Dear Freesurfer experts,
I used 'recon-all' command ('recon-all -i path/EYT1.mgz -s EYrecon -all) in
freesurfer 4.5 and after 8 hours of process, I received the an error and it
stoped.
The error says it can not find files in surf folder... recon-all.log is
attached.
I use virtual machine 10- Ubuntu 12.04 - freesurfer 4.5.
I do appreciate your attention.
BR,
Elahe'
Thu Nov 27 17:35:32 EST 2014
/home/user/Desktop/structural/EY
/usr/local/freesurfer/bin/recon-all
-all -subjid EY
subjid EY
setenv SUBJECTS_DIR /home/user/Desktop/structural
FREESURFER_HOME /usr/local/freesurfer
Actual FREESURFER_HOME /usr/local/freesurfer
build-stamp.txt: freesurfer-Linux-centos4-stable-pub-v4.5.0
Linux ubuntu 3.2.0-23-generic-pae #36-Ubuntu SMP Tue Apr 10 22:19:09 UTC 2012 i686 i686 i386 GNU/Linux
cputime unlimited
filesize unlimited
datasize unlimited
stacksize 8192 kbytes
coredumpsize 0 kbytes
memoryuse unlimited
vmemoryuse unlimited
descriptors 1024
memorylocked 64 kbytes
maxproc 15992
maxlocks unlimited
maxsignal 15992
maxmessage 819200
maxnice 0
maxrtprio 0
maxrttime unlimited
total used free shared buffers cached
Mem: 2061540 595584 1465956 0 90752 283276
-/+ buffers/cache: 221556 1839984
Swap: 0 0 0
########################################
program versions used
$Id: recon-all,v 1.133.2.57 2009/08/06 18:27:48 nicks Exp $
$Id: mri_motion_correct.fsl,v 1.7.2.1 2008/02/29 20:17:11 nicks Exp $
mri_convert -all-info
ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2014/11/27-22:35:32-GMT BuildTimeStamp: Aug 11 2009 08:24:20 CVS: $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ User: user Machine: ubuntu Platform: Linux PlatformVersion: 3.2.0-23-generic-pae CompilerName: GCC CompilerVersion: 30400
FLIRT version 5.5
$Id: talairach_avi,v 1.4.2.1 2009/07/30 19:22:07 nicks Exp $
mri_convert --version
stable4
ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2014/11/27-22:35:33-GMT BuildTimeStamp: Aug 11 2009 08:24:20 CVS: $Id: tkregister2.c,v 1.86.2.12 2009/03/19 22:04:20 greve Exp $ User: user Machine: ubuntu Platform: Linux PlatformVersion: 3.2.0-23-generic-pae CompilerName: GCC CompilerVersion: 30400
Program nu_correct, built from:
Package MNI N3, version 1.10, compiled by nicks@fishie (i686-pc-linux-gnu) on 2007-11-01 at 16:24:51
ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2014/11/27-22:35:33-GMT BuildTimeStamp: Aug 11 2009 08:24:20 CVS: $Id: mri_normalize.c,v 1.52.2.2 2008/05/12 17:34:55 nicks Exp $ User: user Machine: ubuntu Platform: Linux PlatformVersion: 3.2.0-23-generic-pae CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2014/11/27-22:35:34-GMT BuildTimeStamp: Aug 11 2009 08:24:20 CVS: $Id: mri_watershed.cpp,v 1.67.2.5 2009/05/05 19:17:42 nicks Exp $ User: user Machine: ubuntu Platform: Linux PlatformVersion: 3.2.0-23-generic-pae CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2014/11/27-22:35:34-GMT BuildTimeStamp: Aug 11 2009 08:24:20 CVS: $Id: mri_segment.c,v 1.33.2.2 2007/11/21 04:38:38 nicks Exp $ User: user Machine: ubuntu Platform: Linux PlatformVersion: 3.2.0-23-generic-pae CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2014/11/27-22:35:34-GMT BuildTimeStamp: Aug 11 2009 08:24:20 CVS: $Id: mri_label2label.c,v 1.33 2007/08/10 18:23:46 greve Exp $ User: user Machine: ubuntu Platform: Linux PlatformVersion: 3.2.0-23-generic-pae CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2014/11/27-22:35:34-GMT BuildTimeStamp: Aug 11 2009 08:24:20 CVS: $Id: mri_em_register.c,v 1.57.2.2 2008/12/29 17:22:03 nicks Exp $ User: user Machine: ubuntu Platform: Linux PlatformVersion: 3.2.0-23-generic-pae CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2014/11/27-22:35:34-GMT BuildTimeStamp: Aug 11 2009 08:24:20 CVS: $Id: mri_ca_normalize.c,v 1.38.2.3 2009/08/02 15:00:46 nicks Exp $ User: user Machine: ubuntu Platform: Linux PlatformVersion: 3.2.0-23-generic-pae CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2014/11/27-22:35:34-GMT BuildTimeStamp: Aug 11 2009 08:24:20 CVS: $Id: mri_ca_register.c,v 1.63.2.3 2009/07/30 22:39:45 nicks Exp $ User: user Machine: ubuntu Platform: Linux PlatformVersion: 3.2.0-23-generic-pae CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2014/11/27-22:35:35-GMT BuildTimeStamp: Aug 11 2009 08:24:20 CVS: $Id: mri_ca_label.c,v 1.80.2.8 2009/07/30 23:22:53 nicks Exp $ User: user Machine: ubuntu Platform: Linux PlatformVersion: 3.2.0-23-generic-pae CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2014/11/27-22:35:35-GMT BuildTimeStamp: Aug 11 2009 08:24:20 CVS: $Id: mri_pretess.c,v 1.16 2007/01/18 20:23:47 nicks Exp $ User: user Machine: ubuntu Platform: Linux PlatformVersion: 3.2.0-23-generic-pae CompilerName: GCC CompilerVersion: 30400
unknown option -ALL-INFO
ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2014/11/27-22:35:35-GMT BuildTimeStamp: Aug 11 2009 08:24:20 CVS: $Id: mri_fill.c,v 1.111 2007/07/19 20:16:38 fischl Exp $ User: user Machine: ubuntu Platform: Linux PlatformVersion: 3.2.0-23-generic-pae CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2014/11/27-22:35:36-GMT BuildTimeStamp: Aug 11 2009 08:24:20 CVS: $Id: mri_tessellate.c,v 1.32 2007/04/26 21:44:21 fischl Exp $ User: user Machine: ubuntu Platform: Linux PlatformVersion: 3.2.0-23-generic-pae CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2014/11/27-22:35:36-GMT BuildTimeStamp: Aug 11 2009 08:24:20 CVS: $Id: mri_concatenate_lta.c,v 1.3.2.1 2009/05/06 23:40:38 nicks Exp $ User: user Machine: ubuntu Platform: Linux PlatformVersion: 3.2.0-23-generic-pae CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2014/11/27-22:35:36-GMT BuildTimeStamp: Aug 11 2009 08:24:20 CVS: $Id: mri_normalize_tp2.c,v 1.6 2007/01/08 18:10:12 nicks Exp $ User: user Machine: ubuntu Platform: Linux PlatformVersion: 3.2.0-23-generic-pae CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2014/11/27-22:35:36-GMT BuildTimeStamp: Aug 11 2009 08:24:20 CVS: $Id: mris_smooth.c,v 1.21 2007/01/01 18:16:19 fischl Exp $ User: user Machine: ubuntu Platform: Linux PlatformVersion: 3.2.0-23-generic-pae CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2014/11/27-22:35:37-GMT BuildTimeStamp: Aug 11 2009 08:24:20 CVS: $Id: mris_inflate.c,v 1.33.2.3 2008/04/22 19:47:47 nicks Exp $ User: user Machine: ubuntu Platform: Linux PlatformVersion: 3.2.0-23-generic-pae CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2014/11/27-22:35:37-GMT BuildTimeStamp: Aug 11 2009 08:24:20 CVS: $Id: mris_curvature.c,v 1.25 2007/07/20 16:42:32 fischl Exp $ User: user Machine: ubuntu Platform: Linux PlatformVersion: 3.2.0-23-generic-pae CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2014/11/27-22:35:38-GMT BuildTimeStamp: Aug 11 2009 08:24:20 CVS: $Id: mris_sphere.c,v 