INFO: SUBJECTS_DIR is /home/xonobo/FSRFsubjects
Actual FREESURFER_HOME /usr/local/freesurfer
-rw-rw-rw- 1 xonobo xonobo 639806 Apr 10 02:13 /home/xonobo/FSRFsubjects/bert/scripts/recon-all.log
Linux telenetPC 2.6.19-1.2911.fc6 #1 SMP Sat Feb 10 15:16:31 EST 2007 x86_64 x86_64 x86_64 GNU/Linux
#--------------------------------------------
#@# MotionCor Tue Apr 10 02:17:09 CEST 2007
Found 3 runs
/home/xonobo/FSRFsubjects/bert/mri/orig/001.mgz
/home/xonobo/FSRFsubjects/bert/mri/orig/002.mgz
/home/xonobo/FSRFsubjects/bert/mri/orig/003.mgz
#-----------------------------------------------
/home/xonobo/FSRFsubjects/bert

 mri_motion_correct.fsl -o /home/xonobo/FSRFsubjects/bert/mri/rawavg.mgz -wild /home/xonobo/FSRFsubjects/bert/mri/orig/001.mgz /home/xonobo/FSRFsubjects/bert/mri/orig/002.mgz /home/xonobo/FSRFsubjects/bert/mri/orig/003.mgz 

tmpdir is /home/xonobo/FSRFsubjects/bert/mri/tmp-mri_motion_correct.fsl-4704
--------------------------------------------------------------
mri_motion_correct.fsl logfile is /home/xonobo/FSRFsubjects/bert/mri/rawavg.mgz.mri_motion_correct.fsl.log
--------------------------------------------------------------
-----------------------------------------
Converting /home/xonobo/FSRFsubjects/bert/mri/orig/001.mgz 
Tue Apr 10 02:17:15 CEST 2007
/home/xonobo/FSRFsubjects/bert
mri_convert /home/xonobo/FSRFsubjects/bert/mri/orig/001.mgz /home/xonobo/FSRFsubjects/bert/mri/tmp-mri_motion_correct.fsl-4704/cor-1.img -odt float 
reading from /home/xonobo/FSRFsubjects/bert/mri/orig/001.mgz...
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)
changing data type from 0 to 3 (noscale = 0)...
writing to /home/xonobo/FSRFsubjects/bert/mri/tmp-mri_motion_correct.fsl-4704/cor-1.img...
Analyze Output Matrix
-1.000   0.000  -0.000   134.400;
-0.000   0.000   1.000  -111.000;
-0.000  -1.000  -0.000   129.000;
 0.000   0.000   0.000   1.000;
--------------------
INFO: set hdr.hist.orient to -1
-----------------------------------------
Converting /home/xonobo/FSRFsubjects/bert/mri/orig/002.mgz 
Tue Apr 10 02:17:17 CEST 2007
/home/xonobo/FSRFsubjects/bert
mri_convert /home/xonobo/FSRFsubjects/bert/mri/orig/002.mgz /home/xonobo/FSRFsubjects/bert/mri/tmp-mri_motion_correct.fsl-4704/cor-2.img -odt float 
reading from /home/xonobo/FSRFsubjects/bert/mri/orig/002.mgz...
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)
changing data type from 0 to 3 (noscale = 0)...
writing to /home/xonobo/FSRFsubjects/bert/mri/tmp-mri_motion_correct.fsl-4704/cor-2.img...
Analyze Output Matrix
-1.000   0.000  -0.000   134.400;
-0.000   0.000   1.000  -111.000;
-0.000  -1.000  -0.000   129.000;
 0.000   0.000   0.000   1.000;
--------------------
INFO: set hdr.hist.orient to -1
-----------------------------------------
Converting /home/xonobo/FSRFsubjects/bert/mri/orig/003.mgz 
Tue Apr 10 02:17:20 CEST 2007
/home/xonobo/FSRFsubjects/bert
mri_convert /home/xonobo/FSRFsubjects/bert/mri/orig/003.mgz /home/xonobo/FSRFsubjects/bert/mri/tmp-mri_motion_correct.fsl-4704/cor-3.img -odt float 
reading from /home/xonobo/FSRFsubjects/bert/mri/orig/003.mgz...
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)
changing data type from 0 to 3 (noscale = 0)...
writing to /home/xonobo/FSRFsubjects/bert/mri/tmp-mri_motion_correct.fsl-4704/cor-3.img...
Analyze Output Matrix
-1.000   0.000  -0.000   134.400;
-0.000   0.000   1.000  -111.000;
-0.000  -1.000  -0.000   129.000;
 0.000   0.000   0.000   1.000;
--------------------
INFO: set hdr.hist.orient to -1
-----------------------------------------
Motion Correcting /home/xonobo/FSRFsubjects/bert/mri/tmp-mri_motion_correct.fsl-4704/cor-2.img
Tue Apr 10 02:17:23 CEST 2007
/home/xonobo/FSRFsubjects/bert
fsl_rigid_register -maxangle 90 -r /home/xonobo/FSRFsubjects/bert/mri/tmp-mri_motion_correct.fsl-4704/cor-1.img -i /home/xonobo/FSRFsubjects/bert/mri/tmp-mri_motion_correct.fsl-4704/cor-2.img -o /home/xonobo/FSRFsubjects/bert/mri/tmp-mri_motion_correct.fsl-4704/resampled.img -tmpdir /home/xonobo/FSRFsubjects/bert/mri/tmp-mri_motion_correct.fsl-4704 -cleanup
\n\n
$Id: fsl_rigid_register,v 1.14 2006/02/13 20:13:19 greve Exp $
Tue Apr 10 02:17:23 CEST 2007
/home/xonobo/FSRFsubjects/bert/mri/tmp-mri_motion_correct.fsl-4704/resampled.img
Reference is analyze, not converting
Input is analyze, not converting
Output is analyze, not converting
--------------------------------------
/home/xonobo/FSRFsubjects/bert
calling eval flirt -in /home/xonobo/FSRFsubjects/bert/mri/tmp-mri_motion_correct.fsl-4704/cor-2.hdr -out /home/xonobo/FSRFsubjects/bert/mri/tmp-mri_motion_correct.fsl-4704/resampled.hdr -bins 256 -cost corratio -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -interp trilinear -dof 6 -ref /home/xonobo/FSRFsubjects/bert/mri/tmp-mri_motion_correct.fsl-4704/cor-1.hdr -omat /home/xonobo/FSRFsubjects/bert/mri/tmp-mri_motion_correct.fsl-4704/resampled.fslmat
WARNING: Both reference and input images have an sform matrix set
  The output image will use the sform from the reference image
 
