Hello,
New to freesurfer using Linux (successfully reconstructed several images on a
mac) - can you help me determine how to correct the error in this attached
attempt at a recon?
Many thanks,
Linette
Tue Feb 14 22:56:38 EST 2017
/home/cnslab/Desktop/freesurfer/subjects/5098Post
/home/cnslab/Desktop/freesurfer/bin/recon-all
-i /home/cnslab/Desktop/freesurfer/subjects/5098/MPRAGE/IM-0004-0001-0001.dcm -i /home/cnslab/Desktop/freesurfer/subjects/5098/MPRAGE/IM-0004-0002-0001.dcm -all -s 5098Post
subjid 5098Post
setenv SUBJECTS_DIR /home/cnslab/Desktop/freesurfer/subjects
FREESURFER_HOME /home/cnslab/Desktop/freesurfer
Actual FREESURFER_HOME /home/cnslab/Desktop/freesurfer
build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
Linux cnslab 4.4.0-21-generic #37-Ubuntu SMP Mon Apr 18 18:33:37 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 31396
maxlocks unlimited
maxsignal 31396
maxmessage 819200
maxnice 0
maxrtprio 0
maxrttime unlimited
total used free shared buff/cache available
Mem: 8078676 935928 701192 131948 6441556 6935768
Swap: 8290300 0 8290300
########################################
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: 2017/02/15-03:56:38-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: cnslab Machine: cnslab Platform: Linux PlatformVersion: 4.4.0-21-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: 2017/02/15-03:56:38-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: cnslab Machine: cnslab Platform: Linux PlatformVersion: 4.4.0-21-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: 2017/02/15-03:56:39-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: cnslab Machine: cnslab Platform: Linux PlatformVersion: 4.4.0-21-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/15-03:56:39-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: cnslab Machine: cnslab Platform: Linux PlatformVersion: 4.4.0-21-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/15-03:56:39-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: cnslab Machine: cnslab Platform: Linux PlatformVersion: 4.4.0-21-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/15-03:56:39-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: cnslab Machine: cnslab Platform: Linux PlatformVersion: 4.4.0-21-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/15-03:56:39-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: cnslab Machine: cnslab Platform: Linux PlatformVersion: 4.4.0-21-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/15-03:56:39-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: cnslab Machine: cnslab Platform: Linux PlatformVersion: 4.4.0-21-generic CompilerName: GCC CompilerVersion: 40400
======= NUMBER OF OPENMP THREADS = 1 =======
ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/15-03:56:39-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: cnslab Machine: cnslab Platform: Linux PlatformVersion: 4.4.0-21-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/15-03:56:39-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: cnslab Machine: cnslab Platform: Linux PlatformVersion: 4.4.0-21-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/15-03:56:39-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: cnslab Machine: cnslab Platform: Linux PlatformVersion: 4.4.0-21-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/15-03:56:39-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: cnslab Machine: cnslab Platform: Linux PlatformVersion: 4.4.0-21-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/15-03:56:39-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: cnslab Machine: cnslab Platform: Linux PlatformVersion: 4.4.0-21-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/15-03:56:39-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: cnslab Machine: cnslab Platform: Linux PlatformVersion: 4.4.0-21-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/15-03:56:39-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: cnslab Machine: cnslab Platform: Linux PlatformVersion: 4.4.0-21-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/15-03:56:39-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: cnslab Machine: cnslab Platform: Linux PlatformVersion: 4.4.0-21-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/15-03:56:39-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: cnslab Machine: cnslab Platform: Linux PlatformVersion: 4.4.0-21-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/15-03:56:39-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: cnslab Machine: cnslab Platform: Linux PlatformVersion: 4.4.0-21-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/15-03:56:39-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: cnslab Machine: cnslab Platform: Linux PlatformVersion: 4.4.0-21-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/15-03:56:39-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: cnslab Machine: cnslab Platform: Linux