External Email - Use Caution
Hi,
I have been getting this error with one of my subjects Recon-all. I am
attaching the recon-all log file. any help would be appreciated!
Meena
--
—
*Meena M. Makary, Ph.D.*
Assistant Professor | Cairo University <http://bmes.cufe.edu.eg/>
Postdoctoral Fellow | Radiology, Harvard Medical School
<https://connects.catalyst.harvard.edu/Profiles/display/Person/176550>
Postdoctoral Fellow | Athinoula A. Martinos Center, MGH
<https://www.nmr.mgh.harvard.edu/user/4550386>
Career Development and Mentoring Manager | OHBM Student and Postdoc SIG
<https://www.humanbrainmapping.org/i4a/pages/index.cfm?pageid=3449>
Tue Nov 19 16:59:46 EST 2019
/autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-089-BL
/autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/bin/recon-all
-s BIO-ALS-701-089-BL -i /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/Data/BIOMARKER/BIO-ALS-701-089-BL/anat/BIO-ALS-701-089-BL_T1w.nii.gz -all -brainstem-structures -qcache -3T
subjid BIO-ALS-701-089-BL
setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects
FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0
Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0
build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
Linux aura.nmr.mgh.harvard.edu 3.10.0-957.1.3.el7.x86_64 #1 SMP Thu Nov 29 14:49:43 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
cputime unlimited
filesize unlimited
datasize unlimited
stacksize unlimited
coredumpsize 0 kbytes
memoryuse unlimited
vmemoryuse unlimited
descriptors 65535
memorylocked 64 kbytes
maxproc 1030094
maxlocks unlimited
maxsignal 1030094
maxmessage 819200
maxnice 0
maxrtprio 0
maxrttime unlimited
total used free shared buff/cache available
Mem: 263890112 4047388 255097976 216364 4744748 258565876
Swap: 65535996 0 65535996
########################################
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: 2019/11/19-21:59:46-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: mn457 Machine: aura.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.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: 2019/11/19-21:59:46-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: mn457 Machine: aura.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
Program nu_correct, built from:
Package MNI N3, version 1.10, compiled by nicks@kani (i686-pc-linux-gnu) on 2005-11-15 at 21:02:27
ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/11/19-21:59:46-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: mn457 Machine: aura.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/11/19-21:59:46-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: mn457 Machine: aura.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/11/19-21:59:46-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: mn457 Machine: aura.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/11/19-21:59:46-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: mn457 Machine: aura.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/11/19-21:59:46-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: mn457 Machine: aura.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/11/19-21:59:47-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: mn457 Machine: aura.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/11/19-21:59:47-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: mn457 Machine: aura.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/11/19-21:59:47-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: mn457 Machine: aura.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/11/19-21:59:47-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: mn457 Machine: aura.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/11/19-21:59:47-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: mn457 Machine: aura.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/11/19-21:59:47-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: mn457 Machine: aura.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/11/19-21:59:47-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: mn457 Machine: aura.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/11/19-21:59:47-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: mn457 Machine: aura.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/11/19-21:59:47-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: mn457 Machine: aura.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/11/19-21:59:47-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: mn457 Machine: aura.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/11/19-21:59:47-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: mn457 Machine: aura.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/11/19-21:59:47-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: mn457 Machine: aura.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/11/19-21:59:48-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: mn457 Machine: aura.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/11/19-21:59:48-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: mn457 Machine: aura.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/11/19-21:59:48-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: mn457 Machine: aura.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/11/19-21:59:48-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: mn457 Machine: aura.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/11/19-21:59:48-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: mn457 Machine: aura.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/11/19-21:59:48-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: mn457 Machine: aura.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/11/19-21:59:48-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: mn457 Machine: aura.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/11/19-21:59:48-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: mn457 Machine: aura.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2019/11/19-21:59:48-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: mn457 Machine: aura.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/11/19-21:59:48-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: mn457 Machine: aura.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/11/19-21:59:48-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: mn457 Machine: aura.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/11/19-21:59:48-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: mn457 Machine: aura.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/11/19-21:59:48-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: mn457 Machine: aura.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.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: 2019/11/19-21:59:49-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: mn457 Machine: aura.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.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: 2019/11/19-21:59:49-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: mn457 Machine: aura.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/11/19-21:59:49-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: mn457 Machine: aura.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/11/19-21:59:49-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: mn457 Machine: aura.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/11/19-21:59:49-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: mn457 Machine: aura.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/11/19-21:59:49-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: mn457 Machine: aura.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/11/19-21:59:49-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: mn457 Machine: aura.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
#######################################
GCADIR /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/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 /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/average
GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs
#######################################
/autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-089-BL
mri_convert /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/Data/BIOMARKER/BIO-ALS-701-089-BL/anat/BIO-ALS-701-089-BL_T1w.nii.gz /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-089-BL/mri/orig/001.mgz
mri_convert.bin /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/Data/BIOMARKER/BIO-ALS-701-089-BL/anat/BIO-ALS-701-089-BL_T1w.nii.gz /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-089-BL/mri/orig/001.mgz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/Data/BIOMARKER/BIO-ALS-701-089-BL/anat/BIO-ALS-701-089-BL_T1w.nii.gz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (0.159502, -0.987195, 0.00242084)
j_ras = (-0.0951681, -0.0129354, 0.995377)
k_ras = (-0.9826, -0.158995, -0.0960127)
writing to /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-089-BL/mri/orig/001.mgz...