Started at Tue Apr 10 02:17:23 CEST 2007 
Ended   at Tue Apr 10 02:21:22 CEST 2007
 
fsl_rigid_register Done
 
To check results, run:
tkmedit -f /home/xonobo/FSRFsubjects/bert/mri/tmp-mri_motion_correct.fsl-4704/cor-1.img -aux /home/xonobo/FSRFsubjects/bert/mri/tmp-mri_motion_correct.fsl-4704/resampled.img
 
mv /home/xonobo/FSRFsubjects/bert/mri/tmp-mri_motion_correct.fsl-4704/resampled.img /home/xonobo/FSRFsubjects/bert/mri/tmp-mri_motion_correct.fsl-4704/cor-2.img
-----------------------------------------
Motion Correcting /home/xonobo/FSRFsubjects/bert/mri/tmp-mri_motion_correct.fsl-4704/cor-3.img
Tue Apr 10 02:21:23 CEST 2007
/home/xonobo/FSRFsubjects/bert
fsl_rigid_register -maxangle 90 -r /home/xonobo/FSRFsubjects/bert/mri/tmp-mri_motion_correct.fsl-4704/cor-1.img -i /home/xonobo/FSRFsubjects/bert/mri/tmp-mri_motion_correct.fsl-4704/cor-3.img -o /home/xonobo/FSRFsubjects/bert/mri/tmp-mri_motion_correct.fsl-4704/resampled.img -tmpdir /home/xonobo/FSRFsubjects/bert/mri/tmp-mri_motion_correct.fsl-4704 -cleanup
\n\n
$Id: fsl_rigid_register,v 1.14 2006/02/13 20:13:19 greve Exp $
Tue Apr 10 02:21:23 CEST 2007
/home/xonobo/FSRFsubjects/bert/mri/tmp-mri_motion_correct.fsl-4704/resampled.img
Reference is analyze, not converting
Input is analyze, not converting
Output is analyze, not converting
--------------------------------------
/home/xonobo/FSRFsubjects/bert
calling eval flirt -in /home/xonobo/FSRFsubjects/bert/mri/tmp-mri_motion_correct.fsl-4704/cor-3.hdr -out /home/xonobo/FSRFsubjects/bert/mri/tmp-mri_motion_correct.fsl-4704/resampled.hdr -bins 256 -cost corratio -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -interp trilinear -dof 6 -ref /home/xonobo/FSRFsubjects/bert/mri/tmp-mri_motion_correct.fsl-4704/cor-1.hdr -omat /home/xonobo/FSRFsubjects/bert/mri/tmp-mri_motion_correct.fsl-4704/resampled.fslmat
WARNING: Both reference and input images have an sform matrix set
  The output image will use the sform from the reference image
 
