selxavg3-sess log file
/usr/local/freesurfer/stable5_3_0/fsfast/bin/selxavg3-sess
-analysis sycabs_self_lh -s nmr00978 -d /cluster/neuromind/dwakeman/tsc_pilot/subjects/
$Id: selxavg3-sess,v 1.57.2.1 2011/12/09 20:06:47 greve Exp $
uid=3882345(kz221) gid=3882345(kz221) groups=3882345(kz221),1084(megclin),1125(smsgp)
/autofs/cluster/neuromind/dwakeman/tsc_pilot/fsfast
Linux belle 2.6.32-573.22.1.el6.x86_64 #1 SMP Wed Mar 23 03:35:39 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
Wed Jul 13 13:42:24 EDT 2016
preproc-sess -s nmr00978 -d /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects -a sycabs_self_lh -nolog
--------------------------------------------------------------
preproc-sess logfile is /dev/null
--------------------------------------------------------------
$Id: preproc-sess,v 1.45.2.3 2013/01/22 22:09:10 greve Exp $
kz221
setenv FREESURFER_HOME /usr/local/freesurfer/stable5_3_0
setenv SUBJECTS_DIR /cluster/neuromind/dwakeman/tsc_pilot/subjects/
Linux belle 2.6.32-573.22.1.el6.x86_64 #1 SMP Wed Mar 23 03:35:39 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
/autofs/cluster/neuromind/dwakeman/tsc_pilot/fsfast
/usr/local/freesurfer/stable5_3_0/fsfast/bin/preproc-sess
-s nmr00978 -d /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects -a sycabs_self_lh -nolog
Wed Jul 13 13:42:25 EDT 2016
instem   f 
mc   1     f fmcpr 
stc  0     fmcpr
sm   0   
mask 1   brain
nmr00978 Template -----------------------------
mktemplate-sess -s nmr00978 -d /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects -fsd sycabs -nolog -update
 