PlatformVersion: 4.4.0-21-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/15-03:56:39-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: cnslab Machine: cnslab Platform: Linux PlatformVersion: 4.4.0-21-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/15-03:56:40-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: cnslab Machine: cnslab Platform: Linux PlatformVersion: 4.4.0-21-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/15-03:56:40-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: cnslab Machine: cnslab Platform: Linux PlatformVersion: 4.4.0-21-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/15-03:56:40-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: cnslab Machine: cnslab Platform: Linux PlatformVersion: 4.4.0-21-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/15-03:56:40-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: cnslab Machine: cnslab Platform: Linux PlatformVersion: 4.4.0-21-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/15-03:56:40-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: cnslab Machine: cnslab Platform: Linux PlatformVersion: 4.4.0-21-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/15-03:56:40-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: cnslab Machine: cnslab Platform: Linux PlatformVersion: 4.4.0-21-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/15-03:56:40-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: cnslab Machine: cnslab Platform: Linux PlatformVersion: 4.4.0-21-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/15-03:56:40-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: cnslab Machine: cnslab Platform: Linux PlatformVersion: 4.4.0-21-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/15-03:56:40-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: cnslab Machine: cnslab Platform: Linux PlatformVersion: 4.4.0-21-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/15-03:56:40-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: cnslab Machine: cnslab Platform: Linux PlatformVersion: 4.4.0-21-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/15-03:56:40-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: cnslab Machine: cnslab Platform: Linux PlatformVersion: 4.4.0-21-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: 2017/02/15-03:56:40-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: cnslab Machine: cnslab Platform: Linux PlatformVersion: 4.4.0-21-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: 2017/02/15-03:56:40-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: cnslab Machine: cnslab Platform: Linux PlatformVersion: 4.4.0-21-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/15-03:56:40-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: cnslab Machine: cnslab Platform: Linux PlatformVersion: 4.4.0-21-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/15-03:56:40-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: cnslab Machine: cnslab Platform: Linux PlatformVersion: 4.4.0-21-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/15-03:56:40-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: cnslab Machine: cnslab Platform: Linux PlatformVersion: 4.4.0-21-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/15-03:56:40-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: cnslab Machine: cnslab Platform: Linux PlatformVersion: 4.4.0-21-generic CompilerName: GCC CompilerVersion: 40400
#######################################
GCADIR /home/cnslab/Desktop/freesurfer/average
GCA RB_all_2008-03-26.gca
GCASkull RB_all_withskull_2008-03-26.gca
AvgCurvTif average.curvature.filled.buckner40.tif
GCSDIR /home/cnslab/Desktop/freesurfer/average
GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs
#######################################
/home/cnslab/Desktop/freesurfer/subjects/5098Post
mri_convert /home/cnslab/Desktop/freesurfer/subjects/5098/MPRAGE/IM-0004-0001-0001.dcm /home/cnslab/Desktop/freesurfer/subjects/5098Post/mri/orig/001.mgz
mri_convert /home/cnslab/Desktop/freesurfer/subjects/5098/MPRAGE/IM-0004-0001-0001.dcm /home/cnslab/Desktop/freesurfer/subjects/5098Post/mri/orig/001.mgz
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /home/cnslab/Desktop/freesurfer/subjects/5098/MPRAGE/IM-0004-0001-0001.dcm...
Starting DICOMRead2()
dcmfile = /home/cnslab/Desktop/freesurfer/subjects/5098/MPRAGE/IM-0004-0001-0001.dcm
dcmdir = /home/cnslab/Desktop/freesurfer/subjects/5098/MPRAGE
Ref Series No = 8
Found 238 files, checking for dicoms
Found 236 dicom files in series.
First Sorting
Computing Slice Direction
Vs: 0 -1 0
Vs: 0 -1 0
Second Sorting
Counting frames
nframes = 1
nslices = 236
ndcmfiles = 236
PE Dir = ROW (dicom read)
TransferSyntaxUID: --1.2.840.10008.1.2.1--
Loading pixel data
TR=7.36, TE=3.05, TI=650.00, flip angle=11.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (-0, 1, 0)
writing to /home/cnslab/Desktop/freesurfer/subjects/5098Post/mri/orig/001.mgz...
