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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