Dear FreeSurfer Developers,

I am attempting to run recon-all on 7T MP2RAGE images (resolution 
0.7x0.7x0.7mm³) with hippocampus subfield segmentation. I use the freesurfer 
version 5.3 so that I expect an automatic down-sampling to 1x1x1mm³.

I used the data directly from the scanner (without reorientation to standard 
etc.) and used the following command:

recon-all -s $subject.freesurfer -hires -i $subject.mp2rage.nii -expert 
/media/NeuroMet_Project/scripts/expert.opts -all -hippo-subfields"

As expert option I used only: mris_inflate -n 15

The processing starts fine but ends with the following error:

 ERROR: dimension mismatch between input volume and seg
  input 321 321 321
  seg   322 322 322

Could you please help me dealing with this problem?
I attached also the log-file

Thank you so much.

Best Theresa

-------------------------------------------------------------------------
Charité – Universitätsmedizin Berlin
NeuroCure Clinical Research Center NCRC
Dipl.-Biol. Theresa Köbe
AG Kognitive Neurologie
Wiss. Mitarbeiter
Charitéplatz 1, D-10117 Berlin
Tel  +49 30 450 560 185
Fax +49 30 450 7 560 280
Interne Besuchsadresse: CCM, Sauerbruchweg 5, E2
http://www.charite.de/service/lageplan/plan/map/ccm_sauerbruchweg_5/<redir.aspx?REF=mc29RH9tIXK9qgoNB0UJ6dmsQ-pCBih_Q7so140WG76sl9oBFOLTCAFodHRwOi8vd3d3LmNoYXJpdGUuZGUvc2VydmljZS9sYWdlcGxhbi9wbGFuL21hcC9jY21fc2F1ZXJicnVjaHdlZ181Lw..>

Mi 21. Sep 11:07:29 CEST 2016
/media/drive_s/AG/AG-Floeel-Imaging/02-User/TheresaKoebe/NeuroMet_Project/TestFreesurferRecon/Freesurfer/MDC0103.freesurfer
/usr/local/freesurfer-5.3/bin/recon-all
-s MDC0103.freesurfer -hires -i MDC0103.mp2rage.nii -expert /media/drive_s/AG/AG-Floeel-Imaging/02-User/TheresaKoebe/NeuroMet_Project/TestFreesurferRecon/scripts/expert.opts -all -hippo-subfields
subjid MDC0103.freesurfer
setenv SUBJECTS_DIR /media/drive_s/AG/AG-Floeel-Imaging/02-User/TheresaKoebe/NeuroMet_Project/TestFreesurferRecon/Freesurfer
FREESURFER_HOME /usr/local/freesurfer-5.3
Actual FREESURFER_HOME /usr/local/freesurfer-5.3
build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
Linux doc2 3.19.0-64-generic #72~14.04.1-Ubuntu SMP Fri Jun 24 17:59:48 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
cputime      unlimited
filesize     unlimited
datasize     unlimited
stacksize    8192 kbytes
coredumpsize 0 kbytes
memoryuse    unlimited
vmemoryuse   unlimited
descriptors  1024 
memorylocked 64 kbytes
maxproc      63741 
maxlocks     unlimited
maxsignal    63741 
maxmessage   819200 
maxnice      0 
maxrtprio    0 
maxrttime    unlimited

             total       used       free     shared    buffers     cached
Mem:      16348588    7601060    8747528     103052     379096    3403364
-/+ buffers/cache:    3818600   12529988
Swap:     16777212          0   16777212