Session: /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978 ----------------
Wed Jul 13 13:42:25 EDT 2016
Detected input format at nii.gz
/autofs/cluster/neuromind/dwakeman/tsc_pilot/fsfast
mri_convert /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs/009/f.nii.gz /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs/template.nii.gz --frame 0
mri_convert /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs/009/f.nii.gz /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs/template.nii.gz --frame 0 
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs/009/f.nii.gz...
TR=568.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.99997, -0.00137983, 0.00759295)
j_ras = (1.9297e-08, -0.983886, -0.178794)
k_ras = (0.0077173, -0.178789, 0.983857)
keeping frame 0
writing to /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs/template.nii.gz...
  Run: 009 ----------------
  Wed Jul 13 13:42:36 EDT 2016
/autofs/cluster/neuromind/dwakeman/tsc_pilot/fsfast
mri_convert /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs/009/f.nii.gz /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs/009/template.nii.gz --mid-frame
mri_convert /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs/009/f.nii.gz /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs/009/template.nii.gz --mid-frame 
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs/009/f.nii.gz...
TR=568.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.99997, -0.00137983, 0.00759295)
j_ras = (1.9297e-08, -0.983886, -0.178794)
k_ras = (0.0077173, -0.178789, 0.983857)
keeping frame 238
writing to /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs/009/template.nii.gz...
  Run: 010 ----------------
  Wed Jul 13 13:42:46 EDT 2016
/autofs/cluster/neuromind/dwakeman/tsc_pilot/fsfast
mri_convert /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs/010/f.nii.gz /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs/010/template.nii.gz --mid-frame
mri_convert /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs/010/f.nii.gz /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs/010/template.nii.gz --mid-frame 
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs/010/f.nii.gz...
TR=568.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.99997, -0.00137983, 0.00759295)
j_ras = (1.9297e-08, -0.983886, -0.178794)
k_ras = (0.0077173, -0.178789, 0.983857)
keeping frame 238
writing to /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs/010/template.nii.gz...
  Run: 011 ----------------
  Wed Jul 13 13:42:56 EDT 2016
/autofs/cluster/neuromind/dwakeman/tsc_pilot/fsfast
mri_convert /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs/011/f.nii.gz /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs/011/template.nii.gz --mid-frame
mri_convert /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs/011/f.nii.gz /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs/011/template.nii.gz --mid-frame 
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs/011/f.nii.gz...
TR=568.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.99997, -0.00137983, 0.00759295)
j_ras = (1.9297e-08, -0.983886, -0.178794)
k_ras = (0.0077173, -0.178789, 0.983857)
keeping frame 238
writing to /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs/011/template.nii.gz...
Wed Jul 13 13:43:06 EDT 2016
mktemplate-sess completed 
nmr00978 Mask ------------------------
mkbrainmask-sess -maskstem brain -fsd sycabs -s nmr00978 -d /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects -nolog -update
------------------------------------------------
/autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978 
Wed Jul 13 13:43:06 EDT 2016
mkbrainmask -i template.nii.gz -o masks/brain.nii.gz -thresh 0.1 -ndil 1 -nerode 0
FSLMATHS fslmaths.fsl
Scratch Dir is /tmp/mkbrainmask_31088
/autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs
mri_convert template.nii.gz /tmp/mkbrainmask_31088/in.nii
mri_convert template.nii.gz /tmp/mkbrainmask_31088/in.nii 
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from template.nii.gz...
TR=568.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.99997, -0.00137983, 0.00759295)
j_ras = (1.9297e-08, -0.983886, -0.178794)
k_ras = (0.00771731, -0.178789, 0.983857)
writing to /tmp/mkbrainmask_31088/in.nii...
# ---------- Using FSL's BET to Extract Brain------------------ #
/autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs
bet.fsl /tmp/mkbrainmask_31088/in.nii /tmp/mkbrainmask_31088/brain -m -f 0.1
mri_binarize --i /tmp/mkbrainmask_31088/brain_mask.nii --min .01 --o /tmp/mkbrainmask_31088/brain_mask.nii

$Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $
cwd /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs
cmdline mri_binarize --i /tmp/mkbrainmask_31088/brain_mask.nii --min .01 --o /tmp/mkbrainmask_31088/brain_mask.nii 
sysname  Linux
hostname belle
machine  x86_64
user     kz221

input      /tmp/mkbrainmask_31088/brain_mask.nii
frame      0
nErode3d   0
nErode2d   0
output     /tmp/mkbrainmask_31088/brain_mask.nii
Binarizing based on threshold
min        0.01
max        +infinity
binval        1
binvalnot     0
Found 93758 values in range
Counting number of voxels
Found 93758 voxels in final mask
mri_binarize done
Diliating 1
/autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs
mri_binarize --i /tmp/mkbrainmask_31088/brain_mask.nii --min 0.5 --dilate 1 --o /tmp/mkbrainmask_31088/brain_mask.nii

$Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $
cwd /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs
cmdline mri_binarize --i /tmp/mkbrainmask_31088/brain_mask.nii --min 0.5 --dilate 1 --o /tmp/mkbrainmask_31088/brain_mask.nii 
sysname  Linux
hostname belle
machine  x86_64
user     kz221

input      /tmp/mkbrainmask_31088/brain_mask.nii
frame      0
nErode3d   0
nErode2d   0
output     /tmp/mkbrainmask_31088/brain_mask.nii
Binarizing based on threshold
min        0.5
max        +infinity
binval        1
binvalnot     0
Found 93758 values in range
Dilating 1 voxels in 3d
Counting number of voxels
Found 108842 voxels in final mask
mri_binarize done
/autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs
mri_convert /tmp/mkbrainmask_31088/brain_mask.nii masks/brain.nii.gz
mri_convert /tmp/mkbrainmask_31088/brain_mask.nii masks/brain.nii.gz 
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /tmp/mkbrainmask_31088/brain_mask.nii...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.99997, -0.00137983, 0.00759295)
j_ras = (1.9297e-08, -0.983886, -0.178794)
k_ras = (0.00771731, -0.178789, 0.983857)
writing to masks/brain.nii.gz...
 
