This notebook will go through the pipeline for normalizing an fMRI dataset into the MNI template space.
Importing modules
In [2]:
%matplotlib inline
import os, shutil, errno
import sklearn.metrics
import nibabel
import numpy
import nilearn.plotting
import matplotlib.pyplot as plt
from nipype.interfaces import fsl, ants
from nipype.caching import Memory
mem = Memory(base_dir='.')
datadir='/home/vagrant/data'
assert os.path.exists(datadir)
print('Using data from',datadir)
results_dir = os.path.abspath("../results")
if not os.path.exists(results_dir):
os.mkdir(results_dir)
def force_symlink(file1, file2):
try:
os.symlink(file1, file2)
except OSError as e:
if e.errno == errno.EEXIST:
os.remove(file2)
os.symlink(file1, file2)
Using data from /home/vagrant/data
Setting up variables
In [9]:
subject='ses014'
# note - we have to use the anatomy from a different session'
anat_subject='ses018'
bolddir=os.path.join(datadir,'ds031/sub00001',subject,
'functional')
fmapdir=os.path.join(datadir,'ds031/sub00001',subject,
'fieldmap')
meanbold_unwarped_file=os.path.join(results_dir, "meanbold_unwarped.nii.gz")
meanbold=os.path.join(results_dir, "meanbold.nii.gz")
fmapmagdiff=os.path.join(fmapdir, "sub00001_ses014_001_magdiff.nii.gz")
fmapphasediff=os.path.join(fmapdir, "sub00001_ses014_001_phasediff.nii.gz")
fmapmag=os.path.join(fmapdir, "sub00001_ses014_001_magnitude.nii.gz")
fmapmagbrain=os.path.join(results_dir, "fmapmagbrain.nii.gz")
fmap=os.path.join(results_dir, "fieldmap.nii.gz")
boldfile=os.path.join(bolddir,
'sub00001_ses014_task002_run001_bold.nii.gz')
anatomydir=os.path.join(datadir,'ds031/sub00001',anat_subject,
'anatomy')
t1file=os.path.join(anatomydir,'sub00001_ses018_T1w_001.nii.gz')
In [4]:
datadir
Out[4]:
'/home/vagrant/data'
In [ ]:
In [5]:
bias_field_correcton = mem.cache(ants.N4BiasFieldCorrection)
bias_field_correcton_results = bias_field_correcton(input_image = t1file,
dimension = 3,
save_bias = True)
bias_field_correcton_results.outputs
161012-20:51:05,361 workflow INFO:
Executing node 0ee99ba1bb2c1fe9f082ea94b809ecd0 in dir: /home/vagrant/fmri-analysis-vm/analysis/normalization/nipype_mem/nipype-interfaces-ants-segmentation-N4BiasFieldCorrection/0ee99ba1bb2c1fe9f082ea94b809ecd0
161012-20:51:05,363 workflow INFO:
Collecting precomputed outputs
Out[5]:
bias_image = /home/vagrant/fmri-analysis-vm/analysis/normalization/nipype_mem/nipype-interfaces-ants-segmentation-N4BiasFieldCorrection/0ee99ba1bb2c1fe9f082ea94b809ecd0/sub00001_ses018_T1w_001_bias.nii.gz
output_image = /home/vagrant/fmri-analysis-vm/analysis/normalization/nipype_mem/nipype-interfaces-ants-segmentation-N4BiasFieldCorrection/0ee99ba1bb2c1fe9f082ea94b809ecd0/sub00001_ses018_T1w_001_corrected.nii.gz
In [6]:
fig = plt.figure(figsize=(12,6))
nilearn.plotting.plot_anat(t1file, colorbar=True, vmax=3000, display_mode='z', cut_coords=(14, 40),
title="original T1", figure=fig)
fig = plt.figure(figsize=(12,6))
nilearn.plotting.plot_anat(bias_field_correcton_results.outputs.bias_image, display_mode='z',
cut_coords=(14, 40), colorbar=True, title="estimated bias field", figure=fig)
fig = plt.figure(figsize=(12,6))
nilearn.plotting.plot_anat(bias_field_correcton_results.outputs.output_image, colorbar=True,
vmax=3000, display_mode='z', cut_coords=(14, 40), title="corrected T1", figure=fig)
/home/vagrant/miniconda3/lib/python3.5/site-packages/nilearn/image/resampling.py:472: UserWarning: Casting data from int32 to float32
warnings.warn("Casting data from %s to %s" % (data.dtype.name, aux))
Out[6]:
<nilearn.plotting.displays.ZSlicer at 0x7f94e56290f0>
Exercise: Compute the difference between the original and bias-corrected image, and display the difference in the same two slices as above.
In [7]:
bet = mem.cache(fsl.BET)
bet_results = bet(in_file=bias_field_correcton_results.outputs.output_image,
mask=True,
frac=0.3)
bet_results.outputs
161012-20:51:34,521 workflow INFO:
Executing node b759e86642ba486166bb7bcbfeca4cbf in dir: /home/vagrant/fmri-analysis-vm/analysis/normalization/nipype_mem/nipype-interfaces-fsl-preprocess-BET/b759e86642ba486166bb7bcbfeca4cbf
161012-20:51:34,524 workflow INFO:
Collecting precomputed outputs
Out[7]:
inskull_mask_file = <undefined>
inskull_mesh_file = <undefined>
mask_file = /home/vagrant/fmri-analysis-vm/analysis/normalization/nipype_mem/nipype-interfaces-fsl-preprocess-BET/b759e86642ba486166bb7bcbfeca4cbf/sub00001_ses018_T1w_001_corrected_brain_mask.nii.gz
meshfile = <undefined>
out_file = /home/vagrant/fmri-analysis-vm/analysis/normalization/nipype_mem/nipype-interfaces-fsl-preprocess-BET/b759e86642ba486166bb7bcbfeca4cbf/sub00001_ses018_T1w_001_corrected_brain.nii.gz
outline_file = <undefined>
outskin_mask_file = <undefined>
outskin_mesh_file = <undefined>
outskull_mask_file = <undefined>
outskull_mesh_file = <undefined>
skull_mask_file = <undefined>
Visualize brain mask overlaid on anatomy
In [7]:
mask_display=nilearn.plotting.plot_epi(t1file,cmap='gray')
mask_display.add_contours(bet_results.outputs.mask_file, levels=[.5])
/home/vagrant/miniconda3/lib/python3.5/site-packages/nilearn/image/resampling.py:472: UserWarning: Casting data from int32 to float32
warnings.warn("Casting data from %s to %s" % (data.dtype.name, aux))
/home/vagrant/miniconda3/lib/python3.5/site-packages/nilearn/image/resampling.py:472: UserWarning: Casting data from int16 to float32
warnings.warn("Casting data from %s to %s" % (data.dtype.name, aux))
Please note that we are using mean EPI image instead of whole time series.
In [12]:
# first need to prepare the fieldmap
fmp=mem.cache(fsl.PrepareFieldmap)
fmp_results=fmp(in_phase=fmapphasediff,
in_magnitude=fmapmagdiff,
out_fieldmap=fmap)
161012-19:56:30,683 workflow INFO:
Executing node 7195642fa39cc3fc82493c1311d96dbf in dir: /home/vagrant/fmri-analysis-vm/analysis/normalization/nipype_mem/nipype-interfaces-fsl-epi-PrepareFieldmap/7195642fa39cc3fc82493c1311d96dbf
161012-19:56:30,688 workflow INFO:
Running: fsl_prepare_fieldmap SIEMENS /home/vagrant/data/ds031/sub00001/ses014/fieldmap/sub00001_ses014_001_phasediff.nii.gz /home/vagrant/data/ds031/sub00001/ses014/fieldmap/sub00001_ses014_001_magdiff.nii.gz /home/vagrant/fmri-analysis-vm/analysis/results/fieldmap.nii.gz 2.460000
161012-19:56:31,735 interface INFO:
stdout 2016-10-12T19:56:31.735883:Loading volumes
161012-19:56:31,737 interface INFO:
stdout 2016-10-12T19:56:31.735883:Phase loaded
161012-19:56:31,738 interface INFO:
stdout 2016-10-12T19:56:31.735883:Magnitude loaded
161012-19:56:31,739 interface INFO:
stdout 2016-10-12T19:56:31.735883:Mask loaded
161012-19:56:31,740 interface INFO:
stdout 2016-10-12T19:56:31.735883:Rewrapping phase range to [-pi,pi]
161012-19:56:31,742 interface INFO:
stdout 2016-10-12T19:56:31.735883:Number of phase splits = 8
161012-19:56:32,244 interface INFO:
stdout 2016-10-12T19:56:32.244144:Calculating starting matrices (74222 by 74222)
161012-19:56:32,245 interface INFO:
stdout 2016-10-12T19:56:32.244144:Finished connection_matrices
161012-19:56:32,247 interface INFO:
stdout 2016-10-12T19:56:32.244144:152944 constraints left
161012-19:56:40,942 interface INFO:
stdout 2016-10-12T19:56:40.942147:132688 constraints left
---------------------------------------------------------------------------
KeyboardInterrupt Traceback (most recent call last)
<ipython-input-12-d3096ce4ba77> in <module>()
4 fmp_results=fmp(in_phase=fmapphasediff,
5 in_magnitude=fmapmagdiff,
----> 6 out_fieldmap=fmap)
7
8 fmmean=cache(fsl.MeanImage)
/home/vagrant/miniconda3/lib/python3.5/site-packages/nipype/caching/memory.py in __call__(self, **kwargs)
84 cwd = os.getcwd()
85 try:
---> 86 out = node.run()
87 finally:
88 # node.run() changes to the node directory - if something goes wrong
/home/vagrant/miniconda3/lib/python3.5/site-packages/nipype/pipeline/engine/nodes.py in run(self, updatehash)
375 self.inputs.get_traitsfree())
376 try:
--> 377 self._run_interface()
378 except:
379 os.remove(hashfile_unfinished)
/home/vagrant/miniconda3/lib/python3.5/site-packages/nipype/pipeline/engine/nodes.py in _run_interface(self, execute, updatehash)
485 old_cwd = os.getcwd()
486 os.chdir(self.output_dir())
--> 487 self._result = self._run_command(execute)
488 os.chdir(old_cwd)
489
/home/vagrant/miniconda3/lib/python3.5/site-packages/nipype/pipeline/engine/nodes.py in _run_command(self, execute, copyfiles)
615 logger.info('Running: %s' % cmd)
616 try:
--> 617 result = self._interface.run()
618 except Exception as msg:
619 self._result.runtime.stderr = msg
/home/vagrant/miniconda3/lib/python3.5/site-packages/nipype/interfaces/base.py in run(self, **inputs)
1080 version=self.version)
1081 try:
-> 1082 runtime = self._run_wrapper(runtime)
1083 outputs = self.aggregate_outputs(runtime)
1084 runtime.endTime = dt.isoformat(dt.utcnow())