Started at Tue Apr 10 02:21:23 CEST 2007 
Ended   at Tue Apr 10 02:25:26 CEST 2007
 
fsl_rigid_register Done
 
To check results, run:
tkmedit -f /home/xonobo/FSRFsubjects/bert/mri/tmp-mri_motion_correct.fsl-4704/cor-1.img -aux /home/xonobo/FSRFsubjects/bert/mri/tmp-mri_motion_correct.fsl-4704/resampled.img
 
mv /home/xonobo/FSRFsubjects/bert/mri/tmp-mri_motion_correct.fsl-4704/resampled.img /home/xonobo/FSRFsubjects/bert/mri/tmp-mri_motion_correct.fsl-4704/cor-3.img
-----------------------------------------
Averaging 
Tue Apr 10 02:25:26 CEST 2007
/home/xonobo/FSRFsubjects/bert
inhibiting isotropic volume interpolation
1 of 3: reading /home/xonobo/FSRFsubjects/bert/mri/tmp-mri_motion_correct.fsl-4704/cor-1.img...
2 of 3: reading /home/xonobo/FSRFsubjects/bert/mri/tmp-mri_motion_correct.fsl-4704/cor-2.img...
3 of 3: reading /home/xonobo/FSRFsubjects/bert/mri/tmp-mri_motion_correct.fsl-4704/cor-3.img...
writing to /home/xonobo/FSRFsubjects/bert/mri/tmp-mri_motion_correct.fsl-4704/avgvol.img...
alignment and averaging took 0 minutes and 28 seconds.
Analyze Output Matrix
-1.000   0.000   0.000   134.400;
 0.000   0.000   1.000  -111.000;
 0.000  -1.000   0.000   129.000;
 0.000   0.000   0.000   1.000;
--------------------
INFO: set hdr.hist.orient to -1
-----------------------------------------
Converting Average to output 
Tue Apr 10 02:25:54 CEST 2007
/home/xonobo/FSRFsubjects/bert
mri_convert /home/xonobo/FSRFsubjects/bert/mri/tmp-mri_motion_correct.fsl-4704/avgvol.img /home/xonobo/FSRFsubjects/bert/mri/rawavg.mgz -tr 0 -te 0 -TI 0 -flip_angle 0
mri_convert /home/xonobo/FSRFsubjects/bert/mri/tmp-mri_motion_correct.fsl-4704/avgvol.img /home/xonobo/FSRFsubjects/bert/mri/rawavg.mgz -tr 0 -te 0 -TI 0 -flip_angle 0 
reading from /home/xonobo/FSRFsubjects/bert/mri/tmp-mri_motion_correct.fsl-4704/avgvol.img...
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/xonobo/FSRFsubjects/bert/mri/rawavg.mgz...
-----------------------------------------
Started at: Tue Apr 10 02:17:10 CEST 2007
Ended at:   Tue Apr 10 02:26:01 CEST 2007
mri_motion_correct.fsl: done
/home/xonobo/FSRFsubjects/bert

 mri_convert /home/xonobo/FSRFsubjects/bert/mri/rawavg.mgz /home/xonobo/FSRFsubjects/bert/mri/orig.mgz --conform 

mri_convert /home/xonobo/FSRFsubjects/bert/mri/rawavg.mgz /home/xonobo/FSRFsubjects/bert/mri/orig.mgz --conform 
reading from /home/xonobo/FSRFsubjects/bert/mri/rawavg.mgz...
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)
Original Data has (1, 1, 1) mm size and (256, 256, 256) voxels.
Data is conformed to 1 mm size and 256 voxels for all directions
changing data type from 3 to 0 (noscale = 0)...
MRIchangeType: Building histogram 
writing to /home/xonobo/FSRFsubjects/bert/mri/orig.mgz...

