Dear FreeSurfer developers,
I am a new FreeSurfer user and I am trying to run it in a supercomputer
for the first time.
Recon-all finished with errors (see log attached) during skull stripping.
I have searched the archives and only found that it could be a memory
problem, but I am unsure about this.
The version of freesurfer is:
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2
Thank you for your help,
Diana
--------------------------------------------------------
Diana Tordesillas Gutiérrez, PhD
Neuroimaging Unit IDIVAL
IDIVAL Building
Avda. Cardenal Herrera Oria s/n
39011 Santander
Spain
Tel. +34 942202677
diana.tordesil...@humv.es
diana.tordesil...@gmail.com
----------------------------------------------------------
Thu Feb 9 09:53:26 CET 2017
/gpfs/csic_users/res/uc35/uc35002/Sujetos/prueba
/gpfs/res_apps/FREESURFER/freesurfer/bin/recon-all
-all -s prueba
subjid prueba
setenv SUBJECTS_DIR /gpfs/csic_users/res/uc35/uc35002/Sujetos
FREESURFER_HOME /gpfs/res_apps/FREESURFER/freesurfer
Actual FREESURFER_HOME /gpfs/res_projects/apps/FREESURFER/freesurfer
build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
Linux login1 2.6.32-642.6.2.el6.x86_64 #1 SMP Tue Oct 25 15:06:33 CDT 2016 x86_64 x86_64 x86_64 GNU/Linux
cputime 10:00
filesize unlimited
datasize unlimited
stacksize unlimited
coredumpsize 0 kbytes
memoryuse unlimited
vmemoryuse unlimited
descriptors 1024
memorylocked unlimited
maxproc 1024
total used free shared buffers cached
Mem: 65949116 7785820 58163296 732 278420 4237620
-/+ buffers/cache: 3269780 62679336
Swap: 33046524 191752 32854772
########################################
program versions used
$Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $
$Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $
mri_convert.bin -all-info
ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/02/09-08:53:27-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: uc35002 Machine: login1 Platform: Linux PlatformVersion: 2.6.32-642.6.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
FLIRT version 5.5
$Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $
mri_convert.bin --version
stable6
ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/02/09-08:53:27-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: uc35002 Machine: login1 Platform: Linux PlatformVersion: 2.6.32-642.6.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/02/09-08:53:28-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: uc35002 Machine: login1 Platform: Linux PlatformVersion: 2.6.32-642.6.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/02/09-08:53:28-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: uc35002 Machine: login1 Platform: Linux PlatformVersion: 2.6.32-642.6.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/02/09-08:53:28-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: uc35002 Machine: login1 Platform: Linux PlatformVersion: 2.6.32-642.6.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/02/09-08:53:28-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: uc35002 Machine: login1 Platform: Linux PlatformVersion: 2.6.32-642.6.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/02/09-08:53:28-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: uc35002 Machine: login1 Platform: Linux PlatformVersion: 2.6.32-642.6.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/02/09-08:53:29-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: uc35002 Machine: login1 Platform: Linux PlatformVersion: 2.6.32-642.6.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/02/09-08:53:29-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: uc35002 Machine: login1 Platform: Linux PlatformVersion: 2.6.32-642.6.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/02/09-08:53:29-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: uc35002 Machine: login1 Platform: Linux PlatformVersion: 2.6.32-642.6.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/02/09-08:53:29-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: uc35002 Machine: login1 Platform: Linux PlatformVersion: 2.6.32-642.6.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/02/09-08:53:30-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: uc35002 Machine: login1 Platform: Linux PlatformVersion: 2.6.32-642.6.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/02/09-08:53:30-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: uc35002 Machine: login1 Platform: Linux PlatformVersion: 2.6.32-642.6.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/02/09-08:53:30-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: uc35002 Machine: login1 Platform: Linux PlatformVersion: 2.6.32-642.6.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/02/09-08:53:30-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: uc35002 Machine: login1 Platform: Linux PlatformVersion: 2.6.32-642.6.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/02/09-08:53:30-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: uc35002 Machine: login1 Platform: Linux PlatformVersion: 2.6.32-642.6.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/02/09-08:53:30-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: uc35002 Machine: login1 Platform: Linux PlatformVersion: 2.6.32-642.6.