/home/vagrant/miniconda3/lib/python3.5/site-packages/nipype/interfaces/base.py in _run_wrapper(self, runtime)
1723
1724 def _run_wrapper(self, runtime):
-> 1725 runtime = self._run_interface(runtime)
1726 return runtime
1727
/home/vagrant/miniconda3/lib/python3.5/site-packages/nipype/interfaces/fsl/epi.py in _run_interface(self, runtime)
99
100 def _run_interface(self, runtime):
--> 101 runtime = super(PrepareFieldmap, self)._run_interface(runtime)
102
103 if runtime.returncode == 0:
/home/vagrant/miniconda3/lib/python3.5/site-packages/nipype/interfaces/base.py in _run_interface(self, runtime, correct_return_codes)
1754 runtime.environ))
1755 runtime = run_command(runtime, output=self.inputs.terminal_output,
-> 1756 redirect_x=self._redirect_x)
1757 if runtime.returncode is None or \
1758 runtime.returncode not in correct_return_codes:
/home/vagrant/miniconda3/lib/python3.5/site-packages/nipype/interfaces/base.py in run_command(runtime, output, timeout, redirect_x)
1487 proc.poll()
1488 _process()
-> 1489 time.sleep(interval)
1490 _process(drain=1)
1491
KeyboardInterrupt:
In [10]:
fmmean=mem.cache(fsl.MeanImage)
fmmean_results=fmmean(in_file=fmapmag)
fmbet=mem.cache(fsl.BET)
fmbet_results=fmbet(in_file=fmmean_results.outputs.out_file,
out_file=fmapmagbrain)
mcflirt = mem.cache(fsl.MCFLIRT)
mcflirt_results = mcflirt(in_file=boldfile,
mean_vol=True)
boldbet = mem.cache(fsl.BET)
bet_results = boldbet(functional=True,
in_file=mcflirt_results.outputs.mean_img,
mask=True)
161012-20:53:04,517 workflow INFO:
Executing node 93635f8354bcd886e884e26f20008609 in dir: /home/vagrant/fmri-analysis-vm/analysis/normalization/nipype_mem/nipype-interfaces-fsl-maths-MeanImage/93635f8354bcd886e884e26f20008609
161012-20:53:04,518 workflow INFO:
Collecting precomputed outputs
161012-20:53:04,528 workflow INFO:
Executing node 6033b05365e3efe9f47869ad7af44f9b in dir: /home/vagrant/fmri-analysis-vm/analysis/normalization/nipype_mem/nipype-interfaces-fsl-preprocess-BET/6033b05365e3efe9f47869ad7af44f9b
161012-20:53:04,531 workflow INFO:
Collecting precomputed outputs
161012-20:53:04,540 workflow INFO:
Executing node fbfa00c218746e802e49f0bde8aa0174 in dir: /home/vagrant/fmri-analysis-vm/analysis/normalization/nipype_mem/nipype-interfaces-fsl-preprocess-MCFLIRT/fbfa00c218746e802e49f0bde8aa0174
161012-20:53:04,547 workflow INFO:
Running: mcflirt -in /home/vagrant/data/ds031/sub00001/ses014/functional/sub00001_ses014_task002_run001_bold.nii.gz -meanvol -out /home/vagrant/fmri-analysis-vm/analysis/normalization/nipype_mem/nipype-interfaces-fsl-preprocess-MCFLIRT/fbfa00c218746e802e49f0bde8aa0174/sub00001_ses014_task002_run001_bold_mcf.nii.gz
161012-20:55:23,846 workflow INFO:
Executing node fe668b7077efc12dc17112fa1290615d in dir: /home/vagrant/fmri-analysis-vm/analysis/normalization/nipype_mem/nipype-interfaces-fsl-preprocess-BET/fe668b7077efc12dc17112fa1290615d
161012-20:55:23,875 workflow INFO:
Running: bet /home/vagrant/fmri-analysis-vm/analysis/normalization/nipype_mem/nipype-interfaces-fsl-preprocess-MCFLIRT/fbfa00c218746e802e49f0bde8aa0174/sub00001_ses014_task002_run001_bold_mcf.nii.gz_mean_reg.nii.gz /home/vagrant/fmri-analysis-vm/analysis/normalization/nipype_mem/nipype-interfaces-fsl-preprocess-BET/fe668b7077efc12dc17112fa1290615d/sub00001_ses014_task002_run001_bold_mcf.nii.gz_mean_reg_brain.nii.gz -F -m
In [11]:
epi_reg = mem.cache(fsl.EpiReg)
epi_reg_results = epi_reg(epi=bet_results.outputs.out_file,
t1_head=bias_field_correcton_results.outputs.output_image,
t1_brain=bet_results.outputs.out_file,
fmap=fmap,
fmapmag=fmapmag,
fmapmagbrain=fmapmagbrain,
echospacing=2.6/10000.0,
pedir='y',
out_base="epi2struct")
force_symlink(epi_reg_results.outputs.fullwarp, os.path.join(results_dir, "epi_to_t1_warp.nii.gz"))
epi_reg_results.outputs
161012-20:56:03,239 workflow INFO:
Executing node 8aa1a7a3a91b013599dd0026e9a31d4e in dir: /home/vagrant/fmri-analysis-vm/analysis/normalization/nipype_mem/nipype-interfaces-fsl-epi-EpiReg/8aa1a7a3a91b013599dd0026e9a31d4e
161012-20:56:03,244 workflow INFO:
Running: epi_reg --echospacing=0.000260 --fmap=/home/vagrant/fmri-analysis-vm/analysis/results/fieldmap.nii.gz --fmapmag=/home/vagrant/data/ds031/sub00001/ses014/fieldmap/sub00001_ses014_001_magnitude.nii.gz --fmapmagbrain=/home/vagrant/fmri-analysis-vm/analysis/results/fmapmagbrain.nii.gz --noclean --pedir=y --epi=/home/vagrant/fmri-analysis-vm/analysis/normalization/nipype_mem/nipype-interfaces-fsl-preprocess-BET/fe668b7077efc12dc17112fa1290615d/sub00001_ses014_task002_run001_bold_mcf.nii.gz_mean_reg_brain.nii.gz --t1=/home/vagrant/fmri-analysis-vm/analysis/normalization/nipype_mem/nipype-interfaces-ants-segmentation-N4BiasFieldCorrection/0ee99ba1bb2c1fe9f082ea94b809ecd0/sub00001_ses018_T1w_001_corrected.nii.gz --t1brain=/home/vagrant/fmri-analysis-vm/analysis/normalization/nipype_mem/nipype-interfaces-fsl-preprocess-BET/fe668b7077efc12dc17112fa1290615d/sub00001_ses014_task002_run001_bold_mcf.nii.gz_mean_reg_brain.nii.gz --out=epi2struct
161012-20:56:03,788 interface INFO:
stdout 2016-10-12T20:56:03.788448:Running FAST segmentation
161012-20:56:21,172 interface INFO:
stdout 2016-10-12T20:56:21.172276:FLIRT pre-alignment
161012-20:56:25,264 interface INFO:
stdout 2016-10-12T20:56:25.264381:Registering fieldmap to structural
161012-20:57:02,599 interface INFO:
stdout 2016-10-12T20:57:02.599680:Running BBR with fieldmap
161012-20:57:35,853 interface INFO:
stdout 2016-10-12T20:57:35.853379:0.991598 0.996255 -0.020654 -0.083955 0.000000 0.062182 0.845841 0.529799 0.000000 0.060071 -0.533036 0.843958 0.000000 -25.134032 45.338248 9.364755 1.000000
161012-20:57:59,423 interface INFO:
stdout 2016-10-12T20:57:59.423051:Making warp fields and applying registration to EPI series
Out[11]:
epi2str_inv = /home/vagrant/fmri-analysis-vm/analysis/normalization/nipype_mem/nipype-interfaces-fsl-epi-EpiReg/8aa1a7a3a91b013599dd0026e9a31d4e/epi2struct_inv.mat
epi2str_mat = /home/vagrant/fmri-analysis-vm/analysis/normalization/nipype_mem/nipype-interfaces-fsl-epi-EpiReg/8aa1a7a3a91b013599dd0026e9a31d4e/epi2struct.mat
fmap2epi_mat = /home/vagrant/fmri-analysis-vm/analysis/normalization/nipype_mem/nipype-interfaces-fsl-epi-EpiReg/8aa1a7a3a91b013599dd0026e9a31d4e/epi2struct_fieldmaprads2epi.mat
fmap2str_mat = /home/vagrant/fmri-analysis-vm/analysis/normalization/nipype_mem/nipype-interfaces-fsl-epi-EpiReg/8aa1a7a3a91b013599dd0026e9a31d4e/epi2struct_fieldmap2str.mat
fmap_epi = /home/vagrant/fmri-analysis-vm/analysis/normalization/nipype_mem/nipype-interfaces-fsl-epi-EpiReg/8aa1a7a3a91b013599dd0026e9a31d4e/epi2struct_fieldmaprads2epi.nii.gz
fmap_str = /home/vagrant/fmri-analysis-vm/analysis/normalization/nipype_mem/nipype-interfaces-fsl-epi-EpiReg/8aa1a7a3a91b013599dd0026e9a31d4e/epi2struct_fieldmaprads2str.nii.gz
fmapmag_str = /home/vagrant/fmri-analysis-vm/analysis/normalization/nipype_mem/nipype-interfaces-fsl-epi-EpiReg/8aa1a7a3a91b013599dd0026e9a31d4e/epi2struct_fieldmap2str.nii.gz
fullwarp = /home/vagrant/fmri-analysis-vm/analysis/normalization/nipype_mem/nipype-interfaces-fsl-epi-EpiReg/8aa1a7a3a91b013599dd0026e9a31d4e/epi2struct_warp.nii.gz
out_1vol = /home/vagrant/fmri-analysis-vm/analysis/normalization/nipype_mem/nipype-interfaces-fsl-epi-EpiReg/8aa1a7a3a91b013599dd0026e9a31d4e/epi2struct_1vol.nii.gz
out_file = /home/vagrant/fmri-analysis-vm/analysis/normalization/nipype_mem/nipype-interfaces-fsl-epi-EpiReg/8aa1a7a3a91b013599dd0026e9a31d4e/epi2struct.nii.gz
shiftmap = /home/vagrant/fmri-analysis-vm/analysis/normalization/nipype_mem/nipype-interfaces-fsl-epi-EpiReg/8aa1a7a3a91b013599dd0026e9a31d4e/epi2struct_fieldmaprads2epi_shift.nii.gz
wmedge = /home/vagrant/fmri-analysis-vm/analysis/normalization/nipype_mem/nipype-interfaces-fsl-epi-EpiReg/8aa1a7a3a91b013599dd0026e9a31d4e/epi2struct_fast_wmedge.nii.gz
wmseg = /home/vagrant/fmri-analysis-vm/analysis/normalization/nipype_mem/nipype-interfaces-fsl-epi-EpiReg/8aa1a7a3a91b013599dd0026e9a31d4e/epi2struct_fast_wmseg.nii.gz
Boundary based registration used grey/white matter interface to corregister EPI and T1 images. This boundary has been estimated from the T1 image.
In [15]:
mask_display=nilearn.plotting.plot_epi(t1file,cmap='gray', cut_coords=(-20,0,20))
mask_display.add_contours(epi_reg_results.outputs.wmseg, levels=[.5])
/home/vagrant/miniconda3/lib/python3.5/site-packages/nilearn/image/resampling.py:472: UserWarning: Casting data from int32 to float32
warnings.warn("Casting data from %s to %s" % (data.dtype.name, aux))
To evaluate the quality of the corregistration lets overlay the grey-white matter border on top of the EPI image.
In [13]:
mask_display=nilearn.plotting.plot_epi(epi_reg_results.outputs.out_file,cmap='gray', cut_coords=(-20,0,20))
mask_display.add_contours(epi_reg_results.outputs.wmseg, levels=[.5])
To save time we will reduce the number of iterations.