########################################
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: 2016/09/21-09:07:29-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: theresa  Machine: doc2  Platform: Linux  PlatformVersion: 3.19.0-64-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: 2016/09/21-09:07:29-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: theresa  Machine: doc2  Platform: Linux  PlatformVersion: 3.19.0-64-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: 2016/09/21-09:07:29-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: theresa  Machine: doc2  Platform: Linux  PlatformVersion: 3.19.0-64-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_normalize  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2016/09/21-09:07:29-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: theresa  Machine: doc2  Platform: Linux  PlatformVersion: 3.19.0-64-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_watershed  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2016/09/21-09:07:29-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: theresa  Machine: doc2  Platform: Linux  PlatformVersion: 3.19.0-64-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_gcut  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2016/09/21-09:07:29-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: theresa  Machine: doc2  Platform: Linux  PlatformVersion: 3.19.0-64-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_segment  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2016/09/21-09:07:29-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: theresa  Machine: doc2  Platform: Linux  PlatformVersion: 3.19.0-64-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_label2label  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2016/09/21-09:07:29-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: theresa  Machine: doc2  Platform: Linux  PlatformVersion: 3.19.0-64-generic  CompilerName: GCC  CompilerVersion: 40400 


 ======= NUMBER OF OPENMP THREADS = 1 ======= 
ProgramName: mri_em_register  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2016/09/21-09:07:29-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: theresa  Machine: doc2  Platform: Linux  PlatformVersion: 3.19.0-64-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_ca_normalize  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2016/09/21-09:07:29-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: theresa  Machine: doc2  Platform: Linux  PlatformVersion: 3.19.0-64-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_ca_register  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2016/09/21-09:07:30-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: theresa  Machine: doc2  Platform: Linux  PlatformVersion: 3.19.0-64-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_ca_label  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2016/09/21-09:07:30-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: theresa  Machine: doc2  Platform: Linux  PlatformVersion: 3.19.0-64-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_pretess  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2016/09/21-09:07:30-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: theresa  Machine: doc2  Platform: Linux  PlatformVersion: 3.19.0-64-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_fill  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2016/09/21-09:07:30-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: theresa  Machine: doc2  Platform: Linux  PlatformVersion: 3.19.0-64-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_tessellate  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2016/09/21-09:07:30-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: theresa  Machine: doc2  Platform: Linux  PlatformVersion: 3.19.0-64-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_concatenate_lta  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2016/09/21-09:07:30-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: theresa  Machine: doc2  Platform: Linux  PlatformVersion: 3.19.0-64-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_normalize_tp2  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2016/09/21-09:07:30-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: theresa  Machine: doc2  Platform: Linux  PlatformVersion: 3.19.0-64-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_smooth  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2016/09/21-09:07:30-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: theresa  Machine: doc2  Platform: Linux  PlatformVersion: 3.19.0-64-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_inflate  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2016/09/21-09:07:30-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: theresa  Machine: doc2  Platform: Linux  PlatformVersion: 3.19.0-64-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_curvature  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2016/09/21-09:07:30-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: theresa  Machine: doc2  Platform: Linux  PlatformVersion: 3.19.0-64-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_sphere  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2016/09/21-09:07:30-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: theresa  Machine: doc2  Platform: Linux  PlatformVersion: 3.19.0-64-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_fix_topology  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2016/09/21-09:07:30-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: theresa  Machine: doc2  Platform: Linux  PlatformVersion: 3.19.0-64-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_topo_fixer  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2016/09/21-09:07:30-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: theresa  Machine: doc2  Platform: Linux  PlatformVersion: 3.19.0-64-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_ca_label  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2016/09/21-09:07:30-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: theresa  Machine: doc2  Platform: Linux  PlatformVersion: 3.19.0-64-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_euler_number  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2016/09/21-09:07:30-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: theresa  Machine: doc2  Platform: Linux  PlatformVersion: 3.19.0-64-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_make_surfaces  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2016/09/21-09:07:30-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: theresa  Machine: doc2  Platform: Linux  PlatformVersion: 3.19.0-64-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_register  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2016/09/21-09:07:30-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: theresa  Machine: doc2  Platform: Linux  PlatformVersion: 3.19.0-64-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_volmask  ProgramArguments: --all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2016/09/21-09:07:30-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: theresa  Machine: doc2  Platform: Linux  PlatformVersion: 3.19.0-64-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_anatomical_stats  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2016/09/21-09:07:30-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: theresa  Machine: doc2  Platform: Linux  PlatformVersion: 3.19.0-64-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mrisp_paint  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2016/09/21-09:07:31-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: theresa  Machine: doc2  Platform: Linux  PlatformVersion: 3.19.0-64-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_curvature_stats  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2016/09/21-09:07:31-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: theresa  Machine: doc2  Platform: Linux  PlatformVersion: 3.19.0-64-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_calc  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2016/09/21-09:07:31-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: theresa  Machine: doc2  Platform: Linux  PlatformVersion: 3.19.0-64-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: 2016/09/21-09:07:31-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: theresa  Machine: doc2  Platform: Linux  PlatformVersion: 3.19.0-64-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: 2016/09/21-09:07:31-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: theresa  Machine: doc2  Platform: Linux  PlatformVersion: 3.19.0-64-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_and  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2016/09/21-09:07:31-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: theresa  Machine: doc2  Platform: Linux  PlatformVersion: 3.19.0-64-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_or  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2016/09/21-09:07:31-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: theresa  Machine: doc2  Platform: Linux  PlatformVersion: 3.19.0-64-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_fuse_segmentations  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2016/09/21-09:07:31-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: theresa  Machine: doc2  Platform: Linux  PlatformVersion: 3.19.0-64-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_segstats  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2016/09/21-09:07:31-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: theresa  Machine: doc2  Platform: Linux  PlatformVersion: 3.19.0-64-generic  CompilerName: GCC  CompilerVersion: 40400 
#######################################
GCADIR /usr/local/freesurfer-5.3/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-5.3/average
GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs
#######################################
/media/drive_s/AG/AG-Floeel-Imaging/02-User/TheresaKoebe/NeuroMet_Project/TestFreesurferRecon/Freesurfer/MDC0103.freesurfer