/home/cnslab/Desktop/freesurfer/subjects/5098Post
mri_convert /home/cnslab/Desktop/freesurfer/subjects/5098/MPRAGE/IM-0004-0002-0001.dcm /home/cnslab/Desktop/freesurfer/subjects/5098Post/mri/orig/002.mgz
mri_convert /home/cnslab/Desktop/freesurfer/subjects/5098/MPRAGE/IM-0004-0002-0001.dcm /home/cnslab/Desktop/freesurfer/subjects/5098Post/mri/orig/002.mgz
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /home/cnslab/Desktop/freesurfer/subjects/5098/MPRAGE/IM-0004-0002-0001.dcm...
Starting DICOMRead2()
dcmfile = /home/cnslab/Desktop/freesurfer/subjects/5098/MPRAGE/IM-0004-0002-0001.dcm
dcmdir = /home/cnslab/Desktop/freesurfer/subjects/5098/MPRAGE
Ref Series No = 8
Found 238 files, checking for dicoms
Found 236 dicom files in series.
First Sorting
Computing Slice Direction
Vs: 0 -1 0
Vs: 0 -1 0
Second Sorting
Counting frames
nframes = 1
nslices = 236
ndcmfiles = 236
PE Dir = ROW (dicom read)
TransferSyntaxUID: --1.2.840.10008.1.2.1--
Loading pixel data
TR=7.36, TE=3.05, TI=650.00, flip angle=11.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (-0, 1, 0)
writing to /home/cnslab/Desktop/freesurfer/subjects/5098Post/mri/orig/002.mgz...
#--------------------------------------------
#@# MotionCor Tue Feb 14 22:56:48 EST 2017
Found 2 runs
/home/cnslab/Desktop/freesurfer/subjects/5098Post/mri/orig/001.mgz
/home/cnslab/Desktop/freesurfer/subjects/5098Post/mri/orig/002.mgz
Checking for (invalid) multi-frame inputs...
Checking for (invalid) multi-frame inputs...
/home/cnslab/Desktop/freesurfer/subjects/5098Post
mri_robust_template --mov /home/cnslab/Desktop/freesurfer/subjects/5098Post/mri/orig/001.mgz /home/cnslab/Desktop/freesurfer/subjects/5098Post/mri/orig/002.mgz --average 1 --template /home/cnslab/Desktop/freesurfer/subjects/5098Post/mri/rawavg.mgz --satit --inittp 1 --fixtp --noit --iscale --iscaleout /home/cnslab/Desktop/freesurfer/subjects/5098Post/mri/orig/001-iscale.txt /home/cnslab/Desktop/freesurfer/subjects/5098Post/mri/orig/002-iscale.txt --subsample 200 --lta /home/cnslab/Desktop/freesurfer/subjects/5098Post/mri/orig/001.lta /home/cnslab/Desktop/freesurfer/subjects/5098Post/mri/orig/002.lta
$Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $
--mov: Using /home/cnslab/Desktop/freesurfer/subjects/5098Post/mri/orig/001.mgz as movable/source volume.
--mov: Using /home/cnslab/Desktop/freesurfer/subjects/5098Post/mri/orig/002.mgz as movable/source volume.
Total: 2 input volumes
--average: Using method 1 for template computation.
--template: Using /home/cnslab/Desktop/freesurfer/subjects/5098Post/mri/rawavg.mgz as template output volume.
--satit: Will estimate SAT iteratively!
--inittp: Using TP 1 as target for initialization
--fixtp: Will map everything to init TP!
--noit: Will output only first template (no iterations)!
--iscale: Enableing intensity scaling!
--iscaleout: Will perform intensity scaling and output results
--subsample: Will subsample if size is larger than 200 on all axes!
--lta: Will output LTA transforms
reading source '/home/cnslab/Desktop/freesurfer/subjects/5098Post/mri/orig/001.mgz'...
converting source '/home/cnslab/Desktop/freesurfer/subjects/5098Post/mri/orig/001.mgz' to bspline ...
