[fsl@localhost structural]$ preproc-sess -force -surface self lhrh -fwhm 5 -s LD08
--------------------------------------------------------------
preproc-sess logfile is log/preproc-sess.log
--------------------------------------------------------------
$Id: preproc-sess,v 1.31.2.4 2010/07/26 15:55:24 greve Exp $
fsl
setenv FREESURFER_HOME /usr/local/freesurfer
setenv SUBJECTS_DIR /home/fsl/structural
Linux localhost.localdomain 2.6.18-128.1.6.el5 #1 SMP Wed Apr 1 09:10:25 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux
/home/fsl/structural
/usr/local/freesurfer/fsfast/bin/preproc-sess
-force -surface self lhrh -fwhm 5 -s LD08
Tue Apr  5 07:38:35 BST 2011
instem   f 
mc   1     f fmcpr 
stc  0     fmcpr
sm   0   
mask 1   brain
LD08 Template -----------------------------
mktemplate-sess -s LD08 -d /home/fsl/structural -fsd bold
 
Session: /home/fsl/structural/LD08 ----------------
Tue Apr  5 07:38:35 BST 2011
Detected input format at nii
/home/fsl/structural
mri_convert /home/fsl/structural/LD08/bold/001/f.nii /home/fsl/structural/LD08/bold/template.nii --frame 0
mri_convert /home/fsl/structural/LD08/bold/001/f.nii /home/fsl/structural/LD08/bold/template.nii --frame 0 
$Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $
reading from /home/fsl/structural/LD08/bold/001/f.nii...
TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.999754, 0.00122074, 0.0221564)
j_ras = (0.00198375, 0.999446, 0.0332345)
k_ras = (0.0221035, -0.0332703, 0.999202)
keeping frame 0
writing to /home/fsl/structural/LD08/bold/template.nii...
  Run: 001 ----------------
  Tue Apr  5 07:38:36 BST 2011
/home/fsl/structural
mri_convert /home/fsl/structural/LD08/bold/001/f.nii /home/fsl/structural/LD08/bold/001/template.nii --mid-frame
mri_convert /home/fsl/structural/LD08/bold/001/f.nii /home/fsl/structural/LD08/bold/001/template.nii --mid-frame 
$Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $
reading from /home/fsl/structural/LD08/bold/001/f.nii...
TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.999754, 0.00122074, 0.0221564)
j_ras = (0.00198375, 0.999446, 0.0332345)
k_ras = (0.0221035, -0.0332703, 0.999202)
keeping frame 74
writing to /home/fsl/structural/LD08/bold/001/template.nii...
  Run: 002 ----------------
  Tue Apr  5 07:38:37 BST 2011
/home/fsl/structural
mri_convert /home/fsl/structural/LD08/bold/002/f.nii /home/fsl/structural/LD08/bold/002/template.nii --mid-frame
mri_convert /home/fsl/structural/LD08/bold/002/f.nii /home/fsl/structural/LD08/bold/002/template.nii --mid-frame 
$Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $
reading from /home/fsl/structural/LD08/bold/002/f.nii...
TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.999754, 0.00122074, 0.0221564)
j_ras = (0.00198375, 0.999446, 0.0332345)
k_ras = (0.0221035, -0.0332703, 0.999202)
keeping frame 74
writing to /home/fsl/structural/LD08/bold/002/template.nii...
Tue Apr  5 07:38:38 BST 2011
mktemplate-sess completed 
LD08 Mask ------------------------
mkbrainmask-sess -maskstem brain -fsd bold -s LD08 -d /home/fsl/structural
------------------------------------------------
/home/fsl/structural/LD08 
Tue Apr  5 07:38:38 BST 2011
mkbrainmask -i template.nii -o masks/brain.nii -thresh 0.1 -ndil 1 -nerode 0
FSLMATHS fslmaths
Scratch Dir is /tmp/mkbrainmask_10655
/home/fsl/structural/LD08/bold
mri_convert template.nii /tmp/mkbrainmask_10655/in.nii
mri_convert template.nii /tmp/mkbrainmask_10655/in.nii 
$Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $
reading from template.nii...
TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.999754, 0.00122074, 0.0221564)
j_ras = (0.00198375, 0.999446, 0.0332345)
k_ras = (0.0221035, -0.0332703, 0.999202)
writing to /tmp/mkbrainmask_10655/in.nii...
# ---------- Using FSL's BET to Extract Brain------------------ #
/home/fsl/structural/LD08/bold
bet /tmp/mkbrainmask_10655/in.nii /tmp/mkbrainmask_10655/brain -m -f 0.1
mri_binarize --i /tmp/mkbrainmask_10655/brain_mask.nii --min .01 --o /tmp/mkbrainmask_10655/brain_mask.nii