1.47 2007/03/08 18:36:08 greve Exp $ User: user Machine: ubuntu Platform: Linux PlatformVersion: 3.2.0-23-generic-pae CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2014/11/27-22:35:38-GMT BuildTimeStamp: Aug 11 2009 08:24:20 CVS: $Id: mris_fix_topology.c,v 1.43 2007/01/05 16:57:16 nicks Exp $ User: user Machine: ubuntu Platform: Linux PlatformVersion: 3.2.0-23-generic-pae CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2014/11/27-22:35:38-GMT BuildTimeStamp: Aug 11 2009 08:24:20 CVS: $Id: mris_topo_fixer.cpp,v 1.26.2.1 2007/11/18 03:06:20 nicks Exp $ User: user Machine: ubuntu Platform: Linux PlatformVersion: 3.2.0-23-generic-pae CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2014/11/27-22:35:39-GMT BuildTimeStamp: Aug 11 2009 08:24:20 CVS: $Id: mris_ca_label.c,v 1.23 2007/03/23 20:00:07 fischl Exp $ User: user Machine: ubuntu Platform: Linux PlatformVersion: 3.2.0-23-generic-pae CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2014/11/27-22:35:39-GMT BuildTimeStamp: Aug 11 2009 08:24:20 CVS: $Id: mris_euler_number.c,v 1.5 2006/12/29 02:09:10 nicks Exp $ User: user Machine: ubuntu Platform: Linux PlatformVersion: 3.2.0-23-generic-pae CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2014/11/27-22:35:39-GMT BuildTimeStamp: Aug 11 2009 08:24:20 CVS: $Id: mris_make_surfaces.c,v 1.99.2.5 2008/08/21 22:48:22 nicks Exp $ User: user Machine: ubuntu Platform: Linux PlatformVersion: 3.2.0-23-generic-pae CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2014/11/27-22:35:39-GMT BuildTimeStamp: Aug 11 2009 08:24:20 CVS: $Id: mris_register.c,v 1.48 2007/07/19 15:58:50 fischl Exp $ User: user Machine: ubuntu Platform: Linux PlatformVersion: 3.2.0-23-generic-pae CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2014/11/27-22:35:40-GMT BuildTimeStamp: Aug 11 2009 08:24:20 CVS: $Id: mris_anatomical_stats.c,v 1.54.2.7 2009/06/08 23:45:06 nicks Exp $ User: user Machine: ubuntu Platform: Linux PlatformVersion: 3.2.0-23-generic-pae CompilerName: GCC CompilerVersion: 30400
ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2014/11/27-22:35:40-GMT BuildTimeStamp: Aug 11 2009 08:24:20 CVS: $Id: mrisp_paint.c,v 1.8 2007/02/13 16:57:23 fischl Exp $ User: user Machine: ubuntu Platform: Linux PlatformVersion: 3.2.0-23-generic-pae CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2014/11/27-22:35:40-GMT BuildTimeStamp: Aug 11 2009 08:24:20 CVS: $Id: mris_curvature_stats.c,v 1.28.2.5 2009/02/04 21:12:59 nicks Exp $ User: user Machine: ubuntu Platform: Linux PlatformVersion: 3.2.0-23-generic-pae CompilerName: GCC CompilerVersion: 30400
$Id: mri_robust_register.cpp,v 1.22.2.1 2009/05/22 00:58:19 nicks Exp $
ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2014/11/27-22:35:40-GMT BuildTimeStamp: Aug 11 2009 08:24:20 CVS: $Id: mri_robust_register.cpp,v 1.22.2.1 2009/05/22 00:58:19 nicks Exp $ User: user Machine: ubuntu Platform: Linux PlatformVersion: 3.2.0-23-generic-pae CompilerName: GCC CompilerVersion: 30400
$Id: mri_robust_template.cpp,v 1.6.2.4 2009/08/05 16:30:00 nicks Exp $
ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2014/11/27-22:35:41-GMT BuildTimeStamp: Aug 11 2009 08:24:20 CVS: $Id: mri_robust_template.cpp,v 1.6.2.4 2009/08/05 16:30:00 nicks Exp $ User: user Machine: ubuntu Platform: Linux PlatformVersion: 3.2.0-23-generic-pae CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2014/11/27-22:35:41-GMT BuildTimeStamp: Aug 11 2009 08:24:20 CVS: $Id: mri_and.c,v 1.2.2.1 2009/05/22 00:58:19 nicks Exp $ User: user Machine: ubuntu Platform: Linux PlatformVersion: 3.2.0-23-generic-pae CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2014/11/27-22:35:41-GMT BuildTimeStamp: Aug 11 2009 08:24:20 CVS: $Id: mri_or.c,v 1.1.2.1 2009/06/09 19:52:43 nicks Exp $ User: user Machine: ubuntu Platform: Linux PlatformVersion: 3.2.0-23-generic-pae CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2014/11/27-22:35:41-GMT BuildTimeStamp: Aug 11 2009 08:24:20 CVS: $Id: mri_fuse_segmentations.c,v 1.5.2.2 2009/06/10 19:42:00 nicks Exp $ User: user Machine: ubuntu Platform: Linux PlatformVersion: 3.2.0-23-generic-pae CompilerName: GCC CompilerVersion: 30400
#######################################
GCA RB_all_2008-03-26.gca
GCASkull RB_all_withskull_2008-03-26.gca
AvgCurvTif average.curvature.filled.buckner40.tif
GCS curvature.buckner40.filled.desikan_killiany.2009-03-04.gcs
#######################################
#--------------------------------------------
#@# MotionCor Thu Nov 27 17:35:42 EST 2014
ERROR: no run data found in /home/user/Desktop/structural/EY/mri. Make sure to
have a volume called 001.mgz in /home/user/Desktop/structural/EY/mri/orig.
If you have a second run of data call it 002.mgz, etc.
See also: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Conversion
/home/user/Desktop/structural/EY
mri_convert /home/user/Desktop/structural/EY/mri/rawavg.mgz /home/user/Desktop/structural/EY/mri/orig.mgz --conform
mri_convert /home/user/Desktop/structural/EY/mri/rawavg.mgz /home/user/Desktop/structural/EY/mri/orig.mgz --conform
$Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $
reading from /home/user/Desktop/structural/EY/mri/rawavg.mgz...
ERROR: cannot find /home/user/Desktop/structural/EY/mri/rawavg.mgz
mri_add_xform_to_header -c /home/user/Desktop/structural/EY/mri/transforms/talairach.xfm /home/user/Desktop/structural/EY/mri/orig.mgz /home/user/Desktop/structural/EY/mri/orig.mgz
mri_add_xform_to_header: could not open source file /home/user/Desktop/structural/EY/mri/orig.mgz
No such file or directory
#--------------------------------------------
#@# Nu Intensity Correction Thu Nov 27 17:35:43 EST 2014
mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2
ERROR: input volume orig.mgz does not exist
#--------------------------------------------
#@# Talairach Thu Nov 27 17:35:43 EST 2014
/home/user/Desktop/structural/EY/mri
talairach_avi --i nu.mgz --xfm transforms/talairach.auto.xfm
ERROR: input volume nu.mgz does not exist
cp transforms/talairach.auto.xfm transforms/talairach.xfm
cp: cannot stat `transforms/talairach.auto.xfm': No such file or directory
#--------------------------------------------
#@# Talairach Failure Detection Thu Nov 27 17:35:45 EST 2014
/home/user/Desktop/structural/EY/mri
talairach_afd -T 0.005 -xfm transforms/talairach.xfm
ltMNIreadEx: could not open file transforms/talairach.xfm
No such file or directory
ERROR: talairach_afd::Load_xfm(): could not open transforms/talairach.xfm
#--------------------------------------------
#@# Intensity Normalization Thu Nov 27 17:35:45 EST 2014
/home/user/Desktop/structural/EY/mri
mri_normalize -g 1 nu.mgz T1.mgz
using max gradient = 1.000
reading from nu.mgz...
mri_normalize: could not open source file nu.mgz
ERROR: cannot find /home/user/Desktop/structural/EY/mri/nu.mgz
No such file or directory
#--------------------------------------------
#@# Skull Stripping Thu Nov 27 17:35:45 EST 2014
/home/user/Desktop/structural/EY/mri
mri_em_register -skull nu.mgz /usr/local/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta
aligning to atlas containing skull, setting unknown_nbr_spacing = 5
reading 1 input volumes...
logging results to talairach_with_skull.log
reading '/usr/local/freesurfer/average/RB_all_withskull_2008-03-26.gca'...
average std = 23.1 using min determinant for regularization = 53.4
0 singular and 5702 ill-conditioned covariance matrices regularized
reading 'nu.mgz'...
mri_em_register: could not open input volume nu.mgz.
ERROR: cannot find /home/user/Desktop/structural/EY/mri/nu.mgz
No such file or directory
mri_watershed -T1 -brain_atlas /usr/local/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz
Mode: T1 normalized volume
ltaReadFile(transforms/talairach_with_skull.lta): can't open file
Mode: Use the information of atlas (default parms, --help for details)
No such file or directory
mri_watershed Error: Cannot read the transform
cp brainmask.auto.mgz brainmask.mgz
cp: cannot stat `brainmask.auto.mgz': No such file or directory
#-------------------------------------
#@# EM Registration Thu Nov 27 17:36:13 EST 2014
/home/user/Desktop/structural/EY/mri
mri_em_register -mask brainmask.mgz nu.mgz /usr/local/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.lta
using MR volume brainmask.mgz to mask input volume...
reading 1 input volumes...
logging results to talairach.log
reading '/usr/local/freesurfer/average/RB_all_2008-03-26.gca'...
average std = 6.9 using min determinant for regularization = 4.7
0 singular and 1812 ill-conditioned covariance matrices regularized
reading 'nu.mgz'...
mri_em_register: could not open input volume nu.mgz.
ERROR: cannot find /home/user/Desktop/structural/EY/mri/nu.mgz
No such file or directory
#--------------------------------------
#@# CA Normalize Thu Nov 27 17:36:21 EST 2014
/home/user/Desktop/structural/EY/mri
mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /usr/local/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.lta norm.mgz
writing control point volume to ctrl_pts.mgz
using MR volume brainmask.mgz to mask input volume...
reading 1 input volumes
reading atlas from '/usr/local/freesurfer/average/RB_all_2008-03-26.gca'...
reading transform from 'transforms/talairach.lta'...
ltaReadFile(transforms/talairach.lta): can't open file
No such file or directory
mri_ca_normalize: could not open xform file transforms/talairach.lta
No such file or directory
#--------------------------------------
#@# CA Reg Thu Nov 27 17:36:24 EST 2014
/home/user/Desktop/structural/EY/mri
mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /usr/local/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.m3z
ltaReadFile(transforms/talairach.lta): can't open file
not handling expanded ventricles...
No such file or directory
mri_ca_register: could not read transform file transforms/talairach.lta
No such file or directory
#--------------------------------------
#@# CA Reg Inv Thu Nov 27 17:36:24 EST 2014
/home/user/Desktop/structural/EY/mri
mri_ca_register -invert-and-save transforms/talairach.m3z
Loading, Inverting, Saving, Exiting ...
Reading transforms/talairach.m3z
ERROR: cannot find or read transforms/talairach.m3z
#--------------------------------------
#@# Remove Neck Thu Nov 27 17:36:25 EST 2014
INFO: transforms/talairach.m3z not found, using talairach.lta instead
mri_remove_neck -radius 25 nu.mgz transforms/talairach.lta /usr/local/freesurfer/average/RB_all_2008-03-26.gca nu_noneck.mgz
erasing everything more than 25 mm from possible brain
reading atlas '/usr/local/freesurfer/average/RB_all_2008-03-26.gca'...
reading input volume 'nu.mgz'...
mri_remove_neck: could not open input volume nu.mgz.