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/02/09-08:53:30-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: uc35002 Machine: login1 Platform: Linux PlatformVersion: 2.6.32-642.6.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/02/09-08:53:31-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: uc35002 Machine: login1 Platform: Linux PlatformVersion: 2.6.32-642.6.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/02/09-08:53:31-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: uc35002 Machine: login1 Platform: Linux PlatformVersion: 2.6.32-642.6.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/02/09-08:53:31-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: uc35002 Machine: login1 Platform: Linux PlatformVersion: 2.6.32-642.6.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/02/09-08:53:32-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: uc35002 Machine: login1 Platform: Linux PlatformVersion: 2.6.32-642.6.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/02/09-08:53:33-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: uc35002 Machine: login1 Platform: Linux PlatformVersion: 2.6.32-642.6.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/02/09-08:53:33-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: uc35002 Machine: login1 Platform: Linux PlatformVersion: 2.6.32-642.6.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/02/09-08:53:33-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: uc35002 Machine: login1 Platform: Linux PlatformVersion: 2.6.32-642.6.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/02/09-08:53:33-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: uc35002 Machine: login1 Platform: Linux PlatformVersion: 2.6.32-642.6.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/02/09-08:53:34-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: uc35002 Machine: login1 Platform: Linux PlatformVersion: 2.6.32-642.6.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2017/02/09-08:53:34-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: uc35002 Machine: login1 Platform: Linux PlatformVersion: 2.6.32-642.6.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/02/09-08:53:34-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: uc35002 Machine: login1 Platform: Linux PlatformVersion: 2.6.32-642.6.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/02/09-08:53:34-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: uc35002 Machine: login1 Platform: Linux PlatformVersion: 2.6.32-642.6.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/02/09-08:53:34-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: uc35002 Machine: login1 Platform: Linux PlatformVersion: 2.6.32-642.6.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/02/09-08:53:34-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: uc35002 Machine: login1 Platform: Linux PlatformVersion: 2.6.32-642.6.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
$Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $
ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/02/09-08:53:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: uc35002 Machine: login1 Platform: Linux PlatformVersion: 2.6.32-642.6.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
$Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $
ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/02/09-08:53:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: uc35002 Machine: login1 Platform: Linux PlatformVersion: 2.6.32-642.6.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/02/09-08:53:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: uc35002 Machine: login1 Platform: Linux PlatformVersion: 2.6.32-642.6.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/02/09-08:53:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: uc35002 Machine: login1 Platform: Linux PlatformVersion: 2.6.32-642.6.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/02/09-08:53:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: uc35002 Machine: login1 Platform: Linux PlatformVersion: 2.6.32-642.6.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/02/09-08:53:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: uc35002 Machine: login1 Platform: Linux PlatformVersion: 2.6.32-642.6.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/02/09-08:53:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: uc35002 Machine: login1 Platform: Linux PlatformVersion: 2.6.32-642.6.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
#######################################
GCADIR /gpfs/res_apps/FREESURFER/freesurfer/average
GCA RB_all_2016-05-10.vc700.gca
GCASkull RB_all_withskull_2016-05-10.vc700.gca
AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif
GCSDIR /gpfs/res_apps/FREESURFER/freesurfer/average
GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs
#######################################
#--------------------------------------------
#@# MotionCor Thu Feb 9 09:53:35 CET 2017
Found 1 runs
/gpfs/csic_users/res/uc35/uc35002/Sujetos/prueba/mri/orig/001.mgz
Checking for (invalid) multi-frame inputs...