$Id: mri_binarize.c,v 1.23.2.1 2010/07/28 20:07:29 greve Exp $
cwd /home/fsl/structural/LD08/bold
cmdline mri_binarize --i /tmp/mkbrainmask_10655/brain_mask.nii --min .01 --o /tmp/mkbrainmask_10655/brain_mask.nii 
sysname  Linux
hostname localhost.localdomain
machine  x86_64
user     fsl

input      /tmp/mkbrainmask_10655/brain_mask.nii
frame      0
nErode3d   0
nErode2d   0
output     /tmp/mkbrainmask_10655/brain_mask.nii
Binarizing based on threshold
min        0.01
max        +infinity
binval        1
binvalnot     0
Found 40566 values in range
Counting number of voxels
Found 40566 voxels in final mask
mri_binarize done
Diliating 1
/home/fsl/structural/LD08/bold
mri_binarize --i /tmp/mkbrainmask_10655/brain_mask.nii --min 0.5 --dilate 1 --o /tmp/mkbrainmask_10655/brain_mask.nii

$Id: mri_binarize.c,v 1.23.2.1 2010/07/28 20:07:29 greve Exp $
cwd /home/fsl/structural/LD08/bold
cmdline mri_binarize --i /tmp/mkbrainmask_10655/brain_mask.nii --min 0.5 --dilate 1 --o /tmp/mkbrainmask_10655/brain_mask.nii 
sysname  Linux
hostname localhost.localdomain
machine  x86_64
user     fsl

input      /tmp/mkbrainmask_10655/brain_mask.nii
frame      0
nErode3d   0
nErode2d   0
output     /tmp/mkbrainmask_10655/brain_mask.nii
Binarizing based on threshold
min        0.5
max        +infinity
binval        1
binvalnot     0
Found 40566 values in range
Dilating 1 voxels in 3d
Counting number of voxels
Found 46847 voxels in final mask
mri_binarize done
/home/fsl/structural/LD08/bold
mri_convert /tmp/mkbrainmask_10655/brain_mask.nii masks/brain.nii
mri_convert /tmp/mkbrainmask_10655/brain_mask.nii masks/brain.nii 
$Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $
reading from /tmp/mkbrainmask_10655/brain_mask.nii...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.999754, 0.00122074, 0.0221564)
j_ras = (0.00198375, 0.999446, 0.0332345)
k_ras = (0.0221035, -0.0332703, 0.999202)
writing to masks/brain.nii...
 
----------------- mkbrainmask Done -----------------------------
 
mkbrainmask -i 001/template.nii -o 001/masks/brain.nii -thresh 0.1 -ndil 1 -nerode 0
FSLMATHS fslmaths
Scratch Dir is /tmp/mkbrainmask_10765
/home/fsl/structural/LD08/bold
mri_convert 001/template.nii /tmp/mkbrainmask_10765/in.nii
mri_convert 001/template.nii /tmp/mkbrainmask_10765/in.nii 
$Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $
reading from 001/template.nii...
TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.999754, 0.00122074, 0.0221564)
j_ras = (0.00198375, 0.999446, 0.0332345)
k_ras = (0.0221035, -0.0332703, 0.999202)
writing to /tmp/mkbrainmask_10765/in.nii...
# ---------- Using FSL's BET to Extract Brain------------------ #
/home/fsl/structural/LD08/bold
bet /tmp/mkbrainmask_10765/in.nii /tmp/mkbrainmask_10765/brain -m -f 0.1
mri_binarize --i /tmp/mkbrainmask_10765/brain_mask.nii --min .01 --o /tmp/mkbrainmask_10765/brain_mask.nii