 mri_add_xform_to_header -c /home/xonobo/FSRFsubjects/bert/mri/transforms/talairach.xfm /home/xonobo/FSRFsubjects/bert/mri/orig.mgz /home/xonobo/FSRFsubjects/bert/mri/orig.mgz 

INFO: extension is mgz
#--------------------------------------------
#@# Nu Intensity Correction Tue Apr 10 02:26:15 CEST 2007

 mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2 

/home/xonobo/FSRFsubjects/bert/mri
/usr/local/freesurfer/bin/mri_nu_correct.mni
--i orig.mgz --o nu.mgz --n 2
nIters 2
$Id: mri_nu_correct.mni,v 1.3.2.1 2006/11/24 20:16:38 nicks Exp $
Linux telenetPC 2.6.19-1.2911.fc6 #1 SMP Sat Feb 10 15:16:31 EST 2007 x86_64 x86_64 x86_64 GNU/Linux
Tue Apr 10 02:26:15 CEST 2007
Program nu_correct, built from:
Package MNI N3, version 1.10, compiled by nicks@kani (i686-pc-linux-gnu) on 2005-11-15 at 21:02:27
tmpdir is ./tmp.mri_nu_correct.mni.5425
/home/xonobo/FSRFsubjects/bert/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.5425/nu0.mnc
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.5425/nu0.mnc 
reading from orig.mgz...
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 ./tmp.mri_nu_correct.mni.5425/nu0.mnc...
 
--------------------------------------------------------
Iteration 1 Tue Apr 10 02:26:21 CEST 2007
nu_correct -clobber ./tmp.mri_nu_correct.mni.5425/nu0.mnc ./tmp.mri_nu_correct.mni.5425/nu1.mnc
[root@telenetPC:/home/xonobo/FSRFsubjects/bert/mri/] [2007-04-10 02:26:21] running:
  /usr/local/freesurfer/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 /usr/tmp/nu_correct_5494/ ./tmp.mri_nu_correct.mni.5425/nu0.mnc ./tmp.mri_nu_correct.mni.5425/nu1.imp

Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Not implemented yet in cache_volume_range_has_changed()
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Not implemented yet in cache_volume_range_has_changed()
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Not implemented yet in cache_volume_range_has_changed()
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Not implemented yet in cache_volume_range_has_changed()
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Not implemented yet in cache_volume_range_has_changed()
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Not implemented yet in cache_volume_range_has_changed()
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Not implemented yet in cache_volume_range_has_changed()
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Not implemented yet in cache_volume_range_has_changed()
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Not implemented yet in cache_volume_range_has_changed()
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Not implemented yet in cache_volume_range_has_changed()
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Not implemented yet in cache_volume_range_has_changed()
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Not implemented yet in cache_volume_range_has_changed()
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Not implemented yet in cache_volume_range_has_changed()
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Not implemented yet in cache_volume_range_has_changed()
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Not implemented yet in cache_volume_range_has_changed()
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Not implemented yet in cache_volume_range_has_changed()
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Not implemented yet in cache_volume_range_has_changed()
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Not implemented yet in cache_volume_range_has_changed()
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Not implemented yet in cache_volume_range_has_changed()
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Not implemented yet in cache_volume_range_has_changed()
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Not implemented yet in cache_volume_range_has_changed()
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Not implemented yet in cache_volume_range_has_changed()
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Not implemented yet in cache_volume_range_has_changed()
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Not implemented yet in cache_volume_range_has_changed()
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Not implemented yet in cache_volume_range_has_changed()
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Not implemented yet in cache_volume_range_has_changed()
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Not implemented yet in cache_volume_range_has_changed()
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Not implemented yet in cache_volume_range_has_changed()
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Not implemented yet in cache_volume_range_has_changed()
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Not implemented yet in cache_volume_range_has_changed()
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Not implemented yet in cache_volume_range_has_changed()
Number of iterations: 31 
CV of field change: 0.000949366
[root@telenetPC:/home/xonobo/FSRFsubjects/bert/mri/] [2007-04-10 02:27:02] running:
  /usr/local/freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.5425/nu0.mnc /usr/tmp/nu_correct_5494//template.mnc