 mri_convert /media/drive_s/AG/AG-Floeel-Imaging/02-User/TheresaKoebe/NeuroMet_Project/TestFreesurferRecon/MDC0103/MDC0103.mp2rage.nii /media/drive_s/AG/AG-Floeel-Imaging/02-User/TheresaKoebe/NeuroMet_Project/TestFreesurferRecon/Freesurfer/MDC0103.freesurfer/mri/orig/001.mgz 

mri_convert /media/drive_s/AG/AG-Floeel-Imaging/02-User/TheresaKoebe/NeuroMet_Project/TestFreesurferRecon/MDC0103/MDC0103.mp2rage.nii /media/drive_s/AG/AG-Floeel-Imaging/02-User/TheresaKoebe/NeuroMet_Project/TestFreesurferRecon/Freesurfer/MDC0103.freesurfer/mri/orig/001.mgz 
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /media/drive_s/AG/AG-Floeel-Imaging/02-User/TheresaKoebe/NeuroMet_Project/TestFreesurferRecon/MDC0103/MDC0103.mp2rage.nii...
TR=5000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (0, -1, 0)
j_ras = (0, 0, 1)
k_ras = (1, 0, 0)
writing to /media/drive_s/AG/AG-Floeel-Imaging/02-User/TheresaKoebe/NeuroMet_Project/TestFreesurferRecon/Freesurfer/MDC0103.freesurfer/mri/orig/001.mgz...
#--------------------------------------------
#@# MotionCor Mi 21. Sep 11:07:52 CEST 2016
Found 1 runs
/media/drive_s/AG/AG-Floeel-Imaging/02-User/TheresaKoebe/NeuroMet_Project/TestFreesurferRecon/Freesurfer/MDC0103.freesurfer/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 /media/drive_s/AG/AG-Floeel-Imaging/02-User/TheresaKoebe/NeuroMet_Project/TestFreesurferRecon/Freesurfer/MDC0103.freesurfer/mri/orig/001.mgz /media/drive_s/AG/AG-Floeel-Imaging/02-User/TheresaKoebe/NeuroMet_Project/TestFreesurferRecon/Freesurfer/MDC0103.freesurfer/mri/rawavg.mgz 