$Id: mri_binarize.c,v 1.23.2.1 2010/07/28 20:07:29 greve Exp $
cwd /home/fsl/structural/LD08/bold
cmdline mri_binarize --i /tmp/mkbrainmask_10765/brain_mask.nii --min .01 --o /tmp/mkbrainmask_10765/brain_mask.nii 
sysname  Linux
hostname localhost.localdomain
machine  x86_64
user     fsl

input      /tmp/mkbrainmask_10765/brain_mask.nii
frame      0
nErode3d   0
nErode2d   0
output     /tmp/mkbrainmask_10765/brain_mask.nii
Binarizing based on threshold
min        0.01
max        +infinity
binval        1
binvalnot     0
Found 39950 values in range
Counting number of voxels
Found 39950 voxels in final mask
mri_binarize done
Diliating 1
/home/fsl/structural/LD08/bold
mri_binarize --i /tmp/mkbrainmask_10765/brain_mask.nii --min 0.5 --dilate 1 --o /tmp/mkbrainmask_10765/brain_mask.nii

$Id: mri_binarize.c,v 1.23.2.1 2010/07/28 20:07:29 greve Exp $
cwd /home/fsl/structural/LD08/bold
cmdline mri_binarize --i /tmp/mkbrainmask_10765/brain_mask.nii --min 0.5 --dilate 1 --o /tmp/mkbrainmask_10765/brain_mask.nii 
sysname  Linux
hostname localhost.localdomain
machine  x86_64
user     fsl

input      /tmp/mkbrainmask_10765/brain_mask.nii
frame      0
nErode3d   0
nErode2d   0
output     /tmp/mkbrainmask_10765/brain_mask.nii
Binarizing based on threshold
min        0.5
max        +infinity
binval        1
binvalnot     0
Found 39950 values in range
Dilating 1 voxels in 3d
Counting number of voxels
Found 46176 voxels in final mask
mri_binarize done
/home/fsl/structural/LD08/bold
mri_convert /tmp/mkbrainmask_10765/brain_mask.nii 001/masks/brain.nii
mri_convert /tmp/mkbrainmask_10765/brain_mask.nii 001/masks/brain.nii 
$Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $
reading from /tmp/mkbrainmask_10765/brain_mask.nii...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.999754, 0.00122074, 0.0221564)
j_ras = (0.00198375, 0.999446, 0.0332345)
k_ras = (0.0221035, -0.0332703, 0.999202)
writing to 001/masks/brain.nii...
 
----------------- mkbrainmask Done -----------------------------
 
mri_binarize --i 001/masks/brain.nii --min 0.5 --zero-edges --erode 3 --o 001/masks/brain.e3.nii

$Id: mri_binarize.c,v 1.23.2.1 2010/07/28 20:07:29 greve Exp $
cwd /home/fsl/structural/LD08/bold
cmdline mri_binarize --i 001/masks/brain.nii --min 0.5 --zero-edges --erode 3 --o 001/masks/brain.e3.nii 
sysname  Linux
hostname localhost.localdomain
machine  x86_64
user     fsl

input      001/masks/brain.nii
frame      0
nErode3d   3
nErode2d   0
output     001/masks/brain.e3.nii
Binarizing based on threshold
min        0.5
max        +infinity
binval        1
binvalnot     0
Found 42920 values in range
Eroding 3 voxels in 3d
Counting number of voxels
Found 20809 voxels in final mask
mri_binarize done
meanval --i 001/f.nii --m 001/masks/brain.e3.nii --o 001/global.meanval.dat --avgwf 001/global.waveform.dat
Tue Apr  5 07:38:43 BST 2011

setenv SUBJECTS_DIR /home/fsl/structural
cd /home/fsl/structural/LD08/bold
/usr/local/freesurfer/bin/meanval --i 001/f.nii --m 001/masks/brain.e3.nii --o 001/global.meanval.dat --avgwf 001/global.waveform.dat

freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0
Linux localhost.localdomain 2.6.18-128.1.6.el5 #1 SMP Wed Apr 1 09:10:25 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux
mri_segstats --seg 001/masks/brain.e3.nii --id 1 --sum /home/fsl/structural/LD08/bold/001/tmpdir.meanval/blah.10869 --in 001/f.nii --sfavg 001/global.meanval.dat --avgwf 001/global.waveform.dat