In [14]:
ants_reg = mem.cache(ants.Registration)
ants_results = ants_reg(fixed_image = os.path.join(os.getenv('FSLDIR'),'data/standard/MNI152_T1_2mm_brain.nii.gz'),
moving_image = bet_results.outputs.out_file,
transforms = ['Translation', 'Rigid', 'Affine', 'SyN'],
transform_parameters = [(0.1,), (0.1,), (0.1,), (0.2, 3.0, 0.0)],
#number_of_iterations = ([[10000, 111110, 11110]]*3 +
# [[100, 50, 30]]),
number_of_iterations = ([[10, 10, 10]]*3 +
[[1, 5, 3]]),
dimension = 3,
write_composite_transform = True,
metric = ['Mattes'] * 3 + [['Mattes', 'CC']],
metric_weight = [1] * 3 + [[0.5, 0.5]],
radius_or_number_of_bins = [32] * 3 + [[32, 4]],
sampling_strategy = ['Regular'] * 3 + [[None, None]],
sampling_percentage = [0.3] * 3 + [[None, None]],
convergence_threshold = [1.e-8] * 3 + [-0.01],
convergence_window_size = [20] * 3 + [5],
smoothing_sigmas = [[4, 2, 1]] * 3 + [[1, 0.5, 0]],
sigma_units = ['vox'] * 4,
shrink_factors = [[6, 4, 2]] + [[3, 2, 1]]*2 + [[4, 2, 1]],
use_estimate_learning_rate_once = [True] * 4,
use_histogram_matching = [False] * 3 + [True],
initial_moving_transform_com = True,
output_warped_image = True)
force_symlink(ants_results.outputs.composite_transform, os.path.join(results_dir, "t1_to_mni_warp.h5"))
ants_results.outputs
161012-21:03:33,277 workflow INFO:
Executing node 71cf12fd00af0abd2f55c82d0f5ee549 in dir: /home/vagrant/fmri-analysis-vm/analysis/normalization/nipype_mem/nipype-interfaces-ants-registration-Registration/71cf12fd00af0abd2f55c82d0f5ee549
161012-21:03:33,292 workflow INFO:
Running: antsRegistration --collapse-output-transforms 0 --dimensionality 3 --initial-moving-transform [ /usr/share/fsl/5.0/data/standard/MNI152_T1_2mm_brain.nii.gz, /home/vagrant/fmri-analysis-vm/analysis/normalization/nipype_mem/nipype-interfaces-fsl-preprocess-BET/fe668b7077efc12dc17112fa1290615d/sub00001_ses014_task002_run001_bold_mcf.nii.gz_mean_reg_brain.nii.gz, 1 ] --initialize-transforms-per-stage 0 --interpolation Linear --output [ transform, transform_Warped.nii.gz ] --transform Translation[ 0.1 ] --metric Mattes[ /usr/share/fsl/5.0/data/standard/MNI152_T1_2mm_brain.nii.gz, /home/vagrant/fmri-analysis-vm/analysis/normalization/nipype_mem/nipype-interfaces-fsl-preprocess-BET/fe668b7077efc12dc17112fa1290615d/sub00001_ses014_task002_run001_bold_mcf.nii.gz_mean_reg_brain.nii.gz, 1, 32, Regular, 0.3 ] --convergence [ 10x10x10, 1e-08, 20 ] --smoothing-sigmas 4.0x2.0x1.0vox --shrink-factors 6x4x2 --use-estimate-learning-rate-once 1 --use-histogram-matching 0 --transform Rigid[ 0.1 ] --metric Mattes[ /usr/share/fsl/5.0/data/standard/MNI152_T1_2mm_brain.nii.gz, /home/vagrant/fmri-analysis-vm/analysis/normalization/nipype_mem/nipype-interfaces-fsl-preprocess-BET/fe668b7077efc12dc17112fa1290615d/sub00001_ses014_task002_run001_bold_mcf.nii.gz_mean_reg_brain.nii.gz, 1, 32, Regular, 0.3 ] --convergence [ 10x10x10, 1e-08, 20 ] --smoothing-sigmas 4.0x2.0x1.0vox --shrink-factors 3x2x1 --use-estimate-learning-rate-once 1 --use-histogram-matching 0 --transform Affine[ 0.1 ] --metric Mattes[ /usr/share/fsl/5.0/data/standard/MNI152_T1_2mm_brain.nii.gz, /home/vagrant/fmri-analysis-vm/analysis/normalization/nipype_mem/nipype-interfaces-fsl-preprocess-BET/fe668b7077efc12dc17112fa1290615d/sub00001_ses014_task002_run001_bold_mcf.nii.gz_mean_reg_brain.nii.gz, 1, 32, Regular, 0.3 ] --convergence [ 10x10x10, 1e-08, 20 ] --smoothing-sigmas 4.0x2.0x1.0vox --shrink-factors 3x2x1 --use-estimate-learning-rate-once 1 --use-histogram-matching 0 --transform SyN[ 0.2, 3.0, 0.0 ] --metric Mattes[ /usr/share/fsl/5.0/data/standard/MNI152_T1_2mm_brain.nii.gz, /home/vagrant/fmri-analysis-vm/analysis/normalization/nipype_mem/nipype-interfaces-fsl-preprocess-BET/fe668b7077efc12dc17112fa1290615d/sub00001_ses014_task002_run001_bold_mcf.nii.gz_mean_reg_brain.nii.gz, 0.5, 32 ] --metric CC[ /usr/share/fsl/5.0/data/standard/MNI152_T1_2mm_brain.nii.gz, /home/vagrant/fmri-analysis-vm/analysis/normalization/nipype_mem/nipype-interfaces-fsl-preprocess-BET/fe668b7077efc12dc17112fa1290615d/sub00001_ses014_task002_run001_bold_mcf.nii.gz_mean_reg_brain.nii.gz, 0.5, 4 ] --convergence [ 1x5x3, -0.01, 5 ] --smoothing-sigmas 1.0x0.5x0.0vox --shrink-factors 4x2x1 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --winsorize-image-intensities [ 0.0, 1.0 ] --write-composite-transform 1
/home/vagrant/miniconda3/lib/python3.5/site-packages/nipype/interfaces/base.py:432: UserWarning: Input convergence_threshold requires inputs: number_of_iterations
warn(msg)
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stdout 2016-10-12T21:03:33.863177:All_Command_lines_OK
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stdout 2016-10-12T21:03:33.863177:Using double precision for computations.
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stdout 2016-10-12T21:03:33.863177:=============================================================================
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stdout 2016-10-12T21:03:33.863177:The composite transform comprises the following transforms (in order):
161012-21:03:33,865 interface INFO:
stdout 2016-10-12T21:03:33.863177: 1. Center of mass alignment using fixed image: /usr/share/fsl/5.0/data/standard/MNI152_T1_2mm_brain.nii.gz and moving image: /home/vagrant/fmri-analysis-vm/analysis/normalization/nipype_mem/nipype-interfaces-fsl-preprocess-BET/fe668b7077efc12dc17112fa1290615d/sub00001_ses014_task002_run001_bold_mcf.nii.gz_mean_reg_brain.nii.gz (type = Euler3DTransform)
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stdout 2016-10-12T21:03:33.863177:=============================================================================
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stdout 2016-10-12T21:03:33.863177: number of levels = 3
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stdout 2016-10-12T21:03:33.863177: number of levels = 3
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stdout 2016-10-12T21:03:33.863177: number of levels = 3
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stdout 2016-10-12T21:03:33.863177: number of levels = 3
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stdout 2016-10-12T21:03:33.863177: fixed image: /usr/share/fsl/5.0/data/standard/MNI152_T1_2mm_brain.nii.gz
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stdout 2016-10-12T21:03:33.863177: moving image: /home/vagrant/fmri-analysis-vm/analysis/normalization/nipype_mem/nipype-interfaces-fsl-preprocess-BET/fe668b7077efc12dc17112fa1290615d/sub00001_ses014_task002_run001_bold_mcf.nii.gz_mean_reg_brain.nii.gz
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stdout 2016-10-12T21:03:33.863177: fixed image: /usr/share/fsl/5.0/data/standard/MNI152_T1_2mm_brain.nii.gz
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stdout 2016-10-12T21:03:33.863177: moving image: /home/vagrant/fmri-analysis-vm/analysis/normalization/nipype_mem/nipype-interfaces-fsl-preprocess-BET/fe668b7077efc12dc17112fa1290615d/sub00001_ses014_task002_run001_bold_mcf.nii.gz_mean_reg_brain.nii.gz
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stdout 2016-10-12T21:03:33.863177: fixed image: /usr/share/fsl/5.0/data/standard/MNI152_T1_2mm_brain.nii.gz
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stdout 2016-10-12T21:03:33.863177: moving image: /home/vagrant/fmri-analysis-vm/analysis/normalization/nipype_mem/nipype-interfaces-fsl-preprocess-BET/fe668b7077efc12dc17112fa1290615d/sub00001_ses014_task002_run001_bold_mcf.nii.gz_mean_reg_brain.nii.gz
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stdout 2016-10-12T21:03:33.863177: fixed image: /usr/share/fsl/5.0/data/standard/MNI152_T1_2mm_brain.nii.gz
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stdout 2016-10-12T21:03:33.863177: moving image: /home/vagrant/fmri-analysis-vm/analysis/normalization/nipype_mem/nipype-interfaces-fsl-preprocess-BET/fe668b7077efc12dc17112fa1290615d/sub00001_ses014_task002_run001_bold_mcf.nii.gz_mean_reg_brain.nii.gz
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stdout 2016-10-12T21:03:33.863177: fixed image: /usr/share/fsl/5.0/data/standard/MNI152_T1_2mm_brain.nii.gz
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stdout 2016-10-12T21:03:33.863177: moving image: /home/vagrant/fmri-analysis-vm/analysis/normalization/nipype_mem/nipype-interfaces-fsl-preprocess-BET/fe668b7077efc12dc17112fa1290615d/sub00001_ses014_task002_run001_bold_mcf.nii.gz_mean_reg_brain.nii.gz
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stdout 2016-10-12T21:03:33.863177:Dimension = 3
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stdout 2016-10-12T21:03:33.863177:Number of stages = 4
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stdout 2016-10-12T21:03:33.863177:Use Histogram Matching true
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stdout 2016-10-12T21:03:33.863177:Winsorize image intensities true
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stdout 2016-10-12T21:03:33.863177:Lower quantile = 0
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stdout 2016-10-12T21:03:33.863177:Upper quantile = 1
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stdout 2016-10-12T21:03:33.863177:Stage 1 State