MRItoBSpline degree 3
reading source '/home/cnslab/Desktop/freesurfer/subjects/5098Post/mri/orig/002.mgz'...
converting source '/home/cnslab/Desktop/freesurfer/subjects/5098Post/mri/orig/002.mgz' to bspline ...
MRItoBSpline degree 3
MultiRegistration::initializing Xforms (init 1 , maxres 0 , iterate 5 , epsit 0.01 ) :
[init] ========================= TP 2 to TP 1 ==============================
Register TP 2 ( /home/cnslab/Desktop/freesurfer/subjects/5098Post/mri/orig/002.mgz )
to TP 1 ( /home/cnslab/Desktop/freesurfer/subjects/5098Post/mri/orig/001.mgz )
- Max Resolution used: 2
-- gpS ( 64 , 64 , 59 )
-- gpT ( 64 , 64 , 59 )
- running loop to estimate saturation parameter:
Sigma too small: 0 (identical images?)
Sigma too small: 0 (identical images?)
Sigma too small: 0 (identical images?)
Sigma too small: 0 (identical images?)
Sigma too small: 0 (identical images?)
Sigma too small: 0 (identical images?)
Sigma too small: 0 (identical images?)
Sigma too small: 0 (identical images?)
Sigma too small: 0 (identical images?)
Sigma too small: 0 (identical images?)
mapping movs and creating initial template...
allow intensity scaling
using median
Writing final template: /home/cnslab/Desktop/freesurfer/subjects/5098Post/mri/rawavg.mgz
Writing final transforms (warps etc.)...
Determinant( lta[ 0 ]) : 1
Determinant( lta[ 1 ]) : 1
registration took 0 minutes and 30 seconds.
Thank you for using RobustTemplate!
If you find it useful and use it for a publication, please cite:
Within-Subject Template Estimation for Unbiased Longitudinal Image Analysis
M. Reuter, N.J. Schmansky, H.D. Rosas, B. Fischl. NeuroImage 2012.
http://dx.doi.org/10.1016/j.neuroimage.2012.02.084
http://reuter.mit.edu/papers/reuter-long12.pdf
/home/cnslab/Desktop/freesurfer/subjects/5098Post
mri_convert /home/cnslab/Desktop/freesurfer/subjects/5098Post/mri/rawavg.mgz /home/cnslab/Desktop/freesurfer/subjects/5098Post/mri/orig.mgz --conform
mri_convert /home/cnslab/Desktop/freesurfer/subjects/5098Post/mri/rawavg.mgz /home/cnslab/Desktop/freesurfer/subjects/5098Post/mri/orig.mgz --conform
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /home/cnslab/Desktop/freesurfer/subjects/5098Post/mri/rawavg.mgz...
TR=7.36, TE=3.05, TI=650.00, flip angle=11.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (-0, 1, 0)
Original Data has (1, 1, 1) mm size and (256, 256, 236) voxels.
Data is conformed to 1 mm size and 256 voxels for all directions
changing data type from short to uchar (noscale = 0)...
MRIchangeType: Building histogram
Reslicing using trilinear interpolation
writing to /home/cnslab/Desktop/freesurfer/subjects/5098Post/mri/orig.mgz...
mri_add_xform_to_header -c /home/cnslab/Desktop/freesurfer/subjects/5098Post/mri/transforms/talairach.xfm /home/cnslab/Desktop/freesurfer/subjects/5098Post/mri/orig.mgz /home/cnslab/Desktop/freesurfer/subjects/5098Post/mri/orig.mgz
INFO: extension is mgz
#--------------------------------------------
#@# Talairach Tue Feb 14 22:57:24 EST 2017
/home/cnslab/Desktop/freesurfer/subjects/5098Post/mri
mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz
Linux cnslab 4.4.0-21-generic #37-Ubuntu SMP Mon Apr 18 18:33:37 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s 5098Post exited with ERRORS at Tue Feb 14 22:57:26 EST 2017
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