/media/drive_s/AG/AG-Floeel-Imaging/02-User/TheresaKoebe/NeuroMet_Project/TestFreesurferRecon/Freesurfer/MDC0103.freesurfer

 mri_convert /media/drive_s/AG/AG-Floeel-Imaging/02-User/TheresaKoebe/NeuroMet_Project/TestFreesurferRecon/Freesurfer/MDC0103.freesurfer/mri/rawavg.mgz /media/drive_s/AG/AG-Floeel-Imaging/02-User/TheresaKoebe/NeuroMet_Project/TestFreesurferRecon/Freesurfer/MDC0103.freesurfer/mri/orig.mgz --conform_min 

mri_convert /media/drive_s/AG/AG-Floeel-Imaging/02-User/TheresaKoebe/NeuroMet_Project/TestFreesurferRecon/Freesurfer/MDC0103.freesurfer/mri/rawavg.mgz /media/drive_s/AG/AG-Floeel-Imaging/02-User/TheresaKoebe/NeuroMet_Project/TestFreesurferRecon/Freesurfer/MDC0103.freesurfer/mri/orig.mgz --conform_min 
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /media/drive_s/AG/AG-Floeel-Imaging/02-User/TheresaKoebe/NeuroMet_Project/TestFreesurferRecon/Freesurfer/MDC0103.freesurfer/mri/rawavg.mgz...
TR=5000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (0, -1, 0)
j_ras = (0, 0, 1)
k_ras = (1, 0, 0)
Original Data has (0.7, 0.7, 0.7) mm size and (320, 320, 240) voxels.
Data is conformed to 0.7 mm size and 321 voxels for all directions
changing data type from float to uchar (noscale = 0)...
MRIchangeType: Building histogram 
Reslicing using trilinear interpolation 
writing to /media/drive_s/AG/AG-Floeel-Imaging/02-User/TheresaKoebe/NeuroMet_Project/TestFreesurferRecon/Freesurfer/MDC0103.freesurfer/mri/orig.mgz...

 mri_add_xform_to_header -c /media/drive_s/AG/AG-Floeel-Imaging/02-User/TheresaKoebe/NeuroMet_Project/TestFreesurferRecon/Freesurfer/MDC0103.freesurfer/mri/transforms/talairach.xfm /media/drive_s/AG/AG-Floeel-Imaging/02-User/TheresaKoebe/NeuroMet_Project/TestFreesurferRecon/Freesurfer/MDC0103.freesurfer/mri/orig.mgz /media/drive_s/AG/AG-Floeel-Imaging/02-User/TheresaKoebe/NeuroMet_Project/TestFreesurferRecon/Freesurfer/MDC0103.freesurfer/mri/orig.mgz 

INFO: extension is mgz
#--------------------------------------------
#@# Talairach Mi 21. Sep 11:08:09 CEST 2016
/media/drive_s/AG/AG-Floeel-Imaging/02-User/TheresaKoebe/NeuroMet_Project/TestFreesurferRecon/Freesurfer/MDC0103.freesurfer/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 Mi 21. Sep 11:10:53 CEST 2016
/media/drive_s/AG/AG-Floeel-Imaging/02-User/TheresaKoebe/NeuroMet_Project/TestFreesurferRecon/Freesurfer/MDC0103.freesurfer/mri

 talairach_afd -T 0.005 -xfm transforms/talairach.xfm 

talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.8204, pval=0.8469 >= threshold=0.0050)

 awk -f /usr/local/freesurfer-5.3/bin/extract_talairach_avi_QA.awk /media/drive_s/AG/AG-Floeel-Imaging/02-User/TheresaKoebe/NeuroMet_Project/TestFreesurferRecon/Freesurfer/MDC0103.freesurfer/mri/transforms/talairach_avi.log 


 tal_QC_AZS /media/drive_s/AG/AG-Floeel-Imaging/02-User/TheresaKoebe/NeuroMet_Project/TestFreesurferRecon/Freesurfer/MDC0103.freesurfer/mri/transforms/talairach_avi.log 