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stdout 2016-10-12T21:03:33.863177: Image metric = Mattes
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stdout 2016-10-12T21:03:33.863177: Fixed image = Image (0x3114d70)
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stdout 2016-10-12T21:03:33.863177: RTTI typeinfo: itk::Image<double, 3u>
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stdout 2016-10-12T21:03:33.863177: Reference Count: 2
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stdout 2016-10-12T21:03:33.863177: Modified Time: 1783
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stdout 2016-10-12T21:03:34.427056: none
161012-21:03:34,479 interface INFO:
stdout 2016-10-12T21:03:34.427056: Pointer: 0x380cad0
161012-21:03:34,479 interface INFO:
stdout 2016-10-12T21:03:34.427056: Container manages memory: true
161012-21:03:34,480 interface INFO:
stdout 2016-10-12T21:03:34.427056: Size: 626688
161012-21:03:34,486 interface INFO:
stdout 2016-10-12T21:03:34.427056: Capacity: 626688
161012-21:03:34,487 interface INFO:
stdout 2016-10-12T21:03:34.427056:
161012-21:03:34,489 interface INFO:
stdout 2016-10-12T21:03:34.427056: Weighting = 1
161012-21:03:34,499 interface INFO:
stdout 2016-10-12T21:03:34.427056: Sampling strategy = regular
161012-21:03:34,500 interface INFO:
stdout 2016-10-12T21:03:34.427056: Number of bins = 32
161012-21:03:34,501 interface INFO:
stdout 2016-10-12T21:03:34.427056: Radius = 4
161012-21:03:34,502 interface INFO:
stdout 2016-10-12T21:03:34.427056: Sampling percentage = 0.3
161012-21:03:34,503 interface INFO:
stdout 2016-10-12T21:03:34.427056: Transform = Translation
161012-21:03:34,515 interface INFO:
stdout 2016-10-12T21:03:34.427056: Gradient step = 0.1
161012-21:03:34,515 interface INFO:
stdout 2016-10-12T21:03:34.427056: Update field sigma (voxel space) = 0
161012-21:03:34,515 interface INFO:
stdout 2016-10-12T21:03:34.427056: Total field sigma (voxel space) = 0
161012-21:03:34,516 interface INFO:
stdout 2016-10-12T21:03:34.427056: Update field time sigma = 0
161012-21:03:34,516 interface INFO:
stdout 2016-10-12T21:03:34.427056: Total field time sigma = 0
161012-21:03:34,517 interface INFO:
stdout 2016-10-12T21:03:34.427056: Number of time indices = 0
161012-21:03:34,517 interface INFO:
stdout 2016-10-12T21:03:34.427056: Number of time point samples = 0
161012-21:03:34,518 interface INFO:
stdout 2016-10-12T21:03:34.427056:Stage 2 State
161012-21:03:34,518 interface INFO:
stdout 2016-10-12T21:03:34.427056: Image metric = Mattes
161012-21:03:34,519 interface INFO:
stdout 2016-10-12T21:03:34.427056: Fixed image = Image (0x3cd4ae0)
161012-21:03:34,519 interface INFO:
stdout 2016-10-12T21:03:34.427056: RTTI typeinfo: itk::Image<double, 3u>
161012-21:03:34,528 interface INFO:
stdout 2016-10-12T21:03:34.427056: Reference Count: 2
161012-21:03:34,529 interface INFO:
stdout 2016-10-12T21:03:34.427056: Modified Time: 2137
161012-21:03:34,529 interface INFO:
stdout 2016-10-12T21:03:34.427056: Debug: Off
161012-21:03:34,530 interface INFO:
stdout 2016-10-12T21:03:34.427056: Object Name:
161012-21:03:34,530 interface INFO:
stdout 2016-10-12T21:03:34.427056: Observers:
161012-21:03:34,530 interface INFO:
stdout 2016-10-12T21:03:34.427056: none
161012-21:03:34,531 interface INFO:
stdout 2016-10-12T21:03:34.427056: Source: (none)
161012-21:03:34,531 interface INFO:
stdout 2016-10-12T21:03:34.427056: Source output name: (none)
161012-21:03:34,532 interface INFO:
stdout 2016-10-12T21:03:34.427056: Release Data: Off
161012-21:03:34,543 interface INFO:
stdout 2016-10-12T21:03:34.427056: Data Released: False
161012-21:03:34,544 interface INFO:
stdout 2016-10-12T21:03:34.427056: Global Release Data: Off
161012-21:03:34,545 interface INFO:
stdout 2016-10-12T21:03:34.427056: PipelineMTime: 0
161012-21:03:34,545 interface INFO:
stdout 2016-10-12T21:03:34.427056: UpdateMTime: 1959
161012-21:03:34,546 interface INFO:
stdout 2016-10-12T21:03:34.427056: RealTimeStamp: 0 seconds
161012-21:03:34,546 interface INFO:
stdout 2016-10-12T21:03:34.427056: LargestPossibleRegion:
161012-21:03:34,547 interface INFO:
stdout 2016-10-12T21:03:34.427056: Dimension: 3
161012-21:03:34,547 interface INFO:
stdout 2016-10-12T21:03:34.427056: Index: [0, 0, 0]
161012-21:03:34,548 interface INFO:
stdout 2016-10-12T21:03:34.427056: Size: [91, 109, 91]
161012-21:03:34,548 interface INFO:
stdout 2016-10-12T21:03:34.427056: BufferedRegion:
161012-21:03:34,549 interface INFO:
stdout 2016-10-12T21:03:34.427056: Dimension: 3
161012-21:03:34,562 interface INFO:
stdout 2016-10-12T21:03:34.427056: Index: [0, 0, 0]
161012-21:03:34,563 interface INFO:
stdout 2016-10-12T21:03:34.427056: Size: [91, 109, 91]
161012-21:03:34,564 interface INFO:
stdout 2016-10-12T21:03:34.427056: RequestedRegion:
161012-21:03:34,565 interface INFO:
stdout 2016-10-12T21:03:34.427056: Dimension: 3
161012-21:03:34,565 interface INFO:
stdout 2016-10-12T21:03:34.427056: Index: [0, 0, 0]
161012-21:03:34,566 interface INFO:
stdout 2016-10-12T21:03:34.427056: Size: [91, 109, 91]
161012-21:03:34,566 interface INFO:
stdout 2016-10-12T21:03:34.427056: Spacing: [2, 2, 2]
161012-21:03:34,567 interface INFO:
stdout 2016-10-12T21:03:34.427056: Origin: [-90, 126, -72]
161012-21:03:34,568 interface INFO:
stdout 2016-10-12T21:03:34.427056: Direction:
161012-21:03:34,578 interface INFO:
stdout 2016-10-12T21:03:34.427056:1 0 0
161012-21:03:34,580 interface INFO:
stdout 2016-10-12T21:03:34.427056:0 -1 0
161012-21:03:34,580 interface INFO:
stdout 2016-10-12T21:03:34.427056:0 0 1
161012-21:03:34,581 interface INFO:
stdout 2016-10-12T21:03:34.427056:
161012-21:03:34,582 interface INFO:
stdout 2016-10-12T21:03:34.427056: IndexToPointMatrix:
161012-21:03:34,583 interface INFO:
stdout 2016-10-12T21:03:34.427056:2 0 0
161012-21:03:34,584 interface INFO:
stdout 2016-10-12T21:03:34.427056:0 -2 0
161012-21:03:34,585 interface INFO:
stdout 2016-10-12T21:03:34.427056:0 0 2
161012-21:03:34,586 interface INFO:
stdout 2016-10-12T21:03:34.427056:
161012-21:03:34,586 interface INFO:
stdout 2016-10-12T21:03:34.427056: PointToIndexMatrix:
161012-21:03:34,587 interface INFO:
stdout 2016-10-12T21:03:34.427056:0.5 0 0
161012-21:03:34,588 interface INFO:
stdout 2016-10-12T21:03:34.427056:0 -0.5 0
161012-21:03:34,589 interface INFO:
stdout 2016-10-12T21:03:34.427056:0 0 0.5
161012-21:03:34,589 interface INFO:
stdout 2016-10-12T21:03:34.427056:
161012-21:03:34,590 interface INFO:
stdout 2016-10-12T21:03:34.427056: Inverse Direction:
161012-21:03:34,591 interface INFO:
stdout 2016-10-12T21:03:34.427056:1 0 0
161012-21:03:34,591 interface INFO:
stdout 2016-10-12T21:03:34.427056:0 -1 0
161012-21:03:34,592 interface INFO:
stdout 2016-10-12T21:03:34.427056:0 0 1
161012-21:03:34,593 interface INFO:
stdout 2016-10-12T21:03:34.427056:
161012-21:03:34,593 interface INFO:
stdout 2016-10-12T21:03:34.427056: PixelContainer:
161012-21:03:34,595 interface INFO:
stdout 2016-10-12T21:03:34.427056: ImportImageContainer (0x3110130)
161012-21:03:34,595 interface INFO:
stdout 2016-10-12T21:03:34.427056: RTTI typeinfo: itk::ImportImageContainer<unsigned long, double>
161012-21:03:34,596 interface INFO:
stdout 2016-10-12T21:03:34.427056: Reference Count: 1
161012-21:03:34,596 interface INFO:
stdout 2016-10-12T21:03:34.427056: Modified Time: 1956
161012-21:03:34,597 interface INFO:
stdout 2016-10-12T21:03:34.427056: Debug: Off
161012-21:03:34,597 interface INFO:
stdout 2016-10-12T21:03:34.427056: Object Name:
161012-21:03:34,598 interface INFO:
stdout 2016-10-12T21:03:34.427056: Observers:
161012-21:03:34,598 interface INFO:
stdout 2016-10-12T21:03:34.427056: none
161012-21:03:34,599 interface INFO:
stdout 2016-10-12T21:03:34.427056: Pointer: 0x3cd7ae0
161012-21:03:34,599 interface INFO:
stdout 2016-10-12T21:03:34.427056: Container manages memory: true
161012-21:03:34,600 interface INFO:
stdout 2016-10-12T21:03:34.427056: Size: 902629
161012-21:03:34,600 interface INFO:
stdout 2016-10-12T21:03:34.427056: Capacity: 902629
161012-21:03:34,601 interface INFO:
stdout 2016-10-12T21:03:34.427056:
161012-21:03:34,601 interface INFO:
stdout 2016-10-12T21:03:34.427056: Moving image = Image (0x43baa10)
161012-21:03:34,602 interface INFO:
stdout 2016-10-12T21:03:34.427056: RTTI typeinfo: itk::Image<double, 3u>
161012-21:03:34,603 interface INFO:
stdout 2016-10-12T21:03:34.427056: Reference Count: 2
161012-21:03:34,603 interface INFO:
stdout 2016-10-12T21:03:34.427056: Modified Time: 2138
161012-21:03:34,604 interface INFO:
stdout 2016-10-12T21:03:34.427056: Debug: Off
161012-21:03:34,604 interface INFO:
stdout 2016-10-12T21:03:34.427056: Object Name:
161012-21:03:34,604 interface INFO:
stdout 2016-10-12T21:03:34.427056: Observers:
161012-21:03:34,605 interface INFO:
stdout 2016-10-12T21:03:34.427056: none
161012-21:03:34,605 interface INFO:
stdout 2016-10-12T21:03:34.427056: Source: (none)
161012-21:03:34,606 interface INFO:
stdout 2016-10-12T21:03:34.427056: Source output name: (none)
161012-21:03:34,606 interface INFO:
stdout 2016-10-12T21:03:34.427056: Release Data: Off
161012-21:03:34,606 interface INFO:
