Hello,
I recently upgraded from Ubuntu 13.10 to 14.04, and I started getting a
new error message while running "recon-all" with .nii file inputs
(details below). From the error message I believe the problem might be
that Ubuntu 14.04 ships with perl version 5.18 (as opposed to 5.14 for
previous versions), and the Ubuntu 14.04 Perl manpage
(http://manpages.ubuntu.com/manpages/trusty/man1/perl5120delta.1.html),
specifically lists "shellwords.pl" as a newly deprecated library.
My naive instinct was to install perl version 5.14 using perlbrew, and
switch to it whenever a new shell is launched by editing my .bashrc
file, by adding the lines
"source ~/perl5/perlbrew/etc/bashrc"
"perlbrew switch perl-5.14.4"
When I do this my shell recognizes perl-5.14.4 as the active version,
but freesurfer does not. This makes me worry it won't be such a simple
fix. Any Ideas as to the best way to handle this? Am I on the right
track?
Many Thanks!
-Samuel Thorpe
bugr related info:
---------------------------------------------------------------------
FREESURFER_HOME: /usr/local/freesurfer
SUBJECTS_DIR: /usr/local/freesurfer/subjects
"which recon-all" gives "/usr/local/freesurfer/bin/recon-all"
Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
Debian version: jessie/sid
Kernel info: Linux 3.8.0-32-generic x86_64
Linux OS: Ubuntu 14.04 LTS "Trusty Tahr"
example commands executed:
---------------------------------------------------------------------
subject: "bert", "bert_nii"
after converting "/usr/local/freesurfer/subjects/bert/mri/orig/001.mgz"
to .nii using "mri_convert" (operation successful), I attempt,
"recon-all -i /usr/local/freesurfer/subjects/bert/mri/orig/001.nii -s
bert_nii -all"
error message:
---------------------------------------------------------------------
"Can't locate shellwords.pl in @INC (@INC contains:
/usr/local/freesurfer/mni/bin/../lib/mni_autoreg
/usr/local/freesurfer/mni/lib/perl5/5.8.5 /etc/perl
/usr/local/lib/perl/5.18.2 /usr/local/share/perl/5.18.2 /usr/lib/perl5
/usr/share/perl5 /usr/lib/perl/5.18 /usr/share/perl/5.18
/usr/local/lib/site_perl .) at /usr/local/freesurfer/mni/bin/mritotal
line 460."
/usr/local/freesurfer/subjects/bert_nii/script/recon-all.log attached
Fri May 16 13:00:54 EDT 2014
/usr/local/freesurfer/subjects/bert_nii
/usr/local/freesurfer/bin/recon-all
-i /usr/local/freesurfer/subjects/bert/mri/orig/001.nii -s bert_nii -all
subjid bert_nii
setenv SUBJECTS_DIR /usr/local/freesurfer/subjects
FREESURFER_HOME /usr/local/freesurfer
Actual FREESURFER_HOME /usr/local/freesurfer
build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
Linux sam-cdl1 3.8.0-32-generic #47-Ubuntu SMP Tue Oct 1 22:35:23 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
cputime unlimited
filesize unlimited
datasize unlimited
stacksize 8192 kbytes
coredumpsize 0 kbytes
memoryuse unlimited
vmemoryuse unlimited
descriptors 4096
memorylocked 64 kbytes
maxproc 256865
maxlocks unlimited
maxsignal 256865
maxmessage 819200
maxnice 0
maxrtprio 0
maxrttime unlimited
total used free shared buffers cached
Mem: 32898272 5213236 27685036 39844 318804 2828916
-/+ buffers/cache: 2065516 30832756
Swap: 33501180 0 33501180
########################################
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: 2014/05/16-17:00:54-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: sam Machine: sam-cdl1 Platform: Linux PlatformVersion: 3.8.0-32-generic CompilerName: GCC CompilerVersion: 40400
FLIRT version 5.5
$Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $
mri_convert --version
stable5
ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/16-17:00:55-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: sam Machine: sam-cdl1 Platform: Linux PlatformVersion: 3.8.0-32-generic CompilerName: GCC CompilerVersion: 40400
Program nu_correct, built from:
Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37
ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/16-17:00:55-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: sam Machine: sam-cdl1 Platform: Linux PlatformVersion: 3.8.0-32-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/16-17:00:55-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: sam Machine: sam-cdl1 Platform: Linux PlatformVersion: 3.8.0-32-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/16-17:00:55-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: sam Machine: sam-cdl1 Platform: Linux PlatformVersion: 3.8.0-32-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/16-17:00:55-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: sam Machine: sam-cdl1 Platform: Linux PlatformVersion: 3.8.0-32-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/16-17:00:55-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: sam Machine: sam-cdl1 Platform: Linux PlatformVersion: 3.8.0-32-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/16-17:00:55-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: sam Machine: sam-cdl1 Platform: Linux PlatformVersion: 3.8.0-32-generic CompilerName: GCC CompilerVersion: 40400
======= NUMBER OF OPENMP THREADS = 1 =======
ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/16-17:00:55-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: sam Machine: sam-cdl1 Platform: Linux PlatformVersion: 3.8.0-32-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/16-17:00:55-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: sam Machine: sam-cdl1 Platform: Linux PlatformVersion: 3.8.0-32-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/16-17:00:55-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: sam Machine: sam-cdl1 Platform: Linux PlatformVersion: 3.8.0-32-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/16-17:00:55-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: sam Machine: sam-cdl1 Platform: Linux PlatformVersion: 3.8.0-32-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/16-17:00:56-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: sam Machine: sam-cdl1 Platform: Linux PlatformVersion: 3.8.0-32-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/16-17:00:56-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: sam Machine: sam-cdl1 Platform: Linux PlatformVersion: 3.8.0-32-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/16-17:00:56-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: sam Machine: sam-cdl1 Platform: Linux PlatformVersion: 3.8.0-32-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/16-17:00:56-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: sam Machine: sam-cdl1 Platform: Linux PlatformVersion: 3.8.0-32-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/16-17:00:56-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: sam Machine: sam-cdl1 Platform: Linux PlatformVersion: 3.8.0-32-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/16-17:00:56-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: sam Machine: sam-cdl1 Platform: Linux PlatformVersion: 3.8.0-32-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/16-17:00:56-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: sam Machine: sam-cdl1 Platform: Linux PlatformVersion: 3.8.0-32-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/16-17:00:56-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: sam Machine: sam-cdl1 Platform: Linux PlatformVersion: 3.8.0-32-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/16-17:00:56-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: sam Machine: sam-cdl1 Platform: Linux PlatformVersion: 3.8.0-32-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/16-17:00:56-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: sam Machine: sam-cdl1 Platform: Linux PlatformVersion: 3.8.0-32-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/16-17:00:56-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: sam Machine: sam-cdl1 Platform: Linux PlatformVersion: 3.8.0-32-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/16-17:00:56-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: sam Machine: sam-cdl1 Platform: Linux PlatformVersion: 3.8.0-32-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/16-17:00:57-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: sam Machine: sam-cdl1 Platform: Linux PlatformVersion: 3.8.0-32-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/16-17:00:57-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: sam Machine: sam-cdl1 Platform: Linux PlatformVersion: 3.8.0-32-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/16-17:00:57-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: sam Machine: sam-cdl1 Platform: Linux PlatformVersion: 3.8.0-32-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/16-17:00:57-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: sam Machine: sam-cdl1 Platform: Linux PlatformVersion: 3.8.0-32-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/16-17:00:57-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: sam Machine: sam-cdl1 Platform: Linux PlatformVersion: 3.8.0-32-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/16-17:00:57-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: sam Machine: sam-cdl1 Platform: Linux PlatformVersion: 3.8.0-32-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/16-17:00:57-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: sam Machine: sam-cdl1 Platform: Linux PlatformVersion: 3.8.0-32-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/16-17:00:57-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: sam Machine: sam-cdl1 Platform: Linux PlatformVersion: 3.8.0-32-generic CompilerName: GCC CompilerVersion: 40400
$Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $
ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/16-17:00:57-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: sam Machine: sam-cdl1 Platform: Linux PlatformVersion: 3.8.0-32-generic CompilerName: GCC CompilerVersion: 40400
$Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $
ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/16-17:00:57-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: sam Machine: sam-cdl1 Platform: Linux PlatformVersion: 3.8.0-32-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/16-17:00:57-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: sam Machine: sam-cdl1 Platform: Linux PlatformVersion: 3.8.0-32-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/16-17:00:57-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: sam Machine: sam-cdl1 Platform: Linux PlatformVersion: 3.8.0-32-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/16-17:00:57-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: sam Machine: sam-cdl1 Platform: Linux PlatformVersion: 3.8.0-32-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/16-17:00:58-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: sam Machine: sam-cdl1 Platform: Linux PlatformVersion: 3.8.0-32-generic CompilerName: GCC CompilerVersion: 40400
#######################################
GCADIR /usr/local/freesurfer/average
GCA RB_all_2008-03-26.gca
GCASkull RB_all_withskull_2008-03-26.gca
AvgCurvTif average.curvature.filled.buckner40.tif
GCSDIR /usr/local/freesurfer/average
GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs
#######################################
/usr/local/freesurfer/subjects/bert_nii
mri_convert /usr/local/freesurfer/subjects/bert/mri/orig/001.nii /usr/local/freesurfer/subjects/bert_nii/mri/orig/001.mgz
mri_convert /usr/local/freesurfer/subjects/bert/mri/orig/001.nii /usr/local/freesurfer/subjects/bert_nii/mri/orig/001.mgz
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /usr/local/freesurfer/subjects/bert/mri/orig/001.nii...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (1, 0, 0)
j_ras = (0, 1, 0)
k_ras = (0, 0, 1)
writing to /usr/local/freesurfer/subjects/bert_nii/mri/orig/001.mgz...