#--------------------------------------------
#@# MotionCor Tue Nov 19 16:59:58 EST 2019
Found 1 runs
/autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-089-BL/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 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-089-BL/mri/orig/001.mgz /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-089-BL/mri/rawavg.mgz
/autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-089-BL
mri_convert /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-089-BL/mri/rawavg.mgz /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-089-BL/mri/orig.mgz --conform
mri_convert.bin /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-089-BL/mri/rawavg.mgz /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-089-BL/mri/orig.mgz --conform
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-089-BL/mri/rawavg.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (0.159502, -0.987195, 0.00242084)
j_ras = (-0.0951681, -0.0129354, 0.995377)
k_ras = (-0.9826, -0.158995, -0.0960127)
changing data type from float to uchar (noscale = 0)...
MRIchangeType: Building histogram
Reslicing using trilinear interpolation
writing to /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-089-BL/mri/orig.mgz...
mri_add_xform_to_header -c /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-089-BL/mri/transforms/talairach.xfm /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-089-BL/mri/orig.mgz /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-089-BL/mri/orig.mgz
INFO: extension is mgz
#--------------------------------------------
#@# Talairach Tue Nov 19 17:00:08 EST 2019
/autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-089-BL/mri
mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50
/autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-089-BL/mri
/autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/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 aura.nmr.mgh.harvard.edu 3.10.0-957.1.3.el7.x86_64 #1 SMP Thu Nov 29 14:49:43 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
Tue Nov 19 17:00:08 EST 2019
Program nu_correct, built from:
Package MNI N3, version 1.10, compiled by nicks@kani (i686-pc-linux-gnu) on 2005-11-15 at 21:02:27
/usr/bin/bc
tmpdir is ./tmp.mri_nu_correct.mni.19380
/autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-089-BL/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.19380/nu0.mnc -odt float
mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.19380/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, 7.45058e-09)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
changing data type from uchar to float (noscale = 0)...
writing to ./tmp.mri_nu_correct.mni.19380/nu0.mnc...
--------------------------------------------------------
Iteration 1 Tue Nov 19 17:00:11 EST 2019
nu_correct -clobber ./tmp.mri_nu_correct.mni.19380/nu0.mnc ./tmp.mri_nu_correct.mni.19380/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.19380/0/ -iterations 1000 -distance 50
defined(@array) is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/nu_estimate_np_and_em line 165.
(Maybe you should just omit the defined()?)
defined(@array) is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/nu_estimate_np_and_em line 170.
(Maybe you should just omit the defined()?)
defined(@array) is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/nu_estimate_np_and_em line 211.
(Maybe you should just omit the defined()?)
defined(@array) is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/nu_estimate_np_and_em line 1051.
(Maybe you should just omit the defined()?)
defined(@array) is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/nu_estimate_np_and_em line 1054.
(Maybe you should just omit the defined()?)
defined(@array) is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/nu_estimate_np_and_em line 1449.
(Maybe you should just omit the defined()?)
defined(@array) is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/nu_estimate_np_and_em line 1455.