stdout 2016-10-12T21:03:34.427056: Data Released: False
161012-21:03:34,607 interface INFO:
stdout 2016-10-12T21:03:34.427056: Global Release Data: Off
161012-21:03:34,607 interface INFO:
stdout 2016-10-12T21:03:34.427056: PipelineMTime: 0
161012-21:03:34,608 interface INFO:
stdout 2016-10-12T21:03:34.427056: UpdateMTime: 2135
161012-21:03:34,608 interface INFO:
stdout 2016-10-12T21:03:34.427056: RealTimeStamp: 0 seconds
161012-21:03:34,609 interface INFO:
stdout 2016-10-12T21:03:34.427056: LargestPossibleRegion:
161012-21:03:34,610 interface INFO:
stdout 2016-10-12T21:03:34.427056: Dimension: 3
161012-21:03:34,610 interface INFO:
stdout 2016-10-12T21:03:34.427056: Index: [0, 0, 0]
161012-21:03:34,611 interface INFO:
stdout 2016-10-12T21:03:34.427056: Size: [96, 96, 68]
161012-21:03:34,611 interface INFO:
stdout 2016-10-12T21:03:34.427056: BufferedRegion:
161012-21:03:34,612 interface INFO:
stdout 2016-10-12T21:03:34.427056: Dimension: 3
161012-21:03:34,612 interface INFO:
stdout 2016-10-12T21:03:34.427056: Index: [0, 0, 0]
161012-21:03:34,612 interface INFO:
stdout 2016-10-12T21:03:34.427056: Size: [96, 96, 68]
161012-21:03:34,613 interface INFO:
stdout 2016-10-12T21:03:34.427056: RequestedRegion:
161012-21:03:34,613 interface INFO:
stdout 2016-10-12T21:03:34.427056: Dimension: 3
161012-21:03:34,614 interface INFO:
stdout 2016-10-12T21:03:34.427056: Index: [0, 0, 0]
161012-21:03:34,614 interface INFO:
stdout 2016-10-12T21:03:34.427056: Size: [96, 96, 68]
161012-21:03:34,615 interface INFO:
stdout 2016-10-12T21:03:34.427056: Spacing: [2.39583, 2.39583, 2.4]
161012-21:03:34,615 interface INFO:
stdout 2016-10-12T21:03:34.427056: Origin: [-110.153, 63.604, -103.44]
161012-21:03:34,616 interface INFO:
stdout 2016-10-12T21:03:34.427056: Direction:
161012-21:03:34,616 interface INFO:
stdout 2016-10-12T21:03:34.427056:0.99865 -0.0218823 -0.047105
161012-21:03:34,616 interface INFO:
stdout 2016-10-12T21:03:34.427056:0.00754576 -0.836173 0.548413
161012-21:03:34,617 interface INFO:
stdout 2016-10-12T21:03:34.427056:0.0513885 0.548029 0.83488
161012-21:03:34,618 interface INFO:
stdout 2016-10-12T21:03:34.427056:
161012-21:03:34,618 interface INFO:
stdout 2016-10-12T21:03:34.427056: IndexToPointMatrix:
161012-21:03:34,619 interface INFO:
stdout 2016-10-12T21:03:34.427056:2.3926 -0.0524264 -0.113052
161012-21:03:34,619 interface INFO:
stdout 2016-10-12T21:03:34.427056:0.0180784 -2.00333 1.31619
161012-21:03:34,620 interface INFO:
stdout 2016-10-12T21:03:34.427056:0.123118 1.31299 2.00371
161012-21:03:34,620 interface INFO:
stdout 2016-10-12T21:03:34.427056:
161012-21:03:34,621 interface INFO:
stdout 2016-10-12T21:03:34.427056: PointToIndexMatrix:
161012-21:03:34,621 interface INFO:
stdout 2016-10-12T21:03:34.427056:0.416828 0.00314953 0.0214491
161012-21:03:34,622 interface INFO:
stdout 2016-10-12T21:03:34.427056:-0.00913349 -0.349011 0.228742
161012-21:03:34,622 interface INFO:
stdout 2016-10-12T21:03:34.427056:-0.0196271 0.228506 0.347866
161012-21:03:34,623 interface INFO:
stdout 2016-10-12T21:03:34.427056:
161012-21:03:34,623 interface INFO:
stdout 2016-10-12T21:03:34.427056: Inverse Direction:
161012-21:03:34,623 interface INFO:
stdout 2016-10-12T21:03:34.427056:0.99865 0.00754576 0.0513885
161012-21:03:34,624 interface INFO:
stdout 2016-10-12T21:03:34.427056:-0.0218823 -0.836173 0.548029
161012-21:03:34,624 interface INFO:
stdout 2016-10-12T21:03:34.427056:-0.047105 0.548413 0.83488
161012-21:03:34,625 interface INFO:
stdout 2016-10-12T21:03:34.427056:
161012-21:03:34,626 interface INFO:
stdout 2016-10-12T21:03:34.427056: PixelContainer:
161012-21:03:34,626 interface INFO:
stdout 2016-10-12T21:03:34.427056: ImportImageContainer (0x380ad50)
161012-21:03:34,627 interface INFO:
stdout 2016-10-12T21:03:34.427056: RTTI typeinfo: itk::ImportImageContainer<unsigned long, double>
161012-21:03:34,627 interface INFO:
stdout 2016-10-12T21:03:34.427056: Reference Count: 1
161012-21:03:34,628 interface INFO:
stdout 2016-10-12T21:03:34.427056: Modified Time: 2132
161012-21:03:34,628 interface INFO:
stdout 2016-10-12T21:03:34.427056: Debug: Off
161012-21:03:34,629 interface INFO:
stdout 2016-10-12T21:03:34.427056: Object Name:
161012-21:03:34,629 interface INFO:
stdout 2016-10-12T21:03:34.427056: Observers:
161012-21:03:34,630 interface INFO:
stdout 2016-10-12T21:03:34.427056: none
161012-21:03:34,630 interface INFO:
stdout 2016-10-12T21:03:34.427056: Pointer: 0x43be0b0
161012-21:03:34,639 interface INFO:
stdout 2016-10-12T21:03:34.427056: Container manages memory: true
161012-21:03:34,639 interface INFO:
stdout 2016-10-12T21:03:34.427056: Size: 626688
161012-21:03:34,640 interface INFO:
stdout 2016-10-12T21:03:34.427056: Capacity: 626688
161012-21:03:34,640 interface INFO:
stdout 2016-10-12T21:03:34.427056:
161012-21:03:34,641 interface INFO:
stdout 2016-10-12T21:03:34.427056: Weighting = 1
161012-21:03:34,641 interface INFO:
stdout 2016-10-12T21:03:34.427056: Sampling strategy = regular
161012-21:03:34,650 interface INFO:
stdout 2016-10-12T21:03:34.427056: Number of bins = 32
161012-21:03:34,651 interface INFO:
stdout 2016-10-12T21:03:34.427056: Radius = 4
161012-21:03:35,153 interface INFO:
stdout 2016-10-12T21:03:35.153303: Sampling percentage = 0.3
161012-21:03:35,154 interface INFO:
stdout 2016-10-12T21:03:35.153303: Transform = Rigid
161012-21:03:35,156 interface INFO:
stdout 2016-10-12T21:03:35.153303: Gradient step = 0.1
161012-21:03:35,159 interface INFO:
stdout 2016-10-12T21:03:35.153303: Update field sigma (voxel space) = 0
161012-21:03:35,167 interface INFO:
stdout 2016-10-12T21:03:35.153303: Total field sigma (voxel space) = 0
161012-21:03:35,168 interface INFO:
stdout 2016-10-12T21:03:35.153303: Update field time sigma = 0
161012-21:03:35,170 interface INFO:
stdout 2016-10-12T21:03:35.153303: Total field time sigma = 0
161012-21:03:35,172 interface INFO:
stdout 2016-10-12T21:03:35.153303: Number of time indices = 0
161012-21:03:35,174 interface INFO:
stdout 2016-10-12T21:03:35.153303: Number of time point samples = 0
161012-21:03:35,176 interface INFO:
stdout 2016-10-12T21:03:35.153303:Stage 3 State
161012-21:03:35,178 interface INFO:
stdout 2016-10-12T21:03:35.153303: Image metric = Mattes
161012-21:03:35,183 interface INFO:
stdout 2016-10-12T21:03:35.153303: Fixed image = Image (0x48860c0)
161012-21:03:35,186 interface INFO:
stdout 2016-10-12T21:03:35.153303: RTTI typeinfo: itk::Image<double, 3u>
161012-21:03:35,187 interface INFO:
stdout 2016-10-12T21:03:35.153303: Reference Count: 2
161012-21:03:35,188 interface INFO:
stdout 2016-10-12T21:03:35.153303: Modified Time: 2491
161012-21:03:35,189 interface INFO:
stdout 2016-10-12T21:03:35.153303: Debug: Off
161012-21:03:35,194 interface INFO:
stdout 2016-10-12T21:03:35.153303: Object Name:
161012-21:03:35,195 interface INFO:
stdout 2016-10-12T21:03:35.153303: Observers:
161012-21:03:35,196 interface INFO:
stdout 2016-10-12T21:03:35.153303: none
161012-21:03:35,197 interface INFO:
stdout 2016-10-12T21:03:35.153303: Source: (none)
161012-21:03:35,199 interface INFO:
stdout 2016-10-12T21:03:35.153303: Source output name: (none)
161012-21:03:35,200 interface INFO:
stdout 2016-10-12T21:03:35.153303: Release Data: Off
161012-21:03:35,206 interface INFO:
stdout 2016-10-12T21:03:35.153303: Data Released: False
161012-21:03:35,208 interface INFO:
stdout 2016-10-12T21:03:35.153303: Global Release Data: Off
161012-21:03:35,209 interface INFO:
stdout 2016-10-12T21:03:35.153303: PipelineMTime: 0
161012-21:03:35,211 interface INFO:
stdout 2016-10-12T21:03:35.153303: UpdateMTime: 2313
161012-21:03:35,212 interface INFO:
stdout 2016-10-12T21:03:35.153303: RealTimeStamp: 0 seconds
161012-21:03:35,213 interface INFO:
stdout 2016-10-12T21:03:35.153303: LargestPossibleRegion:
161012-21:03:35,214 interface INFO:
stdout 2016-10-12T21:03:35.153303: Dimension: 3
161012-21:03:35,215 interface INFO:
stdout 2016-10-12T21:03:35.153303: Index: [0, 0, 0]
161012-21:03:35,216 interface INFO:
stdout 2016-10-12T21:03:35.153303: Size: [91, 109, 91]
161012-21:03:35,218 interface INFO:
stdout 2016-10-12T21:03:35.153303: BufferedRegion:
161012-21:03:35,223 interface INFO:
stdout 2016-10-12T21:03:35.153303: Dimension: 3
161012-21:03:35,224 interface INFO:
stdout 2016-10-12T21:03:35.153303: Index: [0, 0, 0]
161012-21:03:35,225 interface INFO:
stdout 2016-10-12T21:03:35.153303: Size: [91, 109, 91]
161012-21:03:35,227 interface INFO:
stdout 2016-10-12T21:03:35.153303: RequestedRegion:
161012-21:03:35,228 interface INFO:
stdout 2016-10-12T21:03:35.153303: Dimension: 3
161012-21:03:35,229 interface INFO:
stdout 2016-10-12T21:03:35.153303: Index: [0, 0, 0]
161012-21:03:35,231 interface INFO:
stdout 2016-10-12T21:03:35.153303: Size: [91, 109, 91]
161012-21:03:35,233 interface INFO:
stdout 2016-10-12T21:03:35.153303: Spacing: [2, 2, 2]
161012-21:03:35,234 interface INFO:
stdout 2016-10-12T21:03:35.153303: Origin: [-90, 126, -72]
161012-21:03:35,235 interface INFO:
stdout 2016-10-12T21:03:35.153303: Direction:
161012-21:03:35,238 interface INFO:
stdout 2016-10-12T21:03:35.153303:1 0 0
161012-21:03:35,239 interface INFO:
stdout 2016-10-12T21:03:35.153303:0 -1 0