Transforming slices:......................................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Not implemented yet in cache_volume_range_has_changed()
Transforming slices:................................................................................................................................................................................................................................................................Done
 
 
--------------------------------------------------------
Iteration 2 Tue Apr 10 02:27:07 CEST 2007
nu_correct -clobber ./tmp.mri_nu_correct.mni.5425/nu1.mnc ./tmp.mri_nu_correct.mni.5425/nu2.mnc
[root@telenetPC:/home/xonobo/FSRFsubjects/bert/mri/] [2007-04-10 02:27:07] running:
  /usr/local/freesurfer/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 /usr/tmp/nu_correct_5978/ ./tmp.mri_nu_correct.mni.5425/nu1.mnc ./tmp.mri_nu_correct.mni.5425/nu2.imp

Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Not implemented yet in cache_volume_range_has_changed()
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Not implemented yet in cache_volume_range_has_changed()
Number of iterations: 2 
CV of field change: 0.000645687
[root@telenetPC:/home/xonobo/FSRFsubjects/bert/mri/] [2007-04-10 02:27:12] running:
  /usr/local/freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.5425/nu1.mnc /usr/tmp/nu_correct_5978//template.mnc

Transforming slices:......................................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Not implemented yet in cache_volume_range_has_changed()
Transforming slices:................................................................................................................................................................................................................................................................Done
 
 
 
mri_convert ./tmp.mri_nu_correct.mni.5425/nu2.mnc nu.mgz --like orig.mgz
mri_convert ./tmp.mri_nu_correct.mni.5425/nu2.mnc nu.mgz --like orig.mgz 
reading from ./tmp.mri_nu_correct.mni.5425/nu2.mnc...
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)
INFO: transform src into the like-volume: orig.mgz
writing to nu.mgz...
 
 
Tue Apr 10 02:27:28 CEST 2007
mri_nu_correct.mni done
#--------------------------------------------
#@# Talairach Tue Apr 10 02:27:28 CEST 2007
/home/xonobo/FSRFsubjects/bert/mri

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

/home/xonobo/FSRFsubjects/bert/mri
/usr/local/freesurfer/bin/talairach
--i nu.mgz --xfm transforms/talairach.auto.xfm
$Id: talairach,v 1.2 2005/12/12 23:04:35 greve Exp $
Linux telenetPC 2.6.19-1.2911.fc6 #1 SMP Sat Feb 10 15:16:31 EST 2007 x86_64 x86_64 x86_64 GNU/Linux
Tue Apr 10 02:27:28 CEST 2007
tmpdir is transforms/tmp.talairach.6098
/home/xonobo/FSRFsubjects/bert/mri
mri_convert nu.mgz transforms/tmp.talairach.6098/src.mnc
mri_convert nu.mgz transforms/tmp.talairach.6098/src.mnc 
reading from nu.mgz...
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 transforms/tmp.talairach.6098/src.mnc...
--------------------------------------------
mritotal -verbose -debug -clobber -modeldir /usr/local/freesurfer/mni/bin/../share/mni_autoreg -protocol icbm transforms/tmp.talairach.6098/src.mnc transforms/talairach.auto.xfm
 
 
Tue Apr 10 02:28:03 CEST 2007
talairach done
#--------------------------------------------
#@# Intensity Normalization Tue Apr 10 02:28:03 CEST 2007
/home/xonobo/FSRFsubjects/bert/mri

 mri_normalize -g 1 -f /home/xonobo/FSRFsubjects/bert/tmp/control.dat nu.mgz T1.mgz 

