Log file for mkbrainmask
Sun Sep 30 01:22:51 EDT 2018

setenv SUBJECTS_DIR /media/sda1/nmrclass/tutorial_data/fsfast-tutorial.subjects
cd /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold
/media/sda1/nmrclass/freesurfer/fsfast/bin/mkbrainmask -i template.nii.gz -o masks/brain.nii.gz -reg /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold/register.dof6.lta -ndil 1 -nerode 0

freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-tutorial-2beb96c
$Id: mkbrainmask,v 1.17 2015/12/10 22:51:30 zkaufman Exp $
Linux fsuser3-G5-5587 4.15.0-34-generic #37-Ubuntu SMP Mon Aug 27 15:21:48 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
mri_vol2vol --mov template.nii.gz --reg /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold/register.dof6.lta --inv --interp nearest --o masks/brain.nii.gz --targ /media/sda1/nmrclass/tutorial_data/fsfast-tutorial.subjects/fsf01anat/mri/aparc+aseg.mgz
regio_read_register: loading lta

Matrix from regfile:
 0.99999   0.00268  -0.00300   0.72231;
 0.00352  -0.22242   0.97494  -40.39471;
-0.00195   0.97495   0.22243  -1.18300;
 0.00000   0.00000   0.00000   1.00000;

movvol template.nii.gz
targvol /media/sda1/nmrclass/tutorial_data/fsfast-tutorial.subjects/fsf01anat/mri/aparc+aseg.mgz
outvol masks/brain.nii.gz
regfile /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold/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  1538873989

Invert!
Inverting registration

Final tkRAS-to-tkRAS Matrix is:
 0.99999   0.00352  -0.00195  -0.58232;
 0.00268  -0.22242   0.97495  -7.83319;
-0.00300   0.97494   0.22243   39.64790;
-0.00000  -0.00000  -0.00000   1.00000;


Vox2Vox Matrix is:
 3.43747  -0.00669  -0.01761   19.06136;
-0.01032   0.76460  -4.87472   137.33600;
-0.00921  -3.35138  -1.11210   244.38734;
 0.00000   0.00000   0.00000   1.00000;

Resampling
Output registration matrix is identity

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

$Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $
cwd /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold
cmdline mri_binarize.bin --i masks/brain.nii.gz --o masks/brain.nii.gz --min 0.5 
sysname  Linux
hostname fsuser3-G5-5587
machine  x86_64
user     nmrclass

input      masks/brain.nii.gz
frame      0
nErode3d   0
nErode2d   0
output     masks/brain.nii.gz
Binarizing based on threshold
min        0.5
max        +infinity
binval        1
binvalnot     0
fstart = 0, fend = 0, nframes = 1
Found 24188 values in range
Counting number of voxels in first frame
Found 24188 voxels in final mask
Count: 24188 1429076.079605 122880 19.684245
mri_binarize done
Diliating 1
mri_binarize --i masks/brain.nii.gz --min 0.5 --dilate 1 --o masks/brain.nii.gz

$Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $
cwd /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold
cmdline mri_binarize.bin --i masks/brain.nii.gz --min 0.5 --dilate 1 --o masks/brain.nii.gz 
sysname  Linux
hostname fsuser3-G5-5587
machine  x86_64
user     nmrclass

input      masks/brain.nii.gz
frame      0
nErode3d   0
nErode2d   0
output     masks/brain.nii.gz
Binarizing based on threshold
min        0.5
max        +infinity
binval        1
binvalnot     0
fstart = 0, fend = 0, nframes = 1
Found 24188 values in range
Dilating 1 voxels in 3d
Counting number of voxels in first frame
Found 35032 voxels in final mask
Count: 35032 2069761.585114 122880 28.509115
mri_binarize done
 
Started at Sun Sep 30 01:22:51 EDT 2018 
Ended   at Sun Sep 30 01:22:52 EDT 2018
Mkbrainmask-Run-Time-Sec 1
 
mkbrainmask Done