161012-21:03:35,240 interface INFO:
stdout 2016-10-12T21:03:35.153303:0 0 1
161012-21:03:35,241 interface INFO:
stdout 2016-10-12T21:03:35.153303:
161012-21:03:35,245 interface INFO:
stdout 2016-10-12T21:03:35.153303: IndexToPointMatrix:
161012-21:03:35,247 interface INFO:
stdout 2016-10-12T21:03:35.153303:2 0 0
161012-21:03:35,249 interface INFO:
stdout 2016-10-12T21:03:35.153303:0 -2 0
161012-21:03:35,250 interface INFO:
stdout 2016-10-12T21:03:35.153303:0 0 2
161012-21:03:35,254 interface INFO:
stdout 2016-10-12T21:03:35.153303:
161012-21:03:35,256 interface INFO:
stdout 2016-10-12T21:03:35.153303: PointToIndexMatrix:
161012-21:03:35,257 interface INFO:
stdout 2016-10-12T21:03:35.153303:0.5 0 0
161012-21:03:35,258 interface INFO:
stdout 2016-10-12T21:03:35.153303:0 -0.5 0
161012-21:03:35,259 interface INFO:
stdout 2016-10-12T21:03:35.153303:0 0 0.5
161012-21:03:35,262 interface INFO:
stdout 2016-10-12T21:03:35.153303:
161012-21:03:35,266 interface INFO:
stdout 2016-10-12T21:03:35.153303: Inverse Direction:
161012-21:03:35,267 interface INFO:
stdout 2016-10-12T21:03:35.153303:1 0 0
161012-21:03:35,269 interface INFO:
stdout 2016-10-12T21:03:35.153303:0 -1 0
161012-21:03:35,270 interface INFO:
stdout 2016-10-12T21:03:35.153303:0 0 1
161012-21:03:35,271 interface INFO:
stdout 2016-10-12T21:03:35.153303:
161012-21:03:35,272 interface INFO:
stdout 2016-10-12T21:03:35.153303: PixelContainer:
161012-21:03:35,273 interface INFO:
stdout 2016-10-12T21:03:35.153303: ImportImageContainer (0x3cd5aa0)
161012-21:03:35,274 interface INFO:
stdout 2016-10-12T21:03:35.153303: RTTI typeinfo: itk::ImportImageContainer<unsigned long, double>
161012-21:03:35,275 interface INFO:
stdout 2016-10-12T21:03:35.153303: Reference Count: 1
161012-21:03:35,276 interface INFO:
stdout 2016-10-12T21:03:35.153303: Modified Time: 2310
161012-21:03:35,277 interface INFO:
stdout 2016-10-12T21:03:35.153303: Debug: Off
161012-21:03:35,278 interface INFO:
stdout 2016-10-12T21:03:35.153303: Object Name:
161012-21:03:35,279 interface INFO:
stdout 2016-10-12T21:03:35.153303: Observers:
161012-21:03:35,280 interface INFO:
stdout 2016-10-12T21:03:35.153303: none
161012-21:03:35,281 interface INFO:
stdout 2016-10-12T21:03:35.153303: Pointer: 0x48890c0
161012-21:03:35,283 interface INFO:
stdout 2016-10-12T21:03:35.153303: Container manages memory: true
161012-21:03:35,284 interface INFO:
stdout 2016-10-12T21:03:35.153303: Size: 902629
161012-21:03:35,285 interface INFO:
stdout 2016-10-12T21:03:35.153303: Capacity: 902629
161012-21:03:35,287 interface INFO:
stdout 2016-10-12T21:03:35.153303:
161012-21:03:35,288 interface INFO:
stdout 2016-10-12T21:03:35.153303: Moving image = Image (0x4f6bff0)
161012-21:03:35,289 interface INFO:
stdout 2016-10-12T21:03:35.153303: RTTI typeinfo: itk::Image<double, 3u>
161012-21:03:35,289 interface INFO:
stdout 2016-10-12T21:03:35.153303: Reference Count: 2
161012-21:03:35,290 interface INFO:
stdout 2016-10-12T21:03:35.153303: Modified Time: 2492
161012-21:03:35,291 interface INFO:
stdout 2016-10-12T21:03:35.153303: Debug: Off
161012-21:03:35,293 interface INFO:
stdout 2016-10-12T21:03:35.153303: Object Name:
161012-21:03:35,295 interface INFO:
stdout 2016-10-12T21:03:35.153303: Observers:
161012-21:03:35,296 interface INFO:
stdout 2016-10-12T21:03:35.153303: none
161012-21:03:35,297 interface INFO:
stdout 2016-10-12T21:03:35.153303: Source: (none)
161012-21:03:35,299 interface INFO:
stdout 2016-10-12T21:03:35.153303: Source output name: (none)
161012-21:03:35,301 interface INFO:
stdout 2016-10-12T21:03:35.153303: Release Data: Off
161012-21:03:35,303 interface INFO:
stdout 2016-10-12T21:03:35.153303: Data Released: False
161012-21:03:35,304 interface INFO:
stdout 2016-10-12T21:03:35.153303: Global Release Data: Off
161012-21:03:35,305 interface INFO:
stdout 2016-10-12T21:03:35.153303: PipelineMTime: 0
161012-21:03:35,308 interface INFO:
stdout 2016-10-12T21:03:35.153303: UpdateMTime: 2489
161012-21:03:35,310 interface INFO:
stdout 2016-10-12T21:03:35.153303: RealTimeStamp: 0 seconds
161012-21:03:35,315 interface INFO:
stdout 2016-10-12T21:03:35.153303: LargestPossibleRegion:
161012-21:03:35,316 interface INFO:
stdout 2016-10-12T21:03:35.153303: Dimension: 3
161012-21:03:35,318 interface INFO:
stdout 2016-10-12T21:03:35.153303: Index: [0, 0, 0]
161012-21:03:35,320 interface INFO:
stdout 2016-10-12T21:03:35.153303: Size: [96, 96, 68]
161012-21:03:35,330 interface INFO:
stdout 2016-10-12T21:03:35.153303: BufferedRegion:
161012-21:03:35,332 interface INFO:
stdout 2016-10-12T21:03:35.153303: Dimension: 3
161012-21:03:35,335 interface INFO:
stdout 2016-10-12T21:03:35.153303: Index: [0, 0, 0]
161012-21:03:35,336 interface INFO:
stdout 2016-10-12T21:03:35.153303: Size: [96, 96, 68]
161012-21:03:35,337 interface INFO:
stdout 2016-10-12T21:03:35.153303: RequestedRegion:
161012-21:03:35,338 interface INFO:
stdout 2016-10-12T21:03:35.153303: Dimension: 3
161012-21:03:35,339 interface INFO:
stdout 2016-10-12T21:03:35.153303: Index: [0, 0, 0]
161012-21:03:35,341 interface INFO:
stdout 2016-10-12T21:03:35.153303: Size: [96, 96, 68]
161012-21:03:35,342 interface INFO:
stdout 2016-10-12T21:03:35.153303: Spacing: [2.39583, 2.39583, 2.4]
161012-21:03:35,344 interface INFO:
stdout 2016-10-12T21:03:35.153303: Origin: [-110.153, 63.604, -103.44]
161012-21:03:35,348 interface INFO:
stdout 2016-10-12T21:03:35.153303: Direction:
161012-21:03:35,350 interface INFO:
stdout 2016-10-12T21:03:35.153303:0.99865 -0.0218823 -0.047105
161012-21:03:35,352 interface INFO:
stdout 2016-10-12T21:03:35.153303:0.00754576 -0.836173 0.548413
161012-21:03:35,353 interface INFO:
stdout 2016-10-12T21:03:35.153303:0.0513885 0.548029 0.83488
161012-21:03:35,355 interface INFO:
stdout 2016-10-12T21:03:35.153303:
161012-21:03:35,356 interface INFO:
stdout 2016-10-12T21:03:35.153303: IndexToPointMatrix:
161012-21:03:35,357 interface INFO:
stdout 2016-10-12T21:03:35.153303:2.3926 -0.0524264 -0.113052
161012-21:03:35,358 interface INFO:
stdout 2016-10-12T21:03:35.153303:0.0180784 -2.00333 1.31619
161012-21:03:35,359 interface INFO:
stdout 2016-10-12T21:03:35.153303:0.123118 1.31299 2.00371
161012-21:03:35,363 interface INFO:
stdout 2016-10-12T21:03:35.153303:
161012-21:03:35,365 interface INFO:
stdout 2016-10-12T21:03:35.153303: PointToIndexMatrix:
161012-21:03:35,366 interface INFO:
stdout 2016-10-12T21:03:35.153303:0.416828 0.00314953 0.0214491
161012-21:03:35,367 interface INFO:
stdout 2016-10-12T21:03:35.153303:-0.00913349 -0.349011 0.228742
161012-21:03:35,368 interface INFO:
stdout 2016-10-12T21:03:35.153303:-0.0196271 0.228506 0.347866
161012-21:03:35,369 interface INFO:
stdout 2016-10-12T21:03:35.153303:
161012-21:03:35,371 interface INFO:
stdout 2016-10-12T21:03:35.153303: Inverse Direction:
161012-21:03:35,372 interface INFO:
stdout 2016-10-12T21:03:35.153303:0.99865 0.00754576 0.0513885
161012-21:03:35,373 interface INFO:
stdout 2016-10-12T21:03:35.153303:-0.0218823 -0.836173 0.548029
161012-21:03:35,374 interface INFO:
stdout 2016-10-12T21:03:35.153303:-0.047105 0.548413 0.83488
161012-21:03:35,375 interface INFO:
stdout 2016-10-12T21:03:35.153303:
161012-21:03:35,376 interface INFO:
stdout 2016-10-12T21:03:35.153303: PixelContainer:
161012-21:03:35,377 interface INFO:
stdout 2016-10-12T21:03:35.153303: ImportImageContainer (0x43bb2d0)
161012-21:03:35,378 interface INFO:
stdout 2016-10-12T21:03:35.153303: RTTI typeinfo: itk::ImportImageContainer<unsigned long, double>
161012-21:03:35,379 interface INFO:
stdout 2016-10-12T21:03:35.153303: Reference Count: 1
161012-21:03:35,381 interface INFO:
stdout 2016-10-12T21:03:35.153303: Modified Time: 2486
161012-21:03:35,382 interface INFO:
stdout 2016-10-12T21:03:35.153303: Debug: Off
161012-21:03:35,383 interface INFO:
stdout 2016-10-12T21:03:35.153303: Object Name:
161012-21:03:35,384 interface INFO:
stdout 2016-10-12T21:03:35.153303: Observers:
161012-21:03:35,385 interface INFO:
stdout 2016-10-12T21:03:35.153303: none
161012-21:03:35,386 interface INFO:
stdout 2016-10-12T21:03:35.153303: Pointer: 0x4f6f660
161012-21:03:35,387 interface INFO:
stdout 2016-10-12T21:03:35.153303: Container manages memory: true
161012-21:03:35,388 interface INFO:
stdout 2016-10-12T21:03:35.153303: Size: 626688
161012-21:03:35,389 interface INFO:
stdout 2016-10-12T21:03:35.153303: Capacity: 626688
161012-21:03:35,390 interface INFO:
stdout 2016-10-12T21:03:35.153303:
161012-21:03:35,391 interface INFO:
stdout 2016-10-12T21:03:35.153303: Weighting = 1
161012-21:03:35,392 interface INFO:
stdout 2016-10-12T21:03:35.153303: Sampling strategy = regular
161012-21:03:35,394 interface INFO:
stdout 2016-10-12T21:03:35.153303: Number of bins = 32
161012-21:03:35,396 interface INFO:
stdout 2016-10-12T21:03:35.153303: Radius = 4
161012-21:03:35,398 interface INFO:
stdout 2016-10-12T21:03:35.153303: Sampling percentage = 0.3
161012-21:03:35,399 interface INFO:
stdout 2016-10-12T21:03:35.153303: Transform = Affine
161012-21:03:35,404 interface INFO:
stdout 2016-10-12T21:03:35.153303: Gradient step = 0.1
161012-21:03:35,406 interface INFO:
stdout 2016-10-12T21:03:35.153303: Update field sigma (voxel space) = 0