WARNING: only one run found. This is OK, but motion
correction cannot be performed on one run, so I'll
copy the run to rawavg and continue.
cp /gpfs/csic_users/res/uc35/uc35002/Sujetos/prueba/mri/orig/001.mgz /gpfs/csic_users/res/uc35/uc35002/Sujetos/prueba/mri/rawavg.mgz
/gpfs/csic_users/res/uc35/uc35002/Sujetos/prueba
mri_convert /gpfs/csic_users/res/uc35/uc35002/Sujetos/prueba/mri/rawavg.mgz /gpfs/csic_users/res/uc35/uc35002/Sujetos/prueba/mri/orig.mgz --conform
mri_convert.bin /gpfs/csic_users/res/uc35/uc35002/Sujetos/prueba/mri/rawavg.mgz /gpfs/csic_users/res/uc35/uc35002/Sujetos/prueba/mri/orig.mgz --conform
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /gpfs/csic_users/res/uc35/uc35002/Sujetos/prueba/mri/rawavg.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.00665236, -0.999483, -0.0314457)
j_ras = (-0.025056, 0.0316031, -0.999186)
k_ras = (0.999664, -0.00585904, -0.0252533)
changing data type from float to uchar (noscale = 0)...
MRIchangeType: Building histogram
Reslicing using trilinear interpolation
writing to /gpfs/csic_users/res/uc35/uc35002/Sujetos/prueba/mri/orig.mgz...
mri_add_xform_to_header -c /gpfs/csic_users/res/uc35/uc35002/Sujetos/prueba/mri/transforms/talairach.xfm /gpfs/csic_users/res/uc35/uc35002/Sujetos/prueba/mri/orig.mgz /gpfs/csic_users/res/uc35/uc35002/Sujetos/prueba/mri/orig.mgz
INFO: extension is mgz
#--------------------------------------------
#@# Talairach Thu Feb 9 09:53:44 CET 2017
/gpfs/csic_users/res/uc35/uc35002/Sujetos/prueba/mri
mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50
/gpfs/csic_users/res/uc35/uc35002/Sujetos/prueba/mri
/gpfs/res_apps/FREESURFER/freesurfer/bin/mri_nu_correct.mni
--no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50
nIters 1
$Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $
Linux login1 2.6.32-642.6.2.el6.x86_64 #1 SMP Tue Oct 25 15:06:33 CDT 2016 x86_64 x86_64 x86_64 GNU/Linux
Thu Feb 9 09:53:44 CET 2017
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
/usr/bin/bc
tmpdir is ./tmp.mri_nu_correct.mni.24250
/gpfs/csic_users/res/uc35/uc35002/Sujetos/prueba/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.24250/nu0.mnc -odt float
mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.24250/nu0.mnc -odt float
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from orig.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, -2.6339e-09, -1)
k_ras = (-4.65661e-10, 1, 2.70666e-09)
changing data type from uchar to float (noscale = 0)...
writing to ./tmp.mri_nu_correct.mni.24250/nu0.mnc...
--------------------------------------------------------
Iteration 1 Thu Feb 9 09:53:46 CET 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.24250/nu0.mnc ./tmp.mri_nu_correct.mni.24250/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.24250/0/ -iterations 1000 -distance 50
[uc35002@login1:/gpfs/csic_users/res/uc35/uc35002/Sujetos/prueba/mri/] [2017-02-09 09:53:46] running:
/gpfs/res_apps/FREESURFER/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.24250/0/ ./tmp.mri_nu_correct.mni.24250/nu0.mnc ./tmp.mri_nu_correct.mni.24250/nu1.imp
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
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Number of iterations: 76
CV of field change: 0.000953127
mri_convert ./tmp.mri_nu_correct.mni.24250/nu1.mnc orig_nu.mgz --like orig.mgz --conform
mri_convert.bin ./tmp.mri_nu_correct.mni.24250/nu1.mnc orig_nu.mgz --like orig.mgz --conform
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from ./tmp.mri_nu_correct.mni.24250/nu1.mnc...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, -2.6339e-09, -1)
k_ras = (-4.65661e-10, 1, 2.70666e-09)
INFO: transform src into the like-volume: orig.mgz
changing data type from float to uchar (noscale = 0)...
MRIchangeType: Building histogram
writing to orig_nu.mgz...
Thu Feb 9 09:55:16 CET 2017
mri_nu_correct.mni done
talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm
talairach_avi log file is transforms/talairach_avi.log...