(Maybe you should just omit the defined()?)
defined(@array) is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/nu_estimate_np_and_em line 1457.
(Maybe you should just omit the defined()?)
defined(@array) is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/nu_estimate_np_and_em line 1481.
(Maybe you should just omit the defined()?)
defined(@array) is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/nu_estimate_np_and_em line 1631.
(Maybe you should just omit the defined()?)
defined(@array) is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/nu_estimate_np_and_em line 1633.
(Maybe you should just omit the defined()?)
defined(@array) is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/nu_estimate_np_and_em line 1635.
(Maybe you should just omit the defined()?)
defined(@array) is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/nu_estimate_np_and_em line 1637.
(Maybe you should just omit the defined()?)
defined(@array) is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/nu_estimate_np_and_em line 1639.
(Maybe you should just omit the defined()?)
[mn...@aura.nmr.mgh.harvard.edu:/autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-089-BL/mri/] [2019-11-19 17:00:11] running:
/space/lyon/9/pubsw/Linux2/packages/mni/current/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.19380/0/ ./tmp.mri_nu_correct.mni.19380/nu0.mnc ./tmp.mri_nu_correct.mni.19380/nu1.imp
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Number of iterations: 73
CV of field change: 0.000987598
[mn...@aura.nmr.mgh.harvard.edu:/autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-089-BL/mri/] [2019-11-19 17:01:43] running:
/space/lyon/9/pubsw/Linux2/packages/mni/current/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.19380/nu0.mnc ./tmp.mri_nu_correct.mni.19380/0//template.mnc
Transforming slices:......................................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Transforming slices:................................................................................................................................................................................................................................................................Done
mri_convert ./tmp.mri_nu_correct.mni.19380/nu1.mnc orig_nu.mgz --like orig.mgz --conform
mri_convert.bin ./tmp.mri_nu_correct.mni.19380/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.19380/nu1.mnc...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 7.45058e-09)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
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...
Tue Nov 19 17:01:56 EST 2019
mri_nu_correct.mni done
talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm --atlas 3T18yoSchwartzReactN32_as_orig
talairach_avi log file is transforms/talairach_avi.log...
Started at Tue Nov 19 17:01:56 EST 2019
Ended at Tue Nov 19 17:02:23 EST 2019
talairach_avi done
cp transforms/talairach.auto.xfm transforms/talairach.xfm
#--------------------------------------------
#@# Talairach Failure Detection Tue Nov 19 17:02:25 EST 2019
/autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-089-BL/mri
talairach_afd -T 0.005 -xfm transforms/talairach.xfm
ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0370, pval=0.0034 < threshold=0.0050)
Manual Talairach alignment may be necessary, or
include the -notal-check flag to skip this test,
making sure the -notal-check flag follows -all
or -autorecon1 in the command string.
See:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach
INFO: Trying MINC mritotal to perform Talairach align...
#--------------------------------------------
#@# Talairach Tue Nov 19 17:02:25 EST 2019
/autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-089-BL/mri
mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50
/autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-089-BL/mri
/autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/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 aura.nmr.mgh.harvard.edu 3.10.0-957.1.3.el7.x86_64 #1 SMP Thu Nov 29 14:49:43 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
Tue Nov 19 17:02:25 EST 2019
Program nu_correct, built from:
Package MNI N3, version 1.10, compiled by nicks@kani (i686-pc-linux-gnu) on 2005-11-15 at 21:02:27
/usr/bin/bc
tmpdir is ./tmp.mri_nu_correct.mni.20856
/autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-089-BL/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.20856/nu0.mnc -odt float
mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.20856/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, 7.45058e-09)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
changing data type from uchar to float (noscale = 0)...
writing to ./tmp.mri_nu_correct.mni.20856/nu0.mnc...
--------------------------------------------------------
Iteration 1 Tue Nov 19 17:02:28 EST 2019
nu_correct -clobber ./tmp.mri_nu_correct.mni.20856/nu0.mnc ./tmp.mri_nu_correct.mni.20856/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.20856/0/ -iterations 1000 -distance 50
defined(@array) is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/nu_estimate_np_and_em line 165.
(Maybe you should just omit the defined()?)
defined(@array) is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/nu_estimate_np_and_em line 170.
