directory could not read surface positions from white No such file or directory mris_anatomical_stats -mgz -f ../stats/lh.entorhinal_exvivo.stats -b -l ./lh.entorhinal_exvivo.label MS0435090516.long.MS0435 lh white limiting computations to label ./lh.entorhinal_exvivo.label. reading volume /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/mri/wm.mgz... mghRead(/mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/mri/wm.mgz, -1): could not open file INFO: assuming MGZ format for volumes. mris_anatomical_stats: could not read input volume /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/mri/wm.mgz #-------------------------------------------- #@# Ex-vivo Entorhinal Cortex Label rh Wed Mar 30 12:20:45 EDT 2016 mris_spherical_average -erode 1 -orig white -t 0.4 -o MS0435090516.long.MS0435 label rh.entorhinal rh sphere.reg rh.EC_average rh.entorhinal_exvivo.label painting output onto subject MS0435090516.long.MS0435. processing subject rh.EC_average... reading output surface /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/rh.sphere.reg... MRISreadVertexPosition(white): could not open file /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/surf/rh.white eroding label 1 times before writing thresholding label stat at 0.400 before writing only 1 subject - copying statistics... No such file or directory MRISreadOriginalProperties: could not read surface file white No such file or directory could not read surface positions from white No such file or directory mris_anatomical_stats -mgz -f ../stats/rh.entorhinal_exvivo.stats -b -l ./rh.entorhinal_exvivo.label MS0435090516.long.MS0435 rh white limiting computations to label ./rh.entorhinal_exvivo.label. reading volume /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/mri/wm.mgz... mghRead(/mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/mri/wm.mgz, -1): could not open file INFO: assuming MGZ format for volumes. mris_anatomical_stats: could not read input volume /mnt/fourtb/SAG_3D_BRAVO/MS0435090516.long.MS0435/mri/wm.mgz #------------------------------------------ recon-all -s MS0435090516.long.MS0435 finished without error at Wed Mar 30 12:20:55 EDT 2016