I am able to to initiate recon-all but it fails at various stages during the recon-all process even though I should have plenty memory available to run the process.
FREESURFER_HOME /Applications/freesurfer/
Actual FREESURFER_HOME /Applications/freesurfer
build-stamp.txt: freesurfer-Darwin-lion-stable-pub-v5.3.0
Darwin r5007111.mayo.edu 11.4.2 Darwin Kernel Version 11.4.2: Thu Aug 23 16:25:48 PDT 2012; root:xnu-1699.32.7~1/RELEASE_X86_64 x86_64
cputime unlimited
filesize unlimited
datasize unlimited
stacksize 8192 kbytes
coredumpsize 0 kbytes
memoryuse unlimited
descriptors 256
memorylocked unlimited
maxproc
709
PhysMem: 1987M wired, 5293M active, 2487M inactive, 9767M used, 22G free.
########################################
program versions used
$Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $
$Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $
mri_convert -all-info
ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:12-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id:
mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200
FLIRT version 5.5
$Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $
mri_convert --version
stable5
ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:12-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2
CompilerName: GCC CompilerVersion: 40200
Program nu_correct, built from:
Package MNI N3, version 1.10, compiled by nicks@aspasia.local (i686-apple-darwin10.2.0) on 2010-02-26 at 14:19:30
ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:12-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200
ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:12-GMT
BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200
ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:12-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200
ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:12-GMT BuildTimeStamp:
May 14 2013 09:12:01 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200
ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:12-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200
ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS:
$Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200
ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200
ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id:
mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200
ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200
ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id:
mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200
ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200
ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_fill.c,v 1.118 2011/03/16
21:23:49 nicks Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200
ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200
ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48
nicks Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200
ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200
ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User:
m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200
ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200
ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: m117348 Machine:
r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200
ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200
ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: m117348 Machine: r5007111.mayo.edu
Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200
ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200
ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: m117348 Machine: r5007111.mayo.edu Platform:
Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200
ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200
ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: m117348 Machine: r5007111.mayo.edu Platform:
Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200
ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200
ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin
PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200
ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200
ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin
PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200
ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200
ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin
PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200
$Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $
ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200
$Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $
ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200
ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200
ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200
ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200
ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200
#######################################
GCADIR /Applications/freesurfer//average
GCA RB_all_2008-03-26.gca
GCASkull RB_all_withskull_2008-03-26.gca
AvgCurvTif average.curvature.filled.buckner40.tif
GCSDIR
/Applications/freesurfer//average
GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs
#######################################
/home/m117348/Documents/Schwedt_MRI/1004_out
\n mri_convert /home/m117348/Documents/Schwedt_MRI/1004.mgz /home/m117348/Documents/Schwedt_MRI/1004_out/mri/orig/001.mgz \n
mri_convert /home/m117348/Documents/Schwedt_MRI/1004.mgz /home/m117348/Documents/Schwedt_MRI/1004_out/mri/orig/001.mgz
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /home/m117348/Documents/Schwedt_MRI/1004.mgz...
TR=2400.00, TE=3.16, TI=1000.00, flip angle=8.00
i_ras = (0.0109648, -0.99885, 0.0466696)
j_ras = (-0.0118836, -0.0467993, -0.998834)
k_ras = (-0.999869, -0.0103974, 0.0123829)
writing to /home/m117348/Documents/Schwedt_MRI/1004_out/mri/orig/001.mgz...
#--------------------------------------------
#@# MotionCor Thu May 23 14:05:27 MST 2013
Found 1 runs
/home/m117348/Documents/Schwedt_MRI/1004_out/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.
\n cp /home/m117348/Documents/Schwedt_MRI/1004_out/mri/orig/001.mgz /home/m117348/Documents/Schwedt_MRI/1004_out/mri/rawavg.mgz \n
/home/m117348/Documents/Schwedt_MRI/1004_out
\n mri_convert /home/m117348/Documents/Schwedt_MRI/1004_out/mri/rawavg.mgz /home/m117348/Documents/Schwedt_MRI/1004_out/mri/orig.mgz --conform \n
mri_convert /home/m117348/Documents/Schwedt_MRI/1004_out/mri/rawavg.mgz /home/m117348/Documents/Schwedt_MRI/1004_out/mri/orig.mgz --conform
$Id:
mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /home/m117348/Documents/Schwedt_MRI/1004_out/mri/rawavg.mgz...
TR=2400.00, TE=3.16, TI=1000.00, flip angle=8.00
i_ras = (0.0109648, -0.99885, 0.0466696)
j_ras = (-0.0118836, -0.0467993, -0.998834)
k_ras = (-0.999869, -0.0103974, 0.0123829)
Original Data has (1, 1, 1) mm size and (256, 256, 176) voxels.
Data is conformed to 1 mm size and 256 voxels for all directions
changing data type from short to uchar (noscale = 0)...
MRIchangeType:
Building histogram
Reslicing using trilinear interpolation
writing to /home/m117348/Documents/Schwedt_MRI/1004_out/mri/orig.mgz...
\n mri_add_xform_to_header -c /home/m117348/Documents/Schwedt_MRI/1004_out/mri/transforms/talairach.xfm /home/m117348/Documents/Schwedt_MRI/1004_out/mri/orig.mgz /home/m117348/Documents/Schwedt_MRI/1004_out/mri/orig.mgz \n
INFO: extension is mgz
#--------------------------------------------
#@# Talairach Thu May 23 14:05:55 MST 2013
/home/m117348/Documents/Schwedt_MRI/1004_out/mri
\n mri_nu_correct.mni --n 1
--proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz \n
Darwin r5007111.mayo.edu 11.4.2 Darwin Kernel Version 11.4.2: Thu Aug 23 16:25:48 PDT 2012; root:xnu-1699.32.7~1/RELEASE_X86_64 x86_64
recon-all -s 1004_out exited with ERRORS at Thu May 23 14:06:26 MST 2013
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting