/home/ialtarelli/freesurfer/bin/xhemireg
--s ac_copie
$Id: xhemireg,v 1.22 2012/01/20 20:12:32 greve Exp $
mardi 29 mai 2012, 18:23:42 (UTC+0200)
Linux lscp-iao1 2.6.32-5-amd64 #1 SMP Mon Jan 16 16:22:28 UTC 2012 x86_64 GNU/Linux
/home/ialtarelli/DATABASE/Karla5/ac_copie
setenv SUBJECTS_DIR /home/ialtarelli/DATABASE/Karla5/ 
mardi 29 mai 2012, 18:23:42 (UTC+0200)
mardi 29 mai 2012, 18:23:42 (UTC+0200)
mri_vol2vol --mov mri/orig.mgz --targ mri/orig.mgz --reg /home/ialtarelli/DATABASE/Karla5//ac_copie/xhemi/lrrev.register.dat --o /home/ialtarelli/DATABASE/Karla5//ac_copie/xhemi/mri/orig.mgz --keep-precision --no-save-reg

Matrix from regfile:
-1.000   0.000   0.000   1.000;
 0.000   1.000   0.000   0.000;
 0.000   0.000   1.000   0.000;
 0.000   0.000   0.000   1.000;

movvol mri/orig.mgz
targvol mri/orig.mgz
outvol /home/ialtarelli/DATABASE/Karla5//ac_copie/xhemi/mri/orig.mgz
regfile /home/ialtarelli/DATABASE/Karla5//ac_copie/xhemi/lrrev.register.dat
invert 0
tal    0
talres 2
regheader 0
noresample 0
interp  trilinear (1)
precision  uchar (0)
Gdiag_no  -1
Synth      0
SynthSeed  1338519975
Resampling
Output registration matrix is identity

mri_vol2vol done
mri_vol2vol --mov mri/T1.mgz --targ mri/T1.mgz --reg /home/ialtarelli/DATABASE/Karla5//ac_copie/xhemi/lrrev.register.dat --o /home/ialtarelli/DATABASE/Karla5//ac_copie/xhemi/mri/T1.mgz --keep-precision --no-save-reg

Matrix from regfile:
-1.000   0.000   0.000   1.000;
 0.000   1.000   0.000   0.000;
 0.000   0.000   1.000   0.000;
 0.000   0.000   0.000   1.000;

movvol mri/T1.mgz
targvol mri/T1.mgz
outvol /home/ialtarelli/DATABASE/Karla5//ac_copie/xhemi/mri/T1.mgz
regfile /home/ialtarelli/DATABASE/Karla5//ac_copie/xhemi/lrrev.register.dat
invert 0
tal    0
talres 2
regheader 0
noresample 0
interp  trilinear (1)
precision  uchar (0)
Gdiag_no  -1
Synth      0
SynthSeed  1339218149
Resampling
Output registration matrix is identity

mri_vol2vol done
mri_vol2vol --mov mri/brain.mgz --targ mri/brain.mgz --reg /home/ialtarelli/DATABASE/Karla5//ac_copie/xhemi/lrrev.register.dat --o /home/ialtarelli/DATABASE/Karla5//ac_copie/xhemi/mri/brain.mgz --keep-precision --no-save-reg

Matrix from regfile:
-1.000   0.000   0.000   1.000;
 0.000   1.000   0.000   0.000;
 0.000   0.000   1.000   0.000;
 0.000   0.000   0.000   1.000;

movvol mri/brain.mgz
targvol mri/brain.mgz
outvol /home/ialtarelli/DATABASE/Karla5//ac_copie/xhemi/mri/brain.mgz
regfile /home/ialtarelli/DATABASE/Karla5//ac_copie/xhemi/lrrev.register.dat
invert 0
tal    0
talres 2
regheader 0
noresample 0
interp  trilinear (1)
precision  uchar (0)
Gdiag_no  -1
Synth      0
SynthSeed  1338816872
Resampling
Output registration matrix is identity

mri_vol2vol done
mri_vol2vol --mov mri/brainmask.mgz --targ mri/brainmask.mgz --reg /home/ialtarelli/DATABASE/Karla5//ac_copie/xhemi/lrrev.register.dat --o /home/ialtarelli/DATABASE/Karla5//ac_copie/xhemi/mri/brainmask.mgz --keep-precision --no-save-reg

Matrix from regfile:
-1.000   0.000   0.000   1.000;
 0.000   1.000   0.000   0.000;
 0.000   0.000   1.000   0.000;
 0.000   0.000   0.000   1.000;

movvol mri/brainmask.mgz
targvol mri/brainmask.mgz
outvol /home/ialtarelli/DATABASE/Karla5//ac_copie/xhemi/mri/brainmask.mgz
regfile /home/ialtarelli/DATABASE/Karla5//ac_copie/xhemi/lrrev.register.dat
invert 0
tal    0
talres 2
regheader 0
noresample 0
interp  trilinear (1)
precision  uchar (0)
Gdiag_no  -1
Synth      0
SynthSeed  1338547514
Resampling
Output registration matrix is identity

mri_vol2vol done
mri_vol2vol --mov mri/norm.mgz --targ mri/norm.mgz --reg /home/ialtarelli/DATABASE/Karla5//ac_copie/xhemi/lrrev.register.dat --o /home/ialtarelli/DATABASE/Karla5//ac_copie/xhemi/mri/norm.mgz --keep-precision --no-save-reg