Started at Thu Feb 9 09:55:16 CET 2017
Ended at Thu Feb 9 09:55:51 CET 2017
talairach_avi done
cp transforms/talairach.auto.xfm transforms/talairach.xfm
#--------------------------------------------
#@# Talairach Failure Detection Thu Feb 9 09:55:53 CET 2017
/gpfs/csic_users/res/uc35/uc35002/Sujetos/prueba/mri
talairach_afd -T 0.005 -xfm transforms/talairach.xfm
talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.6942, pval=0.4932 >= threshold=0.0050)
awk -f /gpfs/res_apps/FREESURFER/freesurfer/bin/extract_talairach_avi_QA.awk /gpfs/csic_users/res/uc35/uc35002/Sujetos/prueba/mri/transforms/talairach_avi.log
tal_QC_AZS /gpfs/csic_users/res/uc35/uc35002/Sujetos/prueba/mri/transforms/talairach_avi.log
TalAviQA: 0.97338
z-score: -1
#--------------------------------------------
#@# Nu Intensity Correction Thu Feb 9 09:55:54 CET 2017
mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2
/gpfs/csic_users/res/uc35/uc35002/Sujetos/prueba/mri
/gpfs/res_apps/FREESURFER/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 1.27 2016/02/26 16:19:49 mreuter Exp $
Linux login1 2.6.32-642.6.2.el6.x86_64 #1 SMP Tue Oct 25 15:06:33 CDT 2016 x86_64 x86_64 x86_64 GNU/Linux
Thu Feb 9 09:55:54 CET 2017
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
/usr/bin/bc
tmpdir is ./tmp.mri_nu_correct.mni.27136
/gpfs/csic_users/res/uc35/uc35002/Sujetos/prueba/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.27136/nu0.mnc -odt float
mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.27136/nu0.mnc -odt float
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from orig.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, -2.6339e-09, -1)
k_ras = (-4.65661e-10, 1, 2.70666e-09)
changing data type from uchar to float (noscale = 0)...
writing to ./tmp.mri_nu_correct.mni.27136/nu0.mnc...
--------------------------------------------------------
Iteration 1 Thu Feb 9 09:55:56 CET 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.27136/nu0.mnc ./tmp.mri_nu_correct.mni.27136/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.27136/0/
[uc35002@login1:/gpfs/csic_users/res/uc35/uc35002/Sujetos/prueba/mri/] [2017-02-09 09:55:56] running:
/gpfs/res_apps/FREESURFER/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 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.27136/0/ ./tmp.mri_nu_correct.mni.27136/nu0.mnc ./tmp.mri_nu_correct.mni.27136/nu1.imp
Processing:.................................................................Done
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Processing:.................................................................Done
Number of iterations: 50
CV of field change: 0.0017759
--------------------------------------------------------
Iteration 2 Thu Feb 9 09:56:47 CET 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.27136/nu1.mnc ./tmp.mri_nu_correct.mni.27136/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.27136/1/
[uc35002@login1:/gpfs/csic_users/res/uc35/uc35002/Sujetos/prueba/mri/] [2017-02-09 09:56:47] running:
/gpfs/res_apps/FREESURFER/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 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.27136/1/ ./tmp.mri_nu_correct.mni.27136/nu1.mnc ./tmp.mri_nu_correct.mni.27136/nu2.imp
Processing:.................................................................Done
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Processing:.................................................................Done
Number of iterations: 45
CV of field change: 0.000979965
mri_binarize --i ./tmp.mri_nu_correct.mni.27136/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.27136/ones.mgz
$Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $
cwd /gpfs/csic_users/res/uc35/uc35002/Sujetos/prueba/mri
cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.27136/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.27136/ones.mgz
sysname Linux
hostname login1
machine x86_64
user uc35002
input ./tmp.mri_nu_correct.mni.27136/nu2.mnc
frame 0
nErode3d 0
nErode2d 0
output ./tmp.mri_nu_correct.mni.27136/ones.mgz
Binarizing based on threshold
min -1
max +infinity
binval 1
binvalnot 0
fstart = 0, fend = 0, nframes = 1