using max gradient = 1.000
using control points from file /home/xonobo/FSRFsubjects/bert/tmp/control.dat...
reading from nu.mgz...
normalizing image...
Reading 0 control points...
only using 0 control points from file...
building Voronoi diagram...
performing soap bubble smoothing...
talairach transform
 1.155  -0.024   0.036  -5.713;
 0.015   0.943   0.136  -21.721;
-0.039  -0.161   1.123  -0.750;
 0.000   0.000   0.000   1.000;
INFO: Modifying talairach volume c_(r,a,s) based on average_305
building Voronoi diagram...
performing soap bubble smoothing...
3d normalization pass 1 of 2
building Voronoi diagram...
performing soap bubble smoothing...
3d normalization pass 2 of 2
building Voronoi diagram...
performing soap bubble smoothing...
writing output to T1.mgz
3D bias adjustment took 3 minutes and 54 seconds.
white matter peak found at 110
gm peak at 82 (82), valley at 23 (23)
csf peak at 41, setting threshold to 68
white matter peak found at 110
gm peak at 83 (83), valley at 53 (53)
csf peak at 42, setting threshold to 69
#--------------------------------------------
#@# Skull Stripping Tue Apr 10 02:31:59 CEST 2007
/home/xonobo/FSRFsubjects/bert/mri

 mri_watershed -keep brainmask.auto.mgz brainmask.mgz brainmask.mgz T1.mgz brainmask.auto.mgz 



*********************************************************
The input file is T1.mgz
The output file is brainmask.auto.mgz
If this is incorrect, please exit with CTL-C


*************************WATERSHED**************************
preflooding height equal to 25 percent
Sorting...
      T1-weighted MRI image
      modification of the preflooding height to 15 percent
      Count how many 110 voxels are present :  298937

      Find the largest 110-component...
             heap usage = 369700 Kbytes.
             removing small segments (less than 1 percent of maxarea).done
      And identify it as the main brain basin...done
      Main component: 290035 voxels
      first estimation of the COG coord: x=127 y=114 z=112 r=87
      first estimation of the main basin volume: 2853333 voxels
      global maximum in x=110, y=93, z=70, Imax=255
      CSF=17, WM_intensity=110, WM_VARIANCE=5
      WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110 
done
Analyze

      main basin size= 2007469 voxels, voxel volume =1.000 
                     = 2007469 mmm3 = 2007.469 cm3
done
PostAnalyze...
      ***** 0 basin(s) merged in 1 iteration(s)
      ***** 0 voxel(s) added to the main basin
done

****************TEMPLATE DEFORMATION****************

      second estimation of the COG coord: x=128,y=127, z=119, r=13192 iterations
 Problem with the least square interpolation in GM_MIN calculation.
      before analyzing : CSF_MAX=22, TRANSITION=41, GM_MIN=66, GM=86
      after  analyzing : CSF_MAX=22, TRANSITION=57, GM_MIN=66, GM=64
      mri_strip_skull: done peeling brain
      highly tesselated surface with 10242 vertices
      matching...74 iterations

*********************VALIDATION*********************

No Rigid alignment: Atlas Mode Off
      before rotation: sse = 4.94, sigma = 7.25
      after  rotation: sse = 4.94, sigma = 7.25
Localization of inacurate regions: Erosion-Dilation steps
      the sse mean is  5.44, its var is  6.11   
      before Erosion-Dilatation  5.57% of inacurate vertices
      after  Erosion-Dilatation  5.65% of inacurate vertices
            36.79% of 'positive' inacurate vertices
            63.21% of 'negative' inacurate vertices

      THE SEGMENTATION IS PROBABLY NOT CORRECT
**********************************************
**********************************************
      If the final segmentation is not valid,
      try using the option '-atlas'
**********************************************
**********************************************

Scaling of atlas fields onto current surface fields

********FINAL ITERATIVE TEMPLATE DEFORMATION********
Compute Local values csf/gray
Fine Segmentation...45 iterations

      mri_strip_skull: done peeling brain

Brain Size = 1772841 voxels, voxel volume = 1.000 mm3
           = 1772841 mmm3 = 1772.841 cm3


******************************
Save...done
Keeping brain edits brainmask.auto.mgz brainmask.mgz
  Talairach transform /usr/local/freesurfer/subjects/bert/mri/transforms/talairach.xfm does not exist ...
Loading tal xfm file /home/xonobo/FSRFsubjects/bert/mri/transforms/talairach.xfm
  Talairach transform /usr/local/freesurfer/subjects/bert/mri/transforms/talairach.xfm does not exist ...
Loading tal xfm file /home/xonobo/FSRFsubjects/bert/mri/transforms/talairach.xfm
Keeping edits ...
Saving kept edits to brainmask.mgz .....

#------------------------------------------

recon-all finished without error at Tue Apr 10 02:33:19 CEST 2007
done