ERROR: cannot find /home/user/Desktop/structural/EY/mri/nu.mgz
No such file or directory
#--------------------------------------
#@# SkullLTA Thu Nov 27 17:36:28 EST 2014
mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz /usr/local/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta
aligning to atlas containing skull, setting unknown_nbr_spacing = 5
ltaReadFile(transforms/talairach.lta): can't open file
No such file or directory
Segmentation fault (core dumped)
#--------------------------------------
#@# SubCort Seg Thu Nov 27 17:36:28 EST 2014
mri_ca_label -align -nobigventricles norm.mgz transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz
mri_ca_label: could not read input MR volume from norm.mgz
renormalizing sequences with structure alignment, equivalent to:
-renormalize
-renormalize_mean 0.500
-regularize 0.500
not handling expanded ventricles...
reading 1 input volumes...
reading classifier array from /usr/local/freesurfer/average/RB_all_2008-03-26.gca...
reading input volume from norm.mgz...
ERROR: cannot find /home/user/Desktop/structural/EY/mri/norm.mgz
No such file or directory
mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz EY
reading input aseg from aseg.auto_noCCseg.mgz
writing aseg with cc labels to aseg.auto.mgz
mri_cc: could not read aseg volume from /home/user/Desktop/structural/EY/mri/aseg.auto_noCCseg.mgz
reading aseg from /home/user/Desktop/structural/EY/mri/aseg.auto_noCCseg.mgz
ERROR: cannot find /home/user/Desktop/structural/EY/mri/aseg.auto_noCCseg.mgz
No such file or directory
#--------------------------------------
#@# Merge ASeg Thu Nov 27 17:36:57 EST 2014
cp aseg.auto.mgz aseg.mgz
cp: cannot stat `aseg.auto.mgz': No such file or directory
#--------------------------------------------
#@# Intensity Normalization2 Thu Nov 27 17:36:57 EST 2014
/home/user/Desktop/structural/EY/mri
mri_normalize -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz
using segmentation for initial intensity normalization
reading from norm.mgz...
mri_normalize: could not open source file norm.mgz
using MR volume brainmask.mgz to mask input volume...
ERROR: cannot find /home/user/Desktop/structural/EY/mri/norm.mgz
No such file or directory
#--------------------------------------------
#@# Mask BFS Thu Nov 27 17:36:57 EST 2014
/home/user/Desktop/structural/EY/mri
mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz
threshold mask volume at 5
mri_mask: could not read source volume brain.mgz
ERROR: cannot find /home/user/Desktop/structural/EY/mri/brain.mgz
No such file or directory
#--------------------------------------------
#@# WM Segmentation Thu Nov 27 17:36:58 EST 2014
mri_segment brain.mgz wm.seg.mgz
mri_segment: could not read source volume from brain.mgz
ERROR: cannot find /home/user/Desktop/structural/EY/mri/brain.mgz
No such file or directory
mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.mgz wm.asegedit.mgz
preserving editing changes in input volume...
mri_edit_wm_with_aseg: could not read wm volume from wm.seg.mgz
reading wm segmentation from wm.seg.mgz...
ERROR: cannot find /home/user/Desktop/structural/EY/mri/wm.seg.mgz
No such file or directory
mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz
mri_pretess: could not open wm.asegedit.mgz
ERROR: cannot find /home/user/Desktop/structural/EY/mri/wm.asegedit.mgz
No such file or directory
#--------------------------------------------
#@# Fill Thu Nov 27 17:36:58 EST 2014
/home/user/Desktop/structural/EY/mri
mri_fill -a ../scripts/ponscc.cut.log -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz
logging cutting plane coordinates to ../scripts/ponscc.cut.log...
using segmentation aseg.auto_noCCseg.mgz...