Matrix from regfile:
-1.000   0.000   0.000   1.000;
 0.000   1.000   0.000   0.000;
 0.000   0.000   1.000   0.000;
 0.000   0.000   0.000   1.000;

movvol mri/norm.mgz
targvol mri/norm.mgz
outvol /home/ialtarelli/DATABASE/Karla5//ac_copie/xhemi/mri/norm.mgz
regfile /home/ialtarelli/DATABASE/Karla5//ac_copie/xhemi/lrrev.register.dat
invert 0
tal    0
talres 2
regheader 0
noresample 0
interp  trilinear (1)
precision  uchar (0)
Gdiag_no  -1
Synth      0
SynthSeed  1339303630
Resampling
Output registration matrix is identity

mri_vol2vol done
mri_vol2vol --mov mri/aseg.mgz --targ mri/aseg.mgz --reg /home/ialtarelli/DATABASE/Karla5//ac_copie/xhemi/lrrev.register.dat --o /home/ialtarelli/DATABASE/Karla5//ac_copie/xhemi/mri/aseg.mgz --keep-precision --no-save-reg

Matrix from regfile:
-1.000   0.000   0.000   1.000;
 0.000   1.000   0.000   0.000;
 0.000   0.000   1.000   0.000;
 0.000   0.000   0.000   1.000;

movvol mri/aseg.mgz
targvol mri/aseg.mgz
outvol /home/ialtarelli/DATABASE/Karla5//ac_copie/xhemi/mri/aseg.mgz
regfile /home/ialtarelli/DATABASE/Karla5//ac_copie/xhemi/lrrev.register.dat
invert 0
tal    0
talres 2
regheader 0
noresample 0
interp  trilinear (1)
precision  uchar (0)
Gdiag_no  -1
Synth      0
SynthSeed  1338957273
Resampling
Output registration matrix is identity

mri_vol2vol done
mri_convert /home/ialtarelli/DATABASE/Karla5//ac_copie/xhemi/mri/aseg.mgz /home/ialtarelli/DATABASE/Karla5//ac_copie/xhemi/mri/aseg.mgz --left-right-swap-label
mri_convert /home/ialtarelli/DATABASE/Karla5//ac_copie/xhemi/mri/aseg.mgz /home/ialtarelli/DATABASE/Karla5//ac_copie/xhemi/mri/aseg.mgz --left-right-swap-label 
$Id: mri_convert.c,v 1.194 2012/04/13 03:44:23 greve Exp $
reading from /home/ialtarelli/DATABASE/Karla5//ac_copie/xhemi/mri/aseg.mgz...
Performing left-right swap of labels
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
writing to /home/ialtarelli/DATABASE/Karla5//ac_copie/xhemi/mri/aseg.mgz...
mri_vol2vol --mov mri/aparc+aseg.mgz --targ mri/aparc+aseg.mgz --reg /home/ialtarelli/DATABASE/Karla5//ac_copie/xhemi/lrrev.register.dat --o /home/ialtarelli/DATABASE/Karla5//ac_copie/xhemi/mri/aparc+aseg.mgz --keep-precision --no-save-reg

Matrix from regfile:
-1.000   0.000   0.000   1.000;
 0.000   1.000   0.000   0.000;
 0.000   0.000   1.000   0.000;
 0.000   0.000   0.000   1.000;

movvol mri/aparc+aseg.mgz
targvol mri/aparc+aseg.mgz
outvol /home/ialtarelli/DATABASE/Karla5//ac_copie/xhemi/mri/aparc+aseg.mgz
regfile /home/ialtarelli/DATABASE/Karla5//ac_copie/xhemi/lrrev.register.dat
invert 0
tal    0
talres 2
regheader 0
noresample 0
interp  trilinear (1)
precision  int (1)
Gdiag_no  -1
Synth      0
SynthSeed  1339184551
Resampling
Output registration matrix is identity

mri_vol2vol done
mri_convert /home/ialtarelli/DATABASE/Karla5//ac_copie/xhemi/mri/aparc+aseg.mgz /home/ialtarelli/DATABASE/Karla5//ac_copie/xhemi/mri/aparc+aseg.mgz --left-right-swap-label
mri_convert /home/ialtarelli/DATABASE/Karla5//ac_copie/xhemi/mri/aparc+aseg.mgz /home/ialtarelli/DATABASE/Karla5//ac_copie/xhemi/mri/aparc+aseg.mgz --left-right-swap-label 
$Id: mri_convert.c,v 1.194 2012/04/13 03:44:23 greve Exp $
reading from /home/ialtarelli/DATABASE/Karla5//ac_copie/xhemi/mri/aparc+aseg.mgz...
Performing left-right swap of labels
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
writing to /home/ialtarelli/DATABASE/Karla5//ac_copie/xhemi/mri/aparc+aseg.mgz...
mardi 29 mai 2012, 18:24:20 (UTC+0200)
recon-all -sb ac_copie/xhemi -talairach
Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0
Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0
INFO: SUBJECTS_DIR is /home/ialtarelli/DATABASE/Karla5
Actual FREESURFER_HOME /home/ialtarelli/freesurfer
Linux lscp-iao1 2.6.32-5-amd64 #1 SMP Mon Jan 16 16:22:28 UTC 2012 x86_64 GNU/Linux
#--------------------------------------------
#@# Talairach Tue May 29 18:24:25 CEST 2012
/home/ialtarelli/DATABASE/Karla5/ac_copie/xhemi/mri

 talairach_avi --i nu.mgz --xfm transforms/talairach.auto.xfm 

ERROR: input volume nu.mgz does not exist
Linux lscp-iao1 2.6.32-5-amd64 #1 SMP Mon Jan 16 16:22:28 UTC 2012 x86_64 GNU/Linux

recon-all -s ac_copie/xhemi exited with ERRORS at Tue May 29 18:24:26 CEST 2012