Log file for mkbrainmask
Sun Mar 27 21:53:12 EDT 2016

setenv SUBJECTS_DIR /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects
cd /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold
/usr/local/freesurfer/dev/fsfast/bin/mkbrainmask -i 001/template.nii.gz -o 001/masks/brain.nii.gz -reg /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/001/register.dof6.lta -ndil 1 -nerode 0

freesurfer-Linux-centos6_x86_64-dev-20160325
$Id: mkbrainmask,v 1.17 2015/12/10 22:51:30 zkaufman Exp $
Linux transfer 2.6.32-573.18.1.el6.x86_64 #1 SMP Tue Feb 9 22:46:17 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
mri_vol2vol --mov 001/template.nii.gz --reg /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/001/register.dof6.lta --inv --interp nearest --o 001/masks/brain.nii.gz --targ /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects/fsf01anat/mri/aparc+aseg.mgz
regio_read_register: loading lta

Matrix from regfile:
 1.00000  -0.00030  -0.00116   0.63847;
 0.00106  -0.23893   0.97104  -40.48508;
 0.00057   0.97104   0.23893  -1.35980;
 0.00000   0.00000   0.00000   1.00000;

movvol 001/template.nii.gz
targvol /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects/fsf01anat/mri/aparc+aseg.mgz
outvol 001/masks/brain.nii.gz
regfile /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/001/register.dof6.lta
invert 1
tal    0
talres 2
regheader 0
noresample 0
interp  nearest (0)
precision  float (3)
Gdiag_no  -1
Synth      0
SynthSeed  1459451216

Invert!
Inverting registration

Final tkRAS-to-tkRAS Matrix is:
 1.00000   0.00106   0.00057  -0.59493;
-0.00030  -0.23893   0.97104  -8.35248;
-0.00116   0.97104   0.23893   39.63811;
-0.00000  -0.00000  -0.00000   1.00000;


Vox2Vox Matrix is:
 3.43750   0.00195  -0.00528   18.61178;
-0.00399   0.82132  -4.85518   135.03517;
 0.00103  -3.33794  -1.19465   244.34839;
 0.00000   0.00000   0.00000   1.00000;

Resampling
Output registration matrix is identity

mri_vol2vol done
mri_binarize --i 001/masks/brain.nii.gz --o 001/masks/brain.nii.gz --min 0.5

$Id: mri_binarize.c,v 1.42 2016/01/07 22:23:57 greve Exp $
cwd /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold
cmdline mri_binarize.bin --i 001/masks/brain.nii.gz --o 001/masks/brain.nii.gz --min 0.5 
sysname  Linux
hostname transfer
machine  x86_64
user     zkaufman

input      001/masks/brain.nii.gz
frame      0
nErode3d   0
nErode2d   0
output     001/masks/brain.nii.gz
Binarizing based on threshold
min        0.5
max        +infinity
binval        1
binvalnot     0
fstart = 0, fend = 0, nframes = 1
Found 24269 values in range
Counting number of voxels in first frame
Found 24269 voxels in final mask
Count: 24269 1433861.723827 122880 19.750163
mri_binarize done
Diliating 1
mri_binarize --i 001/masks/brain.nii.gz --min 0.5 --dilate 1 --o 001/masks/brain.nii.gz

$Id: mri_binarize.c,v 1.42 2016/01/07 22:23:57 greve Exp $
cwd /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold
cmdline mri_binarize.bin --i 001/masks/brain.nii.gz --min 0.5 --dilate 1 --o 001/masks/brain.nii.gz 
sysname  Linux
hostname transfer
machine  x86_64
user     zkaufman

input      001/masks/brain.nii.gz
frame      0
nErode3d   0
nErode2d   0
output     001/masks/brain.nii.gz
Binarizing based on threshold
min        0.5
max        +infinity
binval        1
binvalnot     0
fstart = 0, fend = 0, nframes = 1
Found 24269 values in range
Dilating 1 voxels in 3d
Counting number of voxels in first frame
Found 35034 voxels in final mask
Count: 35034 2069879.749168 122880 28.510742
mri_binarize done
 
Started at Sun Mar 27 21:53:12 EDT 2016 
Ended   at Sun Mar 27 21:53:13 EDT 2016
Mkbrainmask-Run-Time-Sec 1
 
mkbrainmask Done