Log file for mkbrainmask
Sun Mar 27 21:53:15 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 003/template.nii.gz -o 003/masks/brain.nii.gz -reg /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/003/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 003/template.nii.gz --reg /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/003/register.dof6.lta --inv --interp nearest --o 003/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:
 0.99985  -0.01758  -0.00046  -0.36206;
-0.00410  -0.25832   0.96605  -41.03094;
 0.01710   0.96590   0.25835  -2.00327;
 0.00000   0.00000   0.00000   1.00000;

movvol 003/template.nii.gz
targvol /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects/fsf01anat/mri/aparc+aseg.mgz
outvol 003/masks/brain.nii.gz
regfile /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/003/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  1459992271

Invert!
Inverting registration

Final tkRAS-to-tkRAS Matrix is:
 0.99985  -0.00410   0.01710   0.22805;
-0.01758  -0.25832   0.96590  -8.67047;
-0.00046   0.96605   0.25835   40.15536;
-0.00000  -0.00000  -0.00000   1.00000;


Vox2Vox Matrix is:
 3.43697   0.05880   0.02050   15.60001;
-0.00158   0.88808  -4.83025   131.93027;
 0.06044  -3.32028  -1.29159   243.01820;
 0.00000   0.00000   0.00000   1.00000;

Resampling
Output registration matrix is identity

mri_vol2vol done
mri_binarize --i 003/masks/brain.nii.gz --o 003/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 003/masks/brain.nii.gz --o 003/masks/brain.nii.gz --min 0.5 
sysname  Linux
hostname transfer
machine  x86_64
user     zkaufman

input      003/masks/brain.nii.gz
frame      0
nErode3d   0
nErode2d   0
output     003/masks/brain.nii.gz
Binarizing based on threshold
min        0.5
max        +infinity
binval        1
binvalnot     0
fstart = 0, fend = 0, nframes = 1
Found 24335 values in range
Counting number of voxels in first frame
Found 24335 voxels in final mask
Count: 24335 1437761.137638 122880 19.803874
mri_binarize done
Diliating 1
mri_binarize --i 003/masks/brain.nii.gz --min 0.5 --dilate 1 --o 003/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 003/masks/brain.nii.gz --min 0.5 --dilate 1 --o 003/masks/brain.nii.gz 
sysname  Linux
hostname transfer
machine  x86_64
user     zkaufman

input      003/masks/brain.nii.gz
frame      0
nErode3d   0
nErode2d   0
output     003/masks/brain.nii.gz
Binarizing based on threshold
min        0.5
max        +infinity
binval        1
binvalnot     0
fstart = 0, fend = 0, nframes = 1
Found 24335 values in range
Dilating 1 voxels in 3d
Counting number of voxels in first frame
Found 35044 voxels in final mask
Count: 35044 2070470.569443 122880 28.518880
mri_binarize done
 
Started at Sun Mar 27 21:53:15 EDT 2016 
Ended   at Sun Mar 27 21:53:17 EDT 2016
Mkbrainmask-Run-Time-Sec 2
 
mkbrainmask Done