----------------- mkbrainmask Done -----------------------------
 
mkbrainmask -i 009/template.nii.gz -o 009/masks/brain.nii.gz -thresh 0.1 -ndil 1 -nerode 0
FSLMATHS fslmaths.fsl
Scratch Dir is /tmp/mkbrainmask_31202
/autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs
mri_convert 009/template.nii.gz /tmp/mkbrainmask_31202/in.nii
mri_convert 009/template.nii.gz /tmp/mkbrainmask_31202/in.nii 
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from 009/template.nii.gz...
TR=568.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.99997, -0.00137983, 0.00759295)
j_ras = (1.9297e-08, -0.983886, -0.178794)
k_ras = (0.00771731, -0.178789, 0.983857)
writing to /tmp/mkbrainmask_31202/in.nii...
# ---------- Using FSL's BET to Extract Brain------------------ #
/autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs
bet.fsl /tmp/mkbrainmask_31202/in.nii /tmp/mkbrainmask_31202/brain -m -f 0.1
mri_binarize --i /tmp/mkbrainmask_31202/brain_mask.nii --min .01 --o /tmp/mkbrainmask_31202/brain_mask.nii

$Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $
cwd /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs
cmdline mri_binarize --i /tmp/mkbrainmask_31202/brain_mask.nii --min .01 --o /tmp/mkbrainmask_31202/brain_mask.nii 
sysname  Linux
hostname belle
machine  x86_64
user     kz221

input      /tmp/mkbrainmask_31202/brain_mask.nii
frame      0
nErode3d   0
nErode2d   0
output     /tmp/mkbrainmask_31202/brain_mask.nii
Binarizing based on threshold
min        0.01
max        +infinity
binval        1
binvalnot     0
Found 97811 values in range
Counting number of voxels
Found 97811 voxels in final mask
mri_binarize done
Diliating 1
/autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs
mri_binarize --i /tmp/mkbrainmask_31202/brain_mask.nii --min 0.5 --dilate 1 --o /tmp/mkbrainmask_31202/brain_mask.nii

$Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $
cwd /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs
cmdline mri_binarize --i /tmp/mkbrainmask_31202/brain_mask.nii --min 0.5 --dilate 1 --o /tmp/mkbrainmask_31202/brain_mask.nii 
sysname  Linux
hostname belle
machine  x86_64
user     kz221

input      /tmp/mkbrainmask_31202/brain_mask.nii
frame      0
nErode3d   0
nErode2d   0
output     /tmp/mkbrainmask_31202/brain_mask.nii
Binarizing based on threshold
min        0.5
max        +infinity
binval        1
binvalnot     0
Found 97811 values in range
Dilating 1 voxels in 3d
Counting number of voxels
Found 113218 voxels in final mask
mri_binarize done
/autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs
mri_convert /tmp/mkbrainmask_31202/brain_mask.nii 009/masks/brain.nii.gz
mri_convert /tmp/mkbrainmask_31202/brain_mask.nii 009/masks/brain.nii.gz 
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /tmp/mkbrainmask_31202/brain_mask.nii...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.99997, -0.00137983, 0.00759295)
j_ras = (1.9297e-08, -0.983886, -0.178794)
k_ras = (0.00771731, -0.178789, 0.983857)
writing to 009/masks/brain.nii.gz...
 