Found 16777216 values in range
Counting number of voxels in first frame
Found 16777216 voxels in final mask
Count: 16777216 16777216.000000 16777216 100.000000
mri_binarize done
mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.27136/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.27136/sum.junk --avgwf ./tmp.mri_nu_correct.mni.27136/input.mean.dat
$Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $
cwd
cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.27136/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.27136/sum.junk --avgwf ./tmp.mri_nu_correct.mni.27136/input.mean.dat
sysname Linux
hostname login1
machine x86_64
user uc35002
UseRobust 0
Loading ./tmp.mri_nu_correct.mni.27136/ones.mgz
Loading orig.mgz
Voxel Volume is 1 mm^3
Generating list of segmentation ids
Found 1 segmentations
Computing statistics for each segmentation
Reporting on 1 segmentations
Using PrintSegStat
Computing spatial average of each frame
0
Writing to ./tmp.mri_nu_correct.mni.27136/input.mean.dat
mri_segstats done
mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.27136/ones.mgz --i ./tmp.mri_nu_correct.mni.27136/nu2.mnc --sum ./tmp.mri_nu_correct.mni.27136/sum.junk --avgwf ./tmp.mri_nu_correct.mni.27136/output.mean.dat
$Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $
cwd
cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.27136/ones.mgz --i ./tmp.mri_nu_correct.mni.27136/nu2.mnc --sum ./tmp.mri_nu_correct.mni.27136/sum.junk --avgwf ./tmp.mri_nu_correct.mni.27136/output.mean.dat
sysname Linux
hostname login1
machine x86_64
user uc35002
UseRobust 0
Loading ./tmp.mri_nu_correct.mni.27136/ones.mgz
Loading ./tmp.mri_nu_correct.mni.27136/nu2.mnc
Voxel Volume is 1 mm^3
Generating list of segmentation ids
Found 1 segmentations
Computing statistics for each segmentation
Reporting on 1 segmentations
Using PrintSegStat
Computing spatial average of each frame
0
Writing to ./tmp.mri_nu_correct.mni.27136/output.mean.dat
mri_segstats done
mris_calc -o ./tmp.mri_nu_correct.mni.27136/nu2.mnc ./tmp.mri_nu_correct.mni.27136/nu2.mnc mul 1.02392327640953655086
Saving result to './tmp.mri_nu_correct.mni.27136/nu2.mnc' (type = MINC ) [ ok ]
mri_convert ./tmp.mri_nu_correct.mni.27136/nu2.mnc nu.mgz --like orig.mgz
mri_convert.bin ./tmp.mri_nu_correct.mni.27136/nu2.mnc nu.mgz --like orig.mgz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from ./tmp.mri_nu_correct.mni.27136/nu2.mnc...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, -2.6339e-09, -1)
k_ras = (-4.65661e-10, 1, 2.70666e-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 6 seconds.
mapping ( 6, 135) to ( 3, 110)
Thu Feb 9 09:58:06 CET 2017
mri_nu_correct.mni done
mri_add_xform_to_header -c /gpfs/csic_users/res/uc35/uc35002/Sujetos/prueba/mri/transforms/talairach.xfm nu.mgz nu.mgz
INFO: extension is mgz
#--------------------------------------------
#@# Intensity Normalization Thu Feb 9 09:58:06 CET 2017
/gpfs/csic_users/res/uc35/uc35002/Sujetos/prueba/mri
mri_normalize -g 1 -mprage nu.mgz T1.mgz
using max gradient = 1.000
assuming input volume is MGH (Van der Kouwe) MP-RAGE
reading from nu.mgz...
normalizing image...
talairach transform
0.99410 -0.03289 -0.03173 0.80250;
0.07821 0.96874 0.24788 -16.24059;
0.00176 -0.23408 1.05151 15.86493;
0.00000 0.00000 0.00000 1.00000;
processing without aseg, no1d=0
MRInormInit():
INFO: Modifying talairach volume c_(r,a,s) based on average_305
MRInormalize():
MRIsplineNormalize(): npeaks = 6
Starting OpenSpline(): npoints = 6
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Iterating 2 times
---------------------------------
3d normalization pass 1 of 2
white matter peak found at 110
white matter peak found at 89
gm peak at 66 (66), valley at 31 (31)
csf peak at 34, setting threshold to 55
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
---------------------------------
3d normalization pass 2 of 2
white matter peak found at 110
white matter peak found at 109
gm peak at 66 (66), valley at 30 (30)
csf peak at 33, setting threshold to 55
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to T1.mgz
3D bias adjustment took 1 minutes and 53 seconds.