$Id: mri_segstats.c,v 1.69.2.1 2010/07/26 16:19:29 greve Exp $
cwd 
cmdline mri_segstats --seg 001/masks/brain.e3.nii --id 1 --sum /home/fsl/structural/LD08/bold/001/tmpdir.meanval/blah.10869 --in 001/f.nii --sfavg 001/global.meanval.dat --avgwf 001/global.waveform.dat 
sysname  Linux
hostname localhost.localdomain
machine  x86_64
user     fsl
Loading 001/masks/brain.e3.nii
Loading 001/f.nii
Voxel Volume is 26.9999 mm^3
Generating list of segmentation ids
Found   1 segmentations
Computing statistics for each segmentation
  0     1   20809  561842

Reporting on   1 segmentations
Computing spatial average of each frame
  0
Writing to 001/global.meanval.dat
0 712.444
Writing to 001/global.waveform.dat
mkbrainmask -i 002/template.nii -o 002/masks/brain.nii -thresh 0.1 -ndil 1 -nerode 0
FSLMATHS fslmaths
Scratch Dir is /tmp/mkbrainmask_10916
/home/fsl/structural/LD08/bold
mri_convert 002/template.nii /tmp/mkbrainmask_10916/in.nii
mri_convert 002/template.nii /tmp/mkbrainmask_10916/in.nii 
$Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $
reading from 002/template.nii...
TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.999754, 0.00122074, 0.0221564)
j_ras = (0.00198375, 0.999446, 0.0332345)
k_ras = (0.0221035, -0.0332703, 0.999202)
writing to /tmp/mkbrainmask_10916/in.nii...
# ---------- Using FSL's BET to Extract Brain------------------ #
/home/fsl/structural/LD08/bold
bet /tmp/mkbrainmask_10916/in.nii /tmp/mkbrainmask_10916/brain -m -f 0.1
mri_binarize --i /tmp/mkbrainmask_10916/brain_mask.nii --min .01 --o /tmp/mkbrainmask_10916/brain_mask.nii

$Id: mri_binarize.c,v 1.23.2.1 2010/07/28 20:07:29 greve Exp $
cwd /home/fsl/structural/LD08/bold
cmdline mri_binarize --i /tmp/mkbrainmask_10916/brain_mask.nii --min .01 --o /tmp/mkbrainmask_10916/brain_mask.nii 
sysname  Linux
hostname localhost.localdomain
machine  x86_64
user     fsl

input      /tmp/mkbrainmask_10916/brain_mask.nii
frame      0
nErode3d   0
nErode2d   0
output     /tmp/mkbrainmask_10916/brain_mask.nii
Binarizing based on threshold
min        0.01
max        +infinity
binval        1
binvalnot     0
Found 40112 values in range
Counting number of voxels
Found 40112 voxels in final mask
mri_binarize done
Diliating 1
/home/fsl/structural/LD08/bold
mri_binarize --i /tmp/mkbrainmask_10916/brain_mask.nii --min 0.5 --dilate 1 --o /tmp/mkbrainmask_10916/brain_mask.nii

$Id: mri_binarize.c,v 1.23.2.1 2010/07/28 20:07:29 greve Exp $
cwd /home/fsl/structural/LD08/bold
cmdline mri_binarize --i /tmp/mkbrainmask_10916/brain_mask.nii --min 0.5 --dilate 1 --o /tmp/mkbrainmask_10916/brain_mask.nii 
sysname  Linux
hostname localhost.localdomain
machine  x86_64
user     fsl

input      /tmp/mkbrainmask_10916/brain_mask.nii
frame      0
nErode3d   0
nErode2d   0
output     /tmp/mkbrainmask_10916/brain_mask.nii
Binarizing based on threshold
min        0.5
max        +infinity
binval        1
binvalnot     0
Found 40112 values in range
Dilating 1 voxels in 3d
Counting number of voxels
Found 46304 voxels in final mask
mri_binarize done
/home/fsl/structural/LD08/bold
mri_convert /tmp/mkbrainmask_10916/brain_mask.nii 002/masks/brain.nii
mri_convert /tmp/mkbrainmask_10916/brain_mask.nii 002/masks/brain.nii 
$Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $
reading from /tmp/mkbrainmask_10916/brain_mask.nii...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.999754, 0.00122074, 0.0221564)
j_ras = (0.00198375, 0.999446, 0.0332345)
k_ras = (0.0221035, -0.0332703, 0.999202)
writing to 002/masks/brain.nii...
 