161012-21:03:35,408 interface INFO:
stdout 2016-10-12T21:03:35.153303: Total field sigma (voxel space) = 0
161012-21:03:35,410 interface INFO:
stdout 2016-10-12T21:03:35.153303: Update field time sigma = 0
161012-21:03:35,412 interface INFO:
stdout 2016-10-12T21:03:35.153303: Total field time sigma = 0
161012-21:03:35,425 interface INFO:
stdout 2016-10-12T21:03:35.153303: Number of time indices = 0
161012-21:03:35,427 interface INFO:
stdout 2016-10-12T21:03:35.153303: Number of time point samples = 0
161012-21:03:35,428 interface INFO:
stdout 2016-10-12T21:03:35.153303:Stage 4 State
161012-21:03:35,429 interface INFO:
stdout 2016-10-12T21:03:35.153303: Image metric = Mattes
161012-21:03:35,430 interface INFO:
stdout 2016-10-12T21:03:35.153303: Fixed image = Image (0x5437670)
161012-21:03:35,431 interface INFO:
stdout 2016-10-12T21:03:35.153303: RTTI typeinfo: itk::Image<double, 3u>
161012-21:03:35,432 interface INFO:
stdout 2016-10-12T21:03:35.153303: Reference Count: 2
161012-21:03:35,433 interface INFO:
stdout 2016-10-12T21:03:35.153303: Modified Time: 2845
161012-21:03:35,434 interface INFO:
stdout 2016-10-12T21:03:35.153303: Debug: Off
161012-21:03:35,435 interface INFO:
stdout 2016-10-12T21:03:35.153303: Object Name:
161012-21:03:35,436 interface INFO:
stdout 2016-10-12T21:03:35.153303: Observers:
161012-21:03:35,438 interface INFO:
stdout 2016-10-12T21:03:35.153303: none
161012-21:03:35,440 interface INFO:
stdout 2016-10-12T21:03:35.153303: Source: (none)
161012-21:03:35,442 interface INFO:
stdout 2016-10-12T21:03:35.153303: Source output name: (none)
161012-21:03:35,459 interface INFO:
stdout 2016-10-12T21:03:35.153303: Release Data: Off
161012-21:03:35,461 interface INFO:
stdout 2016-10-12T21:03:35.153303: Data Released: False
161012-21:03:35,464 interface INFO:
stdout 2016-10-12T21:03:35.153303: Global Release Data: Off
161012-21:03:35,465 interface INFO:
stdout 2016-10-12T21:03:35.153303: PipelineMTime: 0
161012-21:03:35,466 interface INFO:
stdout 2016-10-12T21:03:35.153303: UpdateMTime: 2667
161012-21:03:35,467 interface INFO:
stdout 2016-10-12T21:03:35.153303: RealTimeStamp: 0 seconds
161012-21:03:35,468 interface INFO:
stdout 2016-10-12T21:03:35.153303: LargestPossibleRegion:
161012-21:03:35,469 interface INFO:
stdout 2016-10-12T21:03:35.153303: Dimension: 3
161012-21:03:35,471 interface INFO:
stdout 2016-10-12T21:03:35.153303: Index: [0, 0, 0]
161012-21:03:35,472 interface INFO:
stdout 2016-10-12T21:03:35.153303: Size: [91, 109, 91]
161012-21:03:35,473 interface INFO:
stdout 2016-10-12T21:03:35.153303: BufferedRegion:
161012-21:03:35,475 interface INFO:
stdout 2016-10-12T21:03:35.153303: Dimension: 3
161012-21:03:35,476 interface INFO:
stdout 2016-10-12T21:03:35.153303: Index: [0, 0, 0]
161012-21:03:35,480 interface INFO:
stdout 2016-10-12T21:03:35.153303: Size: [91, 109, 91]
161012-21:03:35,484 interface INFO:
stdout 2016-10-12T21:03:35.153303: RequestedRegion:
161012-21:03:35,486 interface INFO:
stdout 2016-10-12T21:03:35.153303: Dimension: 3
161012-21:03:35,487 interface INFO:
stdout 2016-10-12T21:03:35.153303: Index: [0, 0, 0]
161012-21:03:35,489 interface INFO:
stdout 2016-10-12T21:03:35.153303: Size: [91, 109, 91]
161012-21:03:35,490 interface INFO:
stdout 2016-10-12T21:03:35.153303: Spacing: [2, 2, 2]
161012-21:03:35,491 interface INFO:
stdout 2016-10-12T21:03:35.153303: Origin: [-90, 126, -72]
161012-21:03:35,492 interface INFO:
stdout 2016-10-12T21:03:35.153303: Direction:
161012-21:03:35,495 interface INFO:
stdout 2016-10-12T21:03:35.153303:1 0 0
161012-21:03:35,498 interface INFO:
stdout 2016-10-12T21:03:35.153303:0 -1 0
161012-21:03:35,500 interface INFO:
stdout 2016-10-12T21:03:35.153303:0 0 1
161012-21:03:35,502 interface INFO:
stdout 2016-10-12T21:03:35.153303:
161012-21:03:36,4 interface INFO:
stdout 2016-10-12T21:03:36.004792: IndexToPointMatrix:
161012-21:03:36,6 interface INFO:
stdout 2016-10-12T21:03:36.004792:2 0 0
161012-21:03:36,7 interface INFO:
stdout 2016-10-12T21:03:36.004792:0 -2 0
161012-21:03:36,8 interface INFO:
stdout 2016-10-12T21:03:36.004792:0 0 2
161012-21:03:36,9 interface INFO:
stdout 2016-10-12T21:03:36.004792:
161012-21:03:36,11 interface INFO:
stdout 2016-10-12T21:03:36.004792: PointToIndexMatrix:
161012-21:03:36,12 interface INFO:
stdout 2016-10-12T21:03:36.004792:0.5 0 0
161012-21:03:36,13 interface INFO:
stdout 2016-10-12T21:03:36.004792:0 -0.5 0
161012-21:03:36,14 interface INFO:
stdout 2016-10-12T21:03:36.004792:0 0 0.5
161012-21:03:36,15 interface INFO:
stdout 2016-10-12T21:03:36.004792:
161012-21:03:36,16 interface INFO:
stdout 2016-10-12T21:03:36.004792: Inverse Direction:
161012-21:03:36,16 interface INFO:
stdout 2016-10-12T21:03:36.004792:1 0 0
161012-21:03:36,17 interface INFO:
stdout 2016-10-12T21:03:36.004792:0 -1 0
161012-21:03:36,18 interface INFO:
stdout 2016-10-12T21:03:36.004792:0 0 1
161012-21:03:36,19 interface INFO:
stdout 2016-10-12T21:03:36.004792:
161012-21:03:36,26 interface INFO:
stdout 2016-10-12T21:03:36.004792: PixelContainer:
161012-21:03:36,28 interface INFO:
stdout 2016-10-12T21:03:36.004792: ImportImageContainer (0x3117db0)
161012-21:03:36,29 interface INFO:
stdout 2016-10-12T21:03:36.004792: RTTI typeinfo: itk::ImportImageContainer<unsigned long, double>
161012-21:03:36,30 interface INFO:
stdout 2016-10-12T21:03:36.004792: Reference Count: 1
161012-21:03:36,31 interface INFO:
stdout 2016-10-12T21:03:36.004792: Modified Time: 2664
161012-21:03:36,32 interface INFO:
stdout 2016-10-12T21:03:36.004792: Debug: Off
161012-21:03:36,33 interface INFO:
stdout 2016-10-12T21:03:36.004792: Object Name:
161012-21:03:36,34 interface INFO:
stdout 2016-10-12T21:03:36.004792: Observers:
161012-21:03:36,35 interface INFO:
stdout 2016-10-12T21:03:36.004792: none
161012-21:03:36,36 interface INFO:
stdout 2016-10-12T21:03:36.004792: Pointer: 0x543a760
161012-21:03:36,43 interface INFO:
stdout 2016-10-12T21:03:36.004792: Container manages memory: true
161012-21:03:36,45 interface INFO:
stdout 2016-10-12T21:03:36.004792: Size: 902629
161012-21:03:36,45 interface INFO:
stdout 2016-10-12T21:03:36.004792: Capacity: 902629
161012-21:03:36,46 interface INFO:
stdout 2016-10-12T21:03:36.004792:
161012-21:03:36,47 interface INFO:
stdout 2016-10-12T21:03:36.004792: Moving image = Image (0x5b1d690)
161012-21:03:36,48 interface INFO:
stdout 2016-10-12T21:03:36.004792: RTTI typeinfo: itk::Image<double, 3u>
161012-21:03:36,49 interface INFO:
stdout 2016-10-12T21:03:36.004792: Reference Count: 2
161012-21:03:36,50 interface INFO:
stdout 2016-10-12T21:03:36.004792: Modified Time: 2846
161012-21:03:36,51 interface INFO:
stdout 2016-10-12T21:03:36.004792: Debug: Off
161012-21:03:36,52 interface INFO:
stdout 2016-10-12T21:03:36.004792: Object Name:
161012-21:03:36,52 interface INFO:
stdout 2016-10-12T21:03:36.004792: Observers:
161012-21:03:36,53 interface INFO:
stdout 2016-10-12T21:03:36.004792: none
161012-21:03:36,54 interface INFO:
stdout 2016-10-12T21:03:36.004792: Source: (none)
161012-21:03:36,55 interface INFO:
stdout 2016-10-12T21:03:36.004792: Source output name: (none)
161012-21:03:36,56 interface INFO:
stdout 2016-10-12T21:03:36.004792: Release Data: Off
161012-21:03:36,57 interface INFO:
stdout 2016-10-12T21:03:36.004792: Data Released: False
161012-21:03:36,58 interface INFO:
stdout 2016-10-12T21:03:36.004792: Global Release Data: Off
161012-21:03:36,64 interface INFO:
stdout 2016-10-12T21:03:36.004792: PipelineMTime: 0
161012-21:03:36,66 interface INFO:
stdout 2016-10-12T21:03:36.004792: UpdateMTime: 2843
161012-21:03:36,67 interface INFO:
stdout 2016-10-12T21:03:36.004792: RealTimeStamp: 0 seconds
161012-21:03:36,68 interface INFO:
stdout 2016-10-12T21:03:36.004792: LargestPossibleRegion:
161012-21:03:36,69 interface INFO:
stdout 2016-10-12T21:03:36.004792: Dimension: 3
161012-21:03:36,70 interface INFO:
stdout 2016-10-12T21:03:36.004792: Index: [0, 0, 0]
161012-21:03:36,71 interface INFO:
stdout 2016-10-12T21:03:36.004792: Size: [96, 96, 68]
161012-21:03:36,72 interface INFO:
stdout 2016-10-12T21:03:36.004792: BufferedRegion:
161012-21:03:36,73 interface INFO:
stdout 2016-10-12T21:03:36.004792: Dimension: 3
161012-21:03:36,74 interface INFO:
stdout 2016-10-12T21:03:36.004792: Index: [0, 0, 0]
161012-21:03:36,74 interface INFO:
stdout 2016-10-12T21:03:36.004792: Size: [96, 96, 68]
161012-21:03:36,75 interface INFO:
stdout 2016-10-12T21:03:36.004792: RequestedRegion:
161012-21:03:36,76 interface INFO:
stdout 2016-10-12T21:03:36.004792: Dimension: 3
161012-21:03:36,77 interface INFO:
stdout 2016-10-12T21:03:36.004792: Index: [0, 0, 0]
161012-21:03:36,78 interface INFO:
stdout 2016-10-12T21:03:36.004792: Size: [96, 96, 68]
161012-21:03:36,84 interface INFO:
stdout 2016-10-12T21:03:36.004792: Spacing: [2.39583, 2.39583, 2.4]
161012-21:03:36,87 interface INFO:
stdout 2016-10-12T21:03:36.004792: Origin: [-110.153, 63.604, -103.44]
161012-21:03:36,89 interface INFO:
stdout 2016-10-12T21:03:36.004792: Direction:
161012-21:03:36,91 interface INFO:
stdout 2016-10-12T21:03:36.004792:0.99865 -0.0218823 -0.047105
161012-21:03:36,91 interface INFO:
stdout 2016-10-12T21:03:36.004792:0.00754576 -0.836173 0.548413