#--------------------------------------------
#@# Skull Stripping Thu Feb 9 10:00:00 CET 2017
/gpfs/csic_users/res/uc35/uc35002/Sujetos/prueba/mri
mri_em_register -rusage /gpfs/csic_users/res/uc35/uc35002/Sujetos/prueba/touch/rusage.mri_em_register.skull.dat -skull nu.mgz /gpfs/res_apps/FREESURFER/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta
aligning to atlas containing skull, setting unknown_nbr_spacing = 5
== Number of threads available to mri_em_register for OpenMP = 1 ==
reading 1 input volumes...
logging results to talairach_with_skull.log
reading '/gpfs/res_apps/FREESURFER/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca'...
average std = 22.9 using min determinant for regularization = 52.6
0 singular and 9002 ill-conditioned covariance matrices regularized
reading 'nu.mgz'...
freeing gibbs priors...done.
accounting for voxel sizes in initial transform
bounding unknown intensity as < 8.7 or > 569.1
total sample mean = 77.6 (1399 zeros)
************************************************
spacing=8, using 3243 sample points, tol=1.00e-05...
************************************************
register_mri: find_optimal_transform
find_optimal_transform: nsamples 3243, passno 0, spacing 8
resetting wm mean[0]: 100 --> 108
resetting gm mean[0]: 61 --> 61
input volume #1 is the most T1-like
using real data threshold=13.0
skull bounding box = (48, 32, 11) --> (210, 255, 225)
using (102, 106, 118) as brain centroid...
mean wm in atlas = 108, using box (82,78,92) --> (121, 133,144) to find MRI wm
before smoothing, mri peak at 112
robust fit to distribution - 113 +- 10.1
after smoothing, mri peak at 113, scaling input intensities by 0.956
scaling channel 0 by 0.955752
initial log_p = -4.241
************************************************
First Search limited to translation only.
************************************************
max log p = -4.214965 @ (0.000, 0.000, 0.000)
max log p = -4.144597 @ (-4.545, 4.545, -4.545)
max log p = -4.085411 @ (2.273, 2.273, 6.818)
max log p = -4.085411 @ (0.000, 0.000, 0.000)
max log p = -4.078675 @ (0.568, 1.705, -3.977)
max log p = -4.078675 @ (0.000, 0.000, 0.000)
Found translation: (-1.7, 8.5, -1.7): log p = -4.079
****************************************
Nine parameter search. iteration 0 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.983, old_max_log_p =-4.079 (thresh=-4.1)
1.00000 0.00000 0.00000 -1.70455;
0.00000 1.06580 0.14032 -16.07541;
0.00000 -0.13053 0.99144 16.70401;
0.00000 0.00000 0.00000 1.00000;
****************************************
Nine parameter search. iteration 1 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.930, old_max_log_p =-3.983 (thresh=-4.0)
1.00000 0.00000 0.00000 -1.70455;
0.00000 1.11762 0.28866 -32.20917;
0.00000 -0.26852 0.96465 38.16579;
0.00000 0.00000 0.00000 1.00000;
****************************************
Nine parameter search. iteration 2 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.930, old_max_log_p =-3.930 (thresh=-3.9)
1.00000 0.00000 0.00000 -1.70455;
0.00000 1.11762 0.28866 -32.20917;
0.00000 -0.26852 0.96465 38.16579;
0.00000 0.00000 0.00000 1.00000;
reducing scale to 0.2500
****************************************
Nine parameter search. iteration 3 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.855, old_max_log_p =-3.930 (thresh=-3.9)
0.96206 -0.00711 0.02948 0.73844;
0.00210 1.11720 0.18918 -23.19205;
-0.03391 -0.15759 0.98769 25.64763;
0.00000 0.00000 0.00000 1.00000;
****************************************
Nine parameter search. iteration 4 nscales = 1 ...
****************************************
Killed
Linux login1 2.6.32-642.6.2.el6.x86_64 #1 SMP Tue Oct 25 15:06:33 CDT 2016 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s prueba exited with ERRORS at Thu Feb 9 10:10:00 CET 2017
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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