----------------- mkbrainmask Done -----------------------------
 
mri_binarize --i 002/masks/brain.nii --min 0.5 --zero-edges --erode 3 --o 002/masks/brain.e3.nii

$Id: mri_binarize.c,v 1.23.2.1 2010/07/28 20:07:29 greve Exp $
cwd /home/fsl/structural/LD08/bold
cmdline mri_binarize --i 002/masks/brain.nii --min 0.5 --zero-edges --erode 3 --o 002/masks/brain.e3.nii 
sysname  Linux
hostname localhost.localdomain
machine  x86_64
user     fsl

input      002/masks/brain.nii
frame      0
nErode3d   3
nErode2d   0
output     002/masks/brain.e3.nii
Binarizing based on threshold
min        0.5
max        +infinity
binval        1
binvalnot     0
Found 43025 values in range
Eroding 3 voxels in 3d
Counting number of voxels
Found 20957 voxels in final mask
mri_binarize done
meanval --i 002/f.nii --m 002/masks/brain.e3.nii --o 002/global.meanval.dat --avgwf 002/global.waveform.dat
Tue Apr  5 07:38:46 BST 2011

setenv SUBJECTS_DIR /home/fsl/structural
cd /home/fsl/structural/LD08/bold
/usr/local/freesurfer/bin/meanval --i 002/f.nii --m 002/masks/brain.e3.nii --o 002/global.meanval.dat --avgwf 002/global.waveform.dat

freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0
Linux localhost.localdomain 2.6.18-128.1.6.el5 #1 SMP Wed Apr 1 09:10:25 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux
mri_segstats --seg 002/masks/brain.e3.nii --id 1 --sum /home/fsl/structural/LD08/bold/002/tmpdir.meanval/blah.11020 --in 002/f.nii --sfavg 002/global.meanval.dat --avgwf 002/global.waveform.dat

$Id: mri_segstats.c,v 1.69.2.1 2010/07/26 16:19:29 greve Exp $
cwd 
cmdline mri_segstats --seg 002/masks/brain.e3.nii --id 1 --sum /home/fsl/structural/LD08/bold/002/tmpdir.meanval/blah.11020 --in 002/f.nii --sfavg 002/global.meanval.dat --avgwf 002/global.waveform.dat 
sysname  Linux
hostname localhost.localdomain
machine  x86_64
user     fsl
Loading 002/masks/brain.e3.nii
Loading 002/f.nii
Voxel Volume is 26.9999 mm^3
Generating list of segmentation ids
Found   1 segmentations
Computing statistics for each segmentation
  0     1   20957  565838

Reporting on   1 segmentations
Computing spatial average of each frame
  0
Writing to 002/global.meanval.dat
0 713.694
Writing to 002/global.waveform.dat
Tue Apr  5 07:38:48 BST 2011
mkbrainmask-sess done
LD08 Registration -----------------------------
register-sess -s LD08 -d /home/fsl/structural -fsd bold -dof 6 -per-run
--------------------------------------------------------------
register-sess logfile is /home/fsl/structural/log/register-sess.LD08.log
--------------------------------------------------------------
Tue Apr  5 07:38:48 BST 2011

setenv SUBJECTS_DIR /home/fsl/structural
cd /home/fsl/structural
/usr/local/freesurfer/fsfast/bin/register-sess -s LD08 -d /home/fsl/structural -fsd bold -dof 6 -per-run

freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0
Linux localhost.localdomain 2.6.18-128.1.6.el5 #1 SMP Wed Apr 1 09:10:25 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux
 
Session: /home/fsl/structural/LD08 ----------------
Tue Apr  5 07:38:48 BST 2011
 is not in SUBJECTS_DIR
  SUBJECTS_DIR is /home/fsl/structural
[fsl@localhost structural]$