reading input volume...mri_fill: could not read wm.mgz
ERROR: cannot find /home/user/Desktop/structural/EY/mri/wm.mgz
No such file or directory
#--------------------------------------------
#@# Tessellate lh Thu Nov 27 17:36:59 EST 2014
/home/user/Desktop/structural/EY/scripts
mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz
mri_pretess: could not open ../mri/filled.mgz
ERROR: cannot find ../mri/filled.mgz
No such file or directory
mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix
could not open ../mri/filled-pretess255.mgz
ERROR: cannot find ../mri/filled-pretess255.mgz
No such file or directory
rm -f ../mri/filled-pretess255.mgz
mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix
MRISread(../surf/lh.orig.nofix): could not open file
No such file or directory
Segmentation fault (core dumped)
#--------------------------------------------
#@# Smooth1 lh Thu Nov 27 17:37:00 EST 2014
mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix
/home/user/Desktop/structural/EY/scripts
setting seed for random number generator to 1234
MRISread(../surf/lh.orig.nofix): could not open file
No such file or directory
mris_smooth: could not read surface file ../surf/lh.orig.nofix
No such file or directory
#--------------------------------------------
#@# Inflation1 lh Thu Nov 27 17:37:00 EST 2014
mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix
/home/user/Desktop/structural/EY/scripts
MRISread(../surf/lh.smoothwm.nofix): could not open file
Not saving sulc
No such file or directory
mris_inflate: could not read surface file ../surf/lh.smoothwm.nofix
No such file or directory
#--------------------------------------------
#@# QSphere lh Thu Nov 27 17:37:00 EST 2014
/home/user/Desktop/structural/EY/scripts
mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix
doing quick spherical unfolding.
setting seed for random number genererator to 1234
$Id: mris_sphere.c,v 1.47 2007/03/08 18:36:08 greve Exp $
$Id: mrisurf.c,v 1.557.2.19 2009/08/05 22:10:21 nicks Exp $
MRISread(../surf/lh.inflated.nofix): could not open file
No such file or directory
mris_sphere: could not read surface file ../surf/lh.inflated.nofix
No such file or directory
#--------------------------------------------
#@# Fix Topology lh Thu Nov 27 17:37:00 EST 2014
cp ../surf/lh.orig.nofix ../surf/lh.orig
cp: cannot stat `../surf/lh.orig.nofix': No such file or directory
cp ../surf/lh.inflated.nofix ../surf/lh.inflated
cp: cannot stat `../surf/lh.inflated.nofix': No such file or directory
/home/user/Desktop/structural/EY/scripts
mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 EY lh
reading spherical homeomorphism from 'qsphere.nofix'
using genetic algorithm with optimized parameters
setting seed for random number genererator to 1234
*************************************************************
Topology Correction Parameters
retessellation mode: genetic search
number of patches/generation : 10
number of generations : 10
surface mri loglikelihood coefficient : 1.0
volume mri loglikelihood coefficient : 10.0
normal dot loglikelihood coefficient : 1.0
quadratic curvature loglikelihood coefficient : 1.0
volume resolution : 2
eliminate vertices during search : 1
initial patch selection : 1
select all defect vertices : 0
ordering dependant retessellation: 0
use precomputed edge table : 0
smooth retessellated patch : 2
match retessellated patch : 1
verbose mode : 0
*************************************************************
INFO: assuming .mgz format
$Id: mris_fix_topology.c,v 1.43 2007/01/05 16:57:16 nicks Exp $
$Id: mrisurf.c,v 1.557.2.19 2009/08/05 22:10:21 nicks Exp $
MRISread(/home/user/Desktop/structural/EY/surf/lh.qsphere.nofix): could not open file
reading input surface /home/user/Desktop/structural/EY/surf/lh.qsphere.nofix...
No such file or directory
mris_fix_topology: could not read input surface /home/user/Desktop/structural/EY/surf/lh.qsphere.nofix
No such file or directory
mris_euler_number ../surf/lh.orig
Linux ubuntu 3.2.0-23-generic-pae #36-Ubuntu SMP Tue Apr 10 22:19:09 UTC 2012 i686 i686 i386 GNU/Linux
recon-all exited with ERRORS at Thu Nov 27 17:37:01 EST 2014
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