----------------- mkbrainmask Done -----------------------------
 
mri_binarize --i 009/masks/brain.nii.gz --min 0.5 --zero-edges --erode 3 --o 009/masks/brain.e3.nii.gz

$Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $
cwd /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs
cmdline mri_binarize --i 009/masks/brain.nii.gz --min 0.5 --zero-edges --erode 3 --o 009/masks/brain.e3.nii.gz 
sysname  Linux
hostname belle
machine  x86_64
user     kz221

input      009/masks/brain.nii.gz
frame      0
nErode3d   3
nErode2d   0
output     009/masks/brain.e3.nii.gz
Binarizing based on threshold
min        0.5
max        +infinity
binval        1
binvalnot     0
Found 110421 values in range
Eroding 3 voxels in 3d
Counting number of voxels
Found 66091 voxels in final mask
mri_binarize done
meanval --i 009/f.nii.gz --m 009/masks/brain.e3.nii.gz --o 009/global.meanval.dat --avgwf 009/global.waveform.dat
Wed Jul 13 13:43:10 EDT 2016

setenv SUBJECTS_DIR /cluster/neuromind/dwakeman/tsc_pilot/subjects/
cd /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs
/usr/local/freesurfer/stable5_3_0/bin/meanval --i 009/f.nii.gz --m 009/masks/brain.e3.nii.gz --o 009/global.meanval.dat --avgwf 009/global.waveform.dat

cat: /usr/local/freesurfer/stable5_3_0/build-stamp.txt: No such file or directory
Linux belle 2.6.32-573.22.1.el6.x86_64 #1 SMP Wed Mar 23 03:35:39 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
mri_segstats --seg 009/masks/brain.e3.nii.gz --id 1 --sum /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs/009/tmpdir.meanval.31316/blah.31316 --in 009/f.nii.gz --sfavg 009/global.meanval.dat --avgwf 009/global.waveform.dat

$Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $
cwd 
cmdline mri_segstats --seg 009/masks/brain.e3.nii.gz --id 1 --sum /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs/009/tmpdir.meanval.31316/blah.31316 --in 009/f.nii.gz --sfavg 009/global.meanval.dat --avgwf 009/global.waveform.dat 
sysname  Linux
hostname belle
machine  x86_64
user     kz221
UseRobust  0
Loading 009/masks/brain.e3.nii.gz
Loading 009/f.nii.gz
Voxel Volume is 27 mm^3
Generating list of segmentation ids
Found   1 segmentations
Computing statistics for each segmentation
  0     1                                      66091  1784457.000

Reporting on   1 segmentations
Computing spatial average of each frame
  0
Writing to 009/global.meanval.dat
0 442.671
Writing to 009/global.waveform.dat
mri_segstats done
mkbrainmask -i 010/template.nii.gz -o 010/masks/brain.nii.gz -thresh 0.1 -ndil 1 -nerode 0
FSLMATHS fslmaths.fsl
Scratch Dir is /tmp/mkbrainmask_31412
/autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs
mri_convert 010/template.nii.gz /tmp/mkbrainmask_31412/in.nii
mri_convert 010/template.nii.gz /tmp/mkbrainmask_31412/in.nii 
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from 010/template.nii.gz...
TR=568.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.99997, -0.00137983, 0.00759295)
j_ras = (1.9297e-08, -0.983886, -0.178794)
k_ras = (0.00771731, -0.178789, 0.983857)
writing to /tmp/mkbrainmask_31412/in.nii...
# ---------- Using FSL's BET to Extract Brain------------------ #
/autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs
bet.fsl /tmp/mkbrainmask_31412/in.nii /tmp/mkbrainmask_31412/brain -m -f 0.1
mri_binarize --i /tmp/mkbrainmask_31412/brain_mask.nii --min .01 --o /tmp/mkbrainmask_31412/brain_mask.nii

$Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $
cwd /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs
cmdline mri_binarize --i /tmp/mkbrainmask_31412/brain_mask.nii --min .01 --o /tmp/mkbrainmask_31412/brain_mask.nii 
sysname  Linux
hostname belle
machine  x86_64
user     kz221

input      /tmp/mkbrainmask_31412/brain_mask.nii
frame      0
nErode3d   0
nErode2d   0
output     /tmp/mkbrainmask_31412/brain_mask.nii
Binarizing based on threshold
min        0.01
max        +infinity
binval        1
binvalnot     0
Found 87365 values in range
Counting number of voxels
Found 87365 voxels in final mask
mri_binarize done
Diliating 1
/autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs
mri_binarize --i /tmp/mkbrainmask_31412/brain_mask.nii --min 0.5 --dilate 1 --o /tmp/mkbrainmask_31412/brain_mask.nii

$Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $
cwd /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs
cmdline mri_binarize --i /tmp/mkbrainmask_31412/brain_mask.nii --min 0.5 --dilate 1 --o /tmp/mkbrainmask_31412/brain_mask.nii 
sysname  Linux
hostname belle
machine  x86_64
user     kz221

input      /tmp/mkbrainmask_31412/brain_mask.nii
frame      0
nErode3d   0
nErode2d   0
output     /tmp/mkbrainmask_31412/brain_mask.nii
Binarizing based on threshold
min        0.5
max        +infinity
binval        1
binvalnot     0
Found 87365 values in range
Dilating 1 voxels in 3d
Counting number of voxels
Found 102420 voxels in final mask
mri_binarize done
/autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs
mri_convert /tmp/mkbrainmask_31412/brain_mask.nii 010/masks/brain.nii.gz
mri_convert /tmp/mkbrainmask_31412/brain_mask.nii 010/masks/brain.nii.gz 
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /tmp/mkbrainmask_31412/brain_mask.nii...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.99997, -0.00137983, 0.00759295)
j_ras = (1.9297e-08, -0.983886, -0.178794)
k_ras = (0.00771731, -0.178789, 0.983857)
writing to 010/masks/brain.nii.gz...
 
----------------- mkbrainmask Done -----------------------------
 
mri_binarize --i 010/masks/brain.nii.gz --min 0.5 --zero-edges --erode 3 --o 010/masks/brain.e3.nii.gz

$Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $
cwd /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs
cmdline mri_binarize --i 010/masks/brain.nii.gz --min 0.5 --zero-edges --erode 3 --o 010/masks/brain.e3.nii.gz 
sysname  Linux
hostname belle
machine  x86_64
user     kz221

input      010/masks/brain.nii.gz
frame      0
nErode3d   3
nErode2d   0
output     010/masks/brain.e3.nii.gz
Binarizing based on threshold
min        0.5
max        +infinity
binval        1
binvalnot     0
Found 100377 values in range
Eroding 3 voxels in 3d
Counting number of voxels
Found 58222 voxels in final mask
mri_binarize done
meanval --i 010/f.nii.gz --m 010/masks/brain.e3.nii.gz --o 010/global.meanval.dat --avgwf 010/global.waveform.dat
Wed Jul 13 13:43:24 EDT 2016

setenv SUBJECTS_DIR /cluster/neuromind/dwakeman/tsc_pilot/subjects/
cd /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs
/usr/local/freesurfer/stable5_3_0/bin/meanval --i 010/f.nii.gz --m 010/masks/brain.e3.nii.gz --o 010/global.meanval.dat --avgwf 010/global.waveform.dat

cat: /usr/local/freesurfer/stable5_3_0/build-stamp.txt: No such file or directory
Linux belle 2.6.32-573.22.1.el6.x86_64 #1 SMP Wed Mar 23 03:35:39 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
mri_segstats --seg 010/masks/brain.e3.nii.gz --id 1 --sum /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs/010/tmpdir.meanval.31526/blah.31526 --in 010/f.nii.gz --sfavg 010/global.meanval.dat --avgwf 010/global.waveform.dat

$Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $
cwd 
cmdline mri_segstats --seg 010/masks/brain.e3.nii.gz --id 1 --sum /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs/010/tmpdir.meanval.31526/blah.31526 --in 010/f.nii.gz --sfavg 010/global.meanval.dat --avgwf 010/global.waveform.dat 
sysname  Linux
hostname belle
machine  x86_64
user     kz221
UseRobust  0
Loading 010/masks/brain.e3.nii.gz
Loading 010/f.nii.gz
Voxel Volume is 27 mm^3
Generating list of segmentation ids
Found   1 segmentations
Computing statistics for each segmentation
  0     1                                      58222  1571994.000

Reporting on   1 segmentations
Computing spatial average of each frame
  0
Writing to 010/global.meanval.dat
0 472.463
Writing to 010/global.waveform.dat
mri_segstats done
mkbrainmask -i 011/template.nii.gz -o 011/masks/brain.nii.gz -thresh 0.1 -ndil 1 -nerode 0
FSLMATHS fslmaths.fsl
Scratch Dir is /tmp/mkbrainmask_31629
/autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs
mri_convert 011/template.nii.gz /tmp/mkbrainmask_31629/in.nii
mri_convert 011/template.nii.gz /tmp/mkbrainmask_31629/in.nii 
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from 011/template.nii.gz...
TR=568.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.99997, -0.00137983, 0.00759295)
j_ras = (1.9297e-08, -0.983886, -0.178794)
k_ras = (0.00771731, -0.178789, 0.983857)
writing to /tmp/mkbrainmask_31629/in.nii...
# ---------- Using FSL's BET to Extract Brain------------------ #
/autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs
bet.fsl /tmp/mkbrainmask_31629/in.nii /tmp/mkbrainmask_31629/brain -m -f 0.1
mri_binarize --i /tmp/mkbrainmask_31629/brain_mask.nii --min .01 --o /tmp/mkbrainmask_31629/brain_mask.nii

$Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $
cwd /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs
cmdline mri_binarize --i /tmp/mkbrainmask_31629/brain_mask.nii --min .01 --o /tmp/mkbrainmask_31629/brain_mask.nii 
sysname  Linux
hostname belle
machine  x86_64
user     kz221

input      /tmp/mkbrainmask_31629/brain_mask.nii
frame      0
nErode3d   0
nErode2d   0
output     /tmp/mkbrainmask_31629/brain_mask.nii
Binarizing based on threshold
min        0.01
max        +infinity
binval        1
binvalnot     0
Found 87486 values in range
Counting number of voxels
Found 87486 voxels in final mask
mri_binarize done
Diliating 1
/autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs
mri_binarize --i /tmp/mkbrainmask_31629/brain_mask.nii --min 0.5 --dilate 1 --o /tmp/mkbrainmask_31629/brain_mask.nii

$Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $
cwd /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs
cmdline mri_binarize --i /tmp/mkbrainmask_31629/brain_mask.nii --min 0.5 --dilate 1 --o /tmp/mkbrainmask_31629/brain_mask.nii 
sysname  Linux
hostname belle
machine  x86_64
user     kz221

input      /tmp/mkbrainmask_31629/brain_mask.nii
frame      0
nErode3d   0
nErode2d   0
output     /tmp/mkbrainmask_31629/brain_mask.nii
Binarizing based on threshold
min        0.5
max        +infinity
binval        1
binvalnot     0
Found 87486 values in range
Dilating 1 voxels in 3d
Counting number of voxels
Found 102213 voxels in final mask
mri_binarize done
/autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs
mri_convert /tmp/mkbrainmask_31629/brain_mask.nii 011/masks/brain.nii.gz
mri_convert /tmp/mkbrainmask_31629/brain_mask.nii 011/masks/brain.nii.gz 
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /tmp/mkbrainmask_31629/brain_mask.nii...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.99997, -0.00137983, 0.00759295)
j_ras = (1.9297e-08, -0.983886, -0.178794)
k_ras = (0.00771731, -0.178789, 0.983857)
writing to 011/masks/brain.nii.gz...
 