TalAviQA: 0.97363
z-score: -1
#--------------------------------------------
#@# Nu Intensity Correction Mi 21. Sep 11:10:53 CEST 2016

 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --cm --n 2 

/media/drive_s/AG/AG-Floeel-Imaging/02-User/TheresaKoebe/NeuroMet_Project/TestFreesurferRecon/Freesurfer/MDC0103.freesurfer/mri
/usr/local/freesurfer-5.3/bin/mri_nu_correct.mni
--i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --cm --n 2
nIters 2
$Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $
Linux doc2 3.19.0-64-generic #72~14.04.1-Ubuntu SMP Fri Jun 24 17:59:48 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
Mi 21. Sep 11:10:53 CEST 2016
Program nu_correct, built from:
Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37
tmpdir is ./tmp.mri_nu_correct.mni.407070
/media/drive_s/AG/AG-Floeel-Imaging/02-User/TheresaKoebe/NeuroMet_Project/TestFreesurferRecon/Freesurfer/MDC0103.freesurfer/mri
mri_convert -cm orig.mgz ./tmp.mri_nu_correct.mni.407070/nu0.mnc -odt float
mri_convert -cm orig.mgz ./tmp.mri_nu_correct.mni.407070/nu0.mnc -odt float 
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from orig.mgz...
TR=5000.00, 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)
Original Data has (0.7, 0.7, 0.7) mm size and (321, 321, 321) voxels.
Data is conformed to 0.7 mm size and 322 voxels for all directions
changing data type from uchar to float (noscale = 0)...
Reslicing using trilinear interpolation 
writing to ./tmp.mri_nu_correct.mni.407070/nu0.mnc...
 
--------------------------------------------------------
Iteration 1 Mi 21. Sep 11:11:14 CEST 2016
nu_correct -clobber ./tmp.mri_nu_correct.mni.407070/nu0.mnc ./tmp.mri_nu_correct.mni.407070/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.407070/0/
defined(@array) is deprecated at /usr/local/freesurfer-5.3/mni/bin/nu_estimate_np_and_em line 165.
	(Maybe you should just omit the defined()?)
defined(@array) is deprecated at /usr/local/freesurfer-5.3/mni/bin/nu_estimate_np_and_em line 170.
	(Maybe you should just omit the defined()?)
defined(@array) is deprecated at /usr/local/freesurfer-5.3/mni/bin/nu_estimate_np_and_em line 211.
	(Maybe you should just omit the defined()?)
defined(@array) is deprecated at /usr/local/freesurfer-5.3/mni/bin/nu_estimate_np_and_em line 1051.
	(Maybe you should just omit the defined()?)
defined(@array) is deprecated at /usr/local/freesurfer-5.3/mni/bin/nu_estimate_np_and_em line 1054.
	(Maybe you should just omit the defined()?)
defined(@array) is deprecated at /usr/local/freesurfer-5.3/mni/bin/nu_estimate_np_and_em line 1449.
	(Maybe you should just omit the defined()?)
defined(@array) is deprecated at /usr/local/freesurfer-5.3/mni/bin/nu_estimate_np_and_em line 1455.
	(Maybe you should just omit the defined()?)
defined(@array) is deprecated at /usr/local/freesurfer-5.3/mni/bin/nu_estimate_np_and_em line 1457.
	(Maybe you should just omit the defined()?)
defined(@array) is deprecated at /usr/local/freesurfer-5.3/mni/bin/nu_estimate_np_and_em line 1481.
	(Maybe you should just omit the defined()?)
defined(@array) is deprecated at /usr/local/freesurfer-5.3/mni/bin/nu_estimate_np_and_em line 1631.
	(Maybe you should just omit the defined()?)
defined(@array) is deprecated at /usr/local/freesurfer-5.3/mni/bin/nu_estimate_np_and_em line 1633.
	(Maybe you should just omit the defined()?)
defined(@array) is deprecated at /usr/local/freesurfer-5.3/mni/bin/nu_estimate_np_and_em line 1635.
	(Maybe you should just omit the defined()?)
defined(@array) is deprecated at /usr/local/freesurfer-5.3/mni/bin/nu_estimate_np_and_em line 1637.
	(Maybe you should just omit the defined()?)
defined(@array) is deprecated at /usr/local/freesurfer-5.3/mni/bin/nu_estimate_np_and_em line 1639.
	(Maybe you should just omit the defined()?)
[theresa@doc2:/media/drive_s/AG/AG-Floeel-Imaging/02-User/TheresaKoebe/NeuroMet_Project/TestFreesurferRecon/Freesurfer/MDC0103.freesurfer/mri/] [2016-09-21 11:11:14] running:
  /usr/local/freesurfer-5.3/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.407070/0/ ./tmp.mri_nu_correct.mni.407070/nu0.mnc ./tmp.mri_nu_correct.mni.407070/nu1.imp

Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer-5.3/mni/bin/sharpen_volume line 153.
Processing:..................................................................................Done
Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer-5.3/mni/bin/sharpen_volume line 153.
Processing:..................................................................................Done
Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer-5.3/mni/bin/sharpen_volume line 153.
Processing:..................................................................................Done
Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer-5.3/mni/bin/sharpen_volume line 153.
Processing:..................................................................................Done
Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer-5.3/mni/bin/sharpen_volume line 153.
Processing:..................................................................................Done
Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer-5.3/mni/bin/sharpen_volume line 153.
Processing:..................................................................................Done
Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer-5.3/mni/bin/sharpen_volume line 153.
Processing:..................................................................................Done
Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer-5.3/mni/bin/sharpen_volume line 153.
Processing:..................................................................................Done
Number of iterations: 8 
CV of field change: 0.000899876
[theresa@doc2:/media/drive_s/AG/AG-Floeel-Imaging/02-User/TheresaKoebe/NeuroMet_Project/TestFreesurferRecon/Freesurfer/MDC0103.freesurfer/mri/] [2016-09-21 11:11:47] running:
  /usr/local/freesurfer-5.3/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.407070/nu0.mnc ./tmp.mri_nu_correct.mni.407070/0//template.mnc

Transforming slices:............................................................................................................Done
Transforming slices:..................................................................................................................................................................................................................................................................................................................................Done
 
 
--------------------------------------------------------
Iteration 2 Mi 21. Sep 11:12:20 CEST 2016
nu_correct -clobber ./tmp.mri_nu_correct.mni.407070/nu1.mnc ./tmp.mri_nu_correct.mni.407070/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.407070/1/
defined(@array) is deprecated at /usr/local/freesurfer-5.3/mni/bin/nu_estimate_np_and_em line 165.
	(Maybe you should just omit the defined()?)
defined(@array) is deprecated at /usr/local/freesurfer-5.3/mni/bin/nu_estimate_np_and_em line 170.
	(Maybe you should just omit the defined()?)
defined(@array) is deprecated at /usr/local/freesurfer-5.3/mni/bin/nu_estimate_np_and_em line 211.
	(Maybe you should just omit the defined()?)
defined(@array) is deprecated at /usr/local/freesurfer-5.3/mni/bin/nu_estimate_np_and_em line 1051.
	(Maybe you should just omit the defined()?)
defined(@array) is deprecated at /usr/local/freesurfer-5.3/mni/bin/nu_estimate_np_and_em line 1054.
	(Maybe you should just omit the defined()?)
defined(@array) is deprecated at /usr/local/freesurfer-5.3/mni/bin/nu_estimate_np_and_em line 1449.
	(Maybe you should just omit the defined()?)
defined(@array) is deprecated at /usr/local/freesurfer-5.3/mni/bin/nu_estimate_np_and_em line 1455.
	(Maybe you should just omit the defined()?)
defined(@array) is deprecated at /usr/local/freesurfer-5.3/mni/bin/nu_estimate_np_and_em line 1457.
	(Maybe you should just omit the defined()?)
defined(@array) is deprecated at /usr/local/freesurfer-5.3/mni/bin/nu_estimate_np_and_em line 1481.
	(Maybe you should just omit the defined()?)
defined(@array) is deprecated at /usr/local/freesurfer-5.3/mni/bin/nu_estimate_np_and_em line 1631.
	(Maybe you should just omit the defined()?)
defined(@array) is deprecated at /usr/local/freesurfer-5.3/mni/bin/nu_estimate_np_and_em line 1633.
	(Maybe you should just omit the defined()?)
defined(@array) is deprecated at /usr/local/freesurfer-5.3/mni/bin/nu_estimate_np_and_em line 1635.
	(Maybe you should just omit the defined()?)
defined(@array) is deprecated at /usr/local/freesurfer-5.3/mni/bin/nu_estimate_np_and_em line 1637.
	(Maybe you should just omit the defined()?)
defined(@array) is deprecated at /usr/local/freesurfer-5.3/mni/bin/nu_estimate_np_and_em line 1639.
	(Maybe you should just omit the defined()?)
[theresa@doc2:/media/drive_s/AG/AG-Floeel-Imaging/02-User/TheresaKoebe/NeuroMet_Project/TestFreesurferRecon/Freesurfer/MDC0103.freesurfer/mri/] [2016-09-21 11:12:20] running:
  /usr/local/freesurfer-5.3/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.407070/1/ ./tmp.mri_nu_correct.mni.407070/nu1.mnc ./tmp.mri_nu_correct.mni.407070/nu2.imp

Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer-5.3/mni/bin/sharpen_volume line 153.
Processing:..................................................................................Done
Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer-5.3/mni/bin/sharpen_volume line 153.
Processing:..................................................................................Done
Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer-5.3/mni/bin/sharpen_volume line 153.
Processing:..................................................................................Done
Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer-5.3/mni/bin/sharpen_volume line 153.
Processing:..................................................................................Done
Number of iterations: 4 
CV of field change: 0.000770838
[theresa@doc2:/media/drive_s/AG/AG-Floeel-Imaging/02-User/TheresaKoebe/NeuroMet_Project/TestFreesurferRecon/Freesurfer/MDC0103.freesurfer/mri/] [2016-09-21 11:12:39] running:
  /usr/local/freesurfer-5.3/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.407070/nu1.mnc ./tmp.mri_nu_correct.mni.407070/1//template.mnc

Transforming slices:............................................................................................................Done
Transforming slices:..................................................................................................................................................................................................................................................................................................................................Done
 
 
 
mri_binarize --i ./tmp.mri_nu_correct.mni.407070/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.407070/ones.mgz

$Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $
cwd /media/drive_s/AG/AG-Floeel-Imaging/02-User/TheresaKoebe/NeuroMet_Project/TestFreesurferRecon/Freesurfer/MDC0103.freesurfer/mri
cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.407070/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.407070/ones.mgz 
sysname  Linux
hostname doc2
machine  x86_64
user     theresa

input      ./tmp.mri_nu_correct.mni.407070/nu2.mnc
frame      0
nErode3d   0
nErode2d   0
output     ./tmp.mri_nu_correct.mni.407070/ones.mgz
Binarizing based on threshold
min        -1
max        +infinity
binval        1
binvalnot     0
Found 33386248 values in range
Counting number of voxels
Found 33386248 voxels in final mask
mri_binarize done
mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.407070/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.407070/sum.junk --avgwf ./tmp.mri_nu_correct.mni.407070/input.mean.dat

$Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $
cwd 
cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.407070/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.407070/sum.junk --avgwf ./tmp.mri_nu_correct.mni.407070/input.mean.dat 
sysname  Linux
hostname doc2
machine  x86_64
user     theresa
UseRobust  0
Loading ./tmp.mri_nu_correct.mni.407070/ones.mgz
Loading orig.mgz
ERROR: dimension mismatch between input volume and seg
  input 321 321 321
  seg   322 322 322
Linux doc2 3.19.0-64-generic #72~14.04.1-Ubuntu SMP Fri Jun 24 17:59:48 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s MDC0103.freesurfer exited with ERRORS at Mi 21. Sep 11:13:24 CEST 2016

To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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