#--------------------------------------------
#@# MotionCor Fri May 16 13:01:03 EDT 2014
Found 1 runs
/usr/local/freesurfer/subjects/bert_nii/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 /usr/local/freesurfer/subjects/bert_nii/mri/orig/001.mgz /usr/local/freesurfer/subjects/bert_nii/mri/rawavg.mgz
/usr/local/freesurfer/subjects/bert_nii
mri_convert /usr/local/freesurfer/subjects/bert_nii/mri/rawavg.mgz /usr/local/freesurfer/subjects/bert_nii/mri/orig.mgz --conform
mri_convert /usr/local/freesurfer/subjects/bert_nii/mri/rawavg.mgz /usr/local/freesurfer/subjects/bert_nii/mri/orig.mgz --conform
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /usr/local/freesurfer/subjects/bert_nii/mri/rawavg.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (1, 0, 0)
j_ras = (0, 1, 0)
k_ras = (0, 0, 1)
Original Data has (1, 1, 1) mm size and (256, 256, 256) voxels.
Data is conformed to 1 mm size and 256 voxels for all directions
changing data type from float to uchar (noscale = 0)...
MRIchangeType: Building histogram
Reslicing using trilinear interpolation
writing to /usr/local/freesurfer/subjects/bert_nii/mri/orig.mgz...
mri_add_xform_to_header -c /usr/local/freesurfer/subjects/bert_nii/mri/transforms/talairach.xfm /usr/local/freesurfer/subjects/bert_nii/mri/orig.mgz /usr/local/freesurfer/subjects/bert_nii/mri/orig.mgz
INFO: extension is mgz
#--------------------------------------------
#@# Talairach Fri May 16 13:01:17 EDT 2014
/usr/local/freesurfer/subjects/bert_nii/mri
mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz
talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm
cp transforms/talairach.auto.xfm transforms/talairach.xfm
#--------------------------------------------
#@# Talairach Failure Detection Fri May 16 13:02:29 EDT 2014
/usr/local/freesurfer/subjects/bert_nii/mri
talairach_afd -T 0.005 -xfm transforms/talairach.xfm
talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7679, pval=0.6675 >= threshold=0.0050)
awk -f /usr/local/freesurfer/bin/extract_talairach_avi_QA.awk /usr/local/freesurfer/subjects/bert_nii/mri/transforms/talairach_avi.log
tal_QC_AZS /usr/local/freesurfer/subjects/bert_nii/mri/transforms/talairach_avi.log
TalAviQA: 0.00000
z-score: -222
ERROR: Talairach QA check failed!
z-score = -222 <= -9 = threshold
atlas xform error = 0 < -60 | > 24
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: Attempting MINC mritotal to perform Talairach align
#--------------------------------------------
#@# Talairach Fri May 16 13:02:29 EDT 2014
/usr/local/freesurfer/subjects/bert_nii/mri
mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz
talairach --i orig_nu.mgz --xfm transforms/talairach.auto.xfm
/usr/local/freesurfer/subjects/bert_nii/mri
/usr/local/freesurfer/bin/talairach
--i orig_nu.mgz --xfm transforms/talairach.auto.xfm
$Id: talairach,v 1.7 2011/03/02 20:16:40 nicks Exp $
Linux sam-cdl1 3.8.0-32-generic #47-Ubuntu SMP Tue Oct 1 22:35:23 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
Fri May 16 13:03:05 EDT 2014
tmpdir is transforms/tmp.talairach.24316
/usr/local/freesurfer/subjects/bert_nii/mri
mri_convert orig_nu.mgz transforms/tmp.talairach.24316/src.mnc
mri_convert orig_nu.mgz transforms/tmp.talairach.24316/src.mnc
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from orig_nu.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
writing to transforms/tmp.talairach.24316/src.mnc...
--------------------------------------------
mritotal -verbose -debug -clobber -modeldir /usr/local/freesurfer/mni/bin/../share/mni_autoreg -protocol icbm transforms/tmp.talairach.24316/src.mnc transforms/talairach.auto.xfm
Can't locate shellwords.pl in @INC (@INC contains: /usr/local/freesurfer/mni/bin/../lib/mni_autoreg /usr/local/freesurfer/mni/lib/perl5/5.8.5 /etc/perl /usr/local/lib/perl/5.18.2 /usr/local/share/perl/5.18.2 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.18 /usr/share/perl/5.18 /usr/local/lib/site_perl .) at /usr/local/freesurfer/mni/bin/mritotal line 460.
ERROR: mritotal failed, see transforms/talairach.log
Linux sam-cdl1 3.8.0-32-generic #47-Ubuntu SMP Tue Oct 1 22:35:23 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s bert_nii exited with ERRORS at Fri May 16 13:03:06 EDT 2014
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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