----------------- mkbrainmask Done -----------------------------
 
mri_binarize --i 011/masks/brain.nii.gz --min 0.5 --zero-edges --erode 3 --o 011/masks/brain.e3.nii.gz

$Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $
cwd /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs
cmdline mri_binarize --i 011/masks/brain.nii.gz --min 0.5 --zero-edges --erode 3 --o 011/masks/brain.e3.nii.gz 
sysname  Linux
hostname belle
machine  x86_64
user     kz221

input      011/masks/brain.nii.gz
frame      0
nErode3d   3
nErode2d   0
output     011/masks/brain.e3.nii.gz
Binarizing based on threshold
min        0.5
max        +infinity
binval        1
binvalnot     0
Found 99973 values in range
Eroding 3 voxels in 3d
Counting number of voxels
Found 58324 voxels in final mask
mri_binarize done
meanval --i 011/f.nii.gz --m 011/masks/brain.e3.nii.gz --o 011/global.meanval.dat --avgwf 011/global.waveform.dat
Wed Jul 13 13:43:36 EDT 2016

setenv SUBJECTS_DIR /cluster/neuromind/dwakeman/tsc_pilot/subjects/
cd /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs
/usr/local/freesurfer/stable5_3_0/bin/meanval --i 011/f.nii.gz --m 011/masks/brain.e3.nii.gz --o 011/global.meanval.dat --avgwf 011/global.waveform.dat

cat: /usr/local/freesurfer/stable5_3_0/build-stamp.txt: No such file or directory
Linux belle 2.6.32-573.22.1.el6.x86_64 #1 SMP Wed Mar 23 03:35:39 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
mri_segstats --seg 011/masks/brain.e3.nii.gz --id 1 --sum /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs/011/tmpdir.meanval.31733/blah.31733 --in 011/f.nii.gz --sfavg 011/global.meanval.dat --avgwf 011/global.waveform.dat

$Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $
cwd 
cmdline mri_segstats --seg 011/masks/brain.e3.nii.gz --id 1 --sum /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs/011/tmpdir.meanval.31733/blah.31733 --in 011/f.nii.gz --sfavg 011/global.meanval.dat --avgwf 011/global.waveform.dat 
sysname  Linux
hostname belle
machine  x86_64
user     kz221
UseRobust  0
Loading 011/masks/brain.e3.nii.gz
Loading 011/f.nii.gz
Voxel Volume is 27 mm^3
Generating list of segmentation ids
Found   1 segmentations
Computing statistics for each segmentation
  0     1                                      58324  1574748.000

Reporting on   1 segmentations
Computing spatial average of each frame
  0
Writing to 011/global.meanval.dat
0 472.094
Writing to 011/global.waveform.dat
mri_segstats done
Wed Jul 13 13:43:47 EDT 2016
mkbrainmask-sess done
nmr00978 Registration -----------------------------
register-sess -s nmr00978 -d /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects -fsd sycabs -dof 6 -per-run -nolog -update
--------------------------------------------------------------
register-sess logfile is /dev/null
--------------------------------------------------------------
Wed Jul 13 13:43:48 EDT 2016

setenv SUBJECTS_DIR /cluster/neuromind/dwakeman/tsc_pilot/subjects/
cd /autofs/cluster/neuromind/dwakeman/tsc_pilot/fsfast
/usr/local/freesurfer/stable5_3_0/fsfast/bin/register-sess -s nmr00978 -d /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects -fsd sycabs -dof 6 -per-run -nolog -update

cat: /usr/local/freesurfer/stable5_3_0/build-stamp.txt: No such file or directory
Linux belle 2.6.32-573.22.1.el6.x86_64 #1 SMP Wed Mar 23 03:35:39 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
 
Session: /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978 ----------------
Wed Jul 13 13:43:48 EDT 2016
if: Expression Syntax.