(Maybe you should just omit the defined()?)
defined(@array) is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/nu_estimate_np_and_em line 211.
(Maybe you should just omit the defined()?)
defined(@array) is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/nu_estimate_np_and_em line 1051.
(Maybe you should just omit the defined()?)
defined(@array) is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/nu_estimate_np_and_em line 1054.
(Maybe you should just omit the defined()?)
defined(@array) is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/nu_estimate_np_and_em line 1449.
(Maybe you should just omit the defined()?)
defined(@array) is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/nu_estimate_np_and_em line 1455.
(Maybe you should just omit the defined()?)
defined(@array) is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/nu_estimate_np_and_em line 1457.
(Maybe you should just omit the defined()?)
defined(@array) is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/nu_estimate_np_and_em line 1481.
(Maybe you should just omit the defined()?)
defined(@array) is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/nu_estimate_np_and_em line 1631.
(Maybe you should just omit the defined()?)
defined(@array) is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/nu_estimate_np_and_em line 1633.
(Maybe you should just omit the defined()?)
defined(@array) is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/nu_estimate_np_and_em line 1635.
(Maybe you should just omit the defined()?)
defined(@array) is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/nu_estimate_np_and_em line 1637.
(Maybe you should just omit the defined()?)
defined(@array) is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/nu_estimate_np_and_em line 1639.
(Maybe you should just omit the defined()?)
[mn...@aura.nmr.mgh.harvard.edu:/autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-089-BL/mri/] [2019-11-19 17:02:28] running:
/space/lyon/9/pubsw/Linux2/packages/mni/current/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.20856/0/ ./tmp.mri_nu_correct.mni.20856/nu0.mnc ./tmp.mri_nu_correct.mni.20856/nu1.imp
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153.
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Number of iterations: 73
CV of field change: 0.000987598
[mn...@aura.nmr.mgh.harvard.edu:/autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-089-BL/mri/] [2019-11-19 17:04:01] running:
/space/lyon/9/pubsw/Linux2/packages/mni/current/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.20856/nu0.mnc ./tmp.mri_nu_correct.mni.20856/0//template.mnc
Transforming slices:......................................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Transforming slices:................................................................................................................................................................................................................................................................Done
mri_convert ./tmp.mri_nu_correct.mni.20856/nu1.mnc orig_nu.mgz --like orig.mgz --conform
mri_convert.bin ./tmp.mri_nu_correct.mni.20856/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.20856/nu1.mnc...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 7.45058e-09)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
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...
Tue Nov 19 17:04:14 EST 2019
mri_nu_correct.mni done
talairach --i orig_nu.mgz --xfm transforms/talairach.auto.xfm
/autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-089-BL/mri
/autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/bin/talairach
--i orig_nu.mgz --xfm transforms/talairach.auto.xfm
$Id: talairach,v 1.8 2016/02/16 17:17:20 zkaufman Exp $
Linux aura.nmr.mgh.harvard.edu 3.10.0-957.1.3.el7.x86_64 #1 SMP Thu Nov 29 14:49:43 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
Tue Nov 19 17:04:14 EST 2019
tmpdir is transforms/tmp.talairach.21973
/autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-089-BL/mri
mri_convert orig_nu.mgz transforms/tmp.talairach.21973/src.mnc
mri_convert.bin orig_nu.mgz transforms/tmp.talairach.21973/src.mnc
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from orig_nu.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 7.45058e-09)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
writing to transforms/tmp.talairach.21973/src.mnc...
--------------------------------------------
mritotal -verbose -debug -clobber -modeldir /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/../share/mni_autoreg -protocol icbm transforms/tmp.talairach.21973/src.mnc transforms/talairach.auto.xfm
Can't locate shellwords.pl in @INC (@INC contains: /autofs/cluster/pubsw/1/pubsw/Linux2/packages/mni/1.4/bin/../lib/mni_autoreg /usr/local/freesurfer/stable6_0_0/mni/share/perl5 /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/mritotal line 460.
ERROR: mritotal failed, see transforms/talairach.log
Linux aura.nmr.mgh.harvard.edu 3.10.0-957.1.3.el7.x86_64 #1 SMP Thu Nov 29 14:49:43 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s BIO-ALS-701-089-BL exited with ERRORS at Tue Nov 19 17:04:16 EST 2019
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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