161012-21:03:36,92 interface INFO:
stdout 2016-10-12T21:03:36.004792:0.0513885 0.548029 0.83488
161012-21:03:36,93 interface INFO:
stdout 2016-10-12T21:03:36.004792:
161012-21:03:36,94 interface INFO:
stdout 2016-10-12T21:03:36.004792: IndexToPointMatrix:
161012-21:03:36,95 interface INFO:
stdout 2016-10-12T21:03:36.004792:2.3926 -0.0524264 -0.113052
161012-21:03:36,101 interface INFO:
stdout 2016-10-12T21:03:36.004792:0.0180784 -2.00333 1.31619
161012-21:03:36,103 interface INFO:
stdout 2016-10-12T21:03:36.004792:0.123118 1.31299 2.00371
161012-21:03:36,104 interface INFO:
stdout 2016-10-12T21:03:36.004792:
161012-21:03:36,105 interface INFO:
stdout 2016-10-12T21:03:36.004792: PointToIndexMatrix:
161012-21:03:36,106 interface INFO:
stdout 2016-10-12T21:03:36.004792:0.416828 0.00314953 0.0214491
161012-21:03:36,107 interface INFO:
stdout 2016-10-12T21:03:36.004792:-0.00913349 -0.349011 0.228742
161012-21:03:36,108 interface INFO:
stdout 2016-10-12T21:03:36.004792:-0.0196271 0.228506 0.347866
161012-21:03:36,108 interface INFO:
stdout 2016-10-12T21:03:36.004792:
161012-21:03:36,109 interface INFO:
stdout 2016-10-12T21:03:36.004792: Inverse Direction:
161012-21:03:36,111 interface INFO:
stdout 2016-10-12T21:03:36.004792:0.99865 0.00754576 0.0513885
161012-21:03:36,112 interface INFO:
stdout 2016-10-12T21:03:36.004792:-0.0218823 -0.836173 0.548029
161012-21:03:36,113 interface INFO:
stdout 2016-10-12T21:03:36.004792:-0.047105 0.548413 0.83488
161012-21:03:36,114 interface INFO:
stdout 2016-10-12T21:03:36.004792:
161012-21:03:36,115 interface INFO:
stdout 2016-10-12T21:03:36.004792: PixelContainer:
161012-21:03:36,121 interface INFO:
stdout 2016-10-12T21:03:36.004792: ImportImageContainer (0x4f6cd20)
161012-21:03:36,122 interface INFO:
stdout 2016-10-12T21:03:36.004792: RTTI typeinfo: itk::ImportImageContainer<unsigned long, double>
161012-21:03:36,123 interface INFO:
stdout 2016-10-12T21:03:36.004792: Reference Count: 1
161012-21:03:36,124 interface INFO:
stdout 2016-10-12T21:03:36.004792: Modified Time: 2840
161012-21:03:36,125 interface INFO:
stdout 2016-10-12T21:03:36.004792: Debug: Off
161012-21:03:36,126 interface INFO:
stdout 2016-10-12T21:03:36.004792: Object Name:
161012-21:03:36,127 interface INFO:
stdout 2016-10-12T21:03:36.004792: Observers:
161012-21:03:36,129 interface INFO:
stdout 2016-10-12T21:03:36.004792: none
161012-21:03:36,130 interface INFO:
stdout 2016-10-12T21:03:36.004792: Pointer: 0x5b20d30
161012-21:03:36,131 interface INFO:
stdout 2016-10-12T21:03:36.004792: Container manages memory: true
161012-21:03:36,132 interface INFO:
stdout 2016-10-12T21:03:36.004792: Size: 626688
161012-21:03:36,133 interface INFO:
stdout 2016-10-12T21:03:36.004792: Capacity: 626688
161012-21:03:36,133 interface INFO:
stdout 2016-10-12T21:03:36.004792:
161012-21:03:36,140 interface INFO:
stdout 2016-10-12T21:03:36.004792: Weighting = 0.5
161012-21:03:36,141 interface INFO:
stdout 2016-10-12T21:03:36.004792: Sampling strategy = none
161012-21:03:36,142 interface INFO:
stdout 2016-10-12T21:03:36.004792: Number of bins = 32
161012-21:03:36,143 interface INFO:
stdout 2016-10-12T21:03:36.004792: Radius = 4
161012-21:03:36,144 interface INFO:
stdout 2016-10-12T21:03:36.004792: Sampling percentage = 1
161012-21:03:36,145 interface INFO:
stdout 2016-10-12T21:03:36.004792: Transform = SyN
161012-21:03:36,146 interface INFO:
stdout 2016-10-12T21:03:36.004792: Gradient step = 0.2
161012-21:03:36,148 interface INFO:
stdout 2016-10-12T21:03:36.004792: Update field sigma (voxel space) = 3
161012-21:03:36,148 interface INFO:
stdout 2016-10-12T21:03:36.004792: Total field sigma (voxel space) = 0
161012-21:03:36,149 interface INFO:
stdout 2016-10-12T21:03:36.004792: Update field time sigma = 0
161012-21:03:36,151 interface INFO:
stdout 2016-10-12T21:03:36.004792: Total field time sigma = 0
161012-21:03:36,152 interface INFO:
stdout 2016-10-12T21:03:36.004792: Number of time indices = 0
161012-21:03:36,160 interface INFO:
stdout 2016-10-12T21:03:36.004792: Number of time point samples = 0
161012-21:03:36,161 interface INFO:
stdout 2016-10-12T21:03:36.004792:Registration using 4 total stages.
161012-21:03:36,162 interface INFO:
stdout 2016-10-12T21:03:36.004792:
161012-21:03:36,163 interface INFO:
stdout 2016-10-12T21:03:36.004792:Stage 0
161012-21:03:36,164 interface INFO:
stdout 2016-10-12T21:03:36.004792: iterations = 10x10x10
161012-21:03:36,165 interface INFO:
stdout 2016-10-12T21:03:36.004792: convergence threshold = 1e-08
161012-21:03:36,166 interface INFO:
stdout 2016-10-12T21:03:36.004792: convergence window size = 20
161012-21:03:36,167 interface INFO:
stdout 2016-10-12T21:03:36.004792: number of levels = 3
161012-21:03:36,167 interface INFO:
stdout 2016-10-12T21:03:36.004792: using the Mattes MI metric (number of bins = 32, weight = 1)
161012-21:03:36,168 interface INFO:
stdout 2016-10-12T21:03:36.004792: preprocessing: winsorizing the image intensities
161012-21:03:36,169 interface INFO:
stdout 2016-10-12T21:03:36.004792: preprocessing: histogram matching the images
161012-21:03:36,170 interface INFO:
stdout 2016-10-12T21:03:36.004792: Shrink factors (level 1 out of 3): [6, 6, 6]
161012-21:03:36,171 interface INFO:
stdout 2016-10-12T21:03:36.004792: Shrink factors (level 2 out of 3): [4, 4, 4]
161012-21:03:36,172 interface INFO:
stdout 2016-10-12T21:03:36.004792: Shrink factors (level 3 out of 3): [2, 2, 2]
161012-21:03:36,173 interface INFO:
stdout 2016-10-12T21:03:36.004792: smoothing sigmas per level: [4, 2, 1]
161012-21:03:36,174 interface INFO:
stdout 2016-10-12T21:03:36.004792: regular sampling (percentage = 0.3)
161012-21:03:36,182 interface INFO:
stdout 2016-10-12T21:03:36.004792:
161012-21:03:36,185 interface INFO:
stdout 2016-10-12T21:03:36.004792:*** Running translation registration ***
161012-21:03:36,187 interface INFO:
stdout 2016-10-12T21:03:36.004792:
161012-21:03:36,188 interface INFO:
stdout 2016-10-12T21:03:36.004792:DIAGNOSTIC,Iteration,metricValue,convergenceValue,ITERATION_TIME_INDEX,SINCE_LAST
161012-21:03:36,189 interface INFO:
stdout 2016-10-12T21:03:36.004792: 2DIAGNOSTIC, 1, -1.023022911156e+00, 1.797693134862e+308, 1.1559e+00, 1.1559e+00,
161012-21:03:36,189 interface INFO:
stdout 2016-10-12T21:03:36.004792: 2DIAGNOSTIC, 2, -1.024708791949e+00, 1.797693134862e+308, 1.1639e+00, 8.0080e-03,
161012-21:03:36,190 interface INFO:
stdout 2016-10-12T21:03:36.004792: 2DIAGNOSTIC, 3, -1.027608474108e+00, 1.797693134862e+308, 1.1668e+00, 2.9130e-03,
161012-21:03:36,191 interface INFO:
stdout 2016-10-12T21:03:36.004792: 2DIAGNOSTIC, 4, -1.029838842266e+00, 1.797693134862e+308, 1.1735e+00, 6.6969e-03,
161012-21:03:36,192 interface INFO:
stdout 2016-10-12T21:03:36.004792: 2DIAGNOSTIC, 5, -1.030611132298e+00, 1.797693134862e+308, 1.1796e+00, 6.0430e-03,
161012-21:03:36,193 interface INFO:
stdout 2016-10-12T21:03:36.004792: 2DIAGNOSTIC, 6, -1.030784265624e+00, 1.797693134862e+308, 1.1829e+00, 3.2952e-03,
161012-21:03:36,193 interface INFO:
stdout 2016-10-12T21:03:36.004792: 2DIAGNOSTIC, 7, -1.030839471925e+00, 1.797693134862e+308, 1.1888e+00, 5.9268e-03,
161012-21:03:36,195 interface INFO:
stdout 2016-10-12T21:03:36.004792: 2DIAGNOSTIC, 8, -1.030843406994e+00, 1.797693134862e+308, 1.1949e+00, 6.1259e-03,
161012-21:03:36,197 interface INFO:
stdout 2016-10-12T21:03:36.004792: 2DIAGNOSTIC, 9, -1.030843674612e+00, 1.797693134862e+308, 1.2053e+00, 1.0326e-02,
161012-21:03:36,198 interface INFO:
stdout 2016-10-12T21:03:36.004792: 2DIAGNOSTIC, 10, -1.030843862959e+00, 1.797693134862e+308, 1.2160e+00, 1.0726e-02,
161012-21:03:36,199 interface INFO:
stdout 2016-10-12T21:03:36.004792:DIAGNOSTIC,Iteration,metricValue,convergenceValue,ITERATION_TIME_INDEX,SINCE_LAST
161012-21:03:36,200 interface INFO:
stdout 2016-10-12T21:03:36.004792: 2DIAGNOSTIC, 1, -7.169325681728e-01, 1.797693134862e+308, 1.8630e+00, 6.4703e-01,
161012-21:03:36,701 interface INFO:
stdout 2016-10-12T21:03:36.701806: 2DIAGNOSTIC, 2, -7.193099357506e-01, 1.797693134862e+308, 1.8734e+00, 1.0349e-02,
161012-21:03:36,704 interface INFO:
stdout 2016-10-12T21:03:36.701806: 2DIAGNOSTIC, 3, -7.222789338392e-01, 1.797693134862e+308, 1.8848e+00, 1.1486e-02,
161012-21:03:36,708 interface INFO:
stdout 2016-10-12T21:03:36.701806: 2DIAGNOSTIC, 4, -7.263304619988e-01, 1.797693134862e+308, 1.8964e+00, 1.1586e-02,
161012-21:03:36,709 interface INFO:
stdout 2016-10-12T21:03:36.701806: 2DIAGNOSTIC, 5, -7.301026327848e-01, 1.797693134862e+308, 1.9092e+00, 1.2787e-02,
161012-21:03:36,710 interface INFO:
stdout 2016-10-12T21:03:36.701806: 2DIAGNOSTIC, 6, -7.305749740111e-01, 1.797693134862e+308, 1.9256e+00, 1.6401e-02,
161012-21:03:36,712 interface INFO:
stdout 2016-10-12T21:03:36.701806: 2DIAGNOSTIC, 7, -7.322713575812e-01, 1.797693134862e+308, 1.9426e+00, 1.6959e-02,
161012-21:03:36,713 interface INFO:
stdout 2016-10-12T21:03:36.701806: 2DIAGNOSTIC, 8, -7.323514350348e-01, 1.797693134862e+308, 1.9669e+00, 2.4342e-02,
161012-21:03:36,717 interface INFO:
stdout 2016-10-12T21:03:36.701806: 2DIAGNOSTIC, 9, -7.324147252610e-01, 1.797693134862e+308, 1.9896e+00, 2.2687e-02,
161012-21:03:36,718 interface INFO:
stdout 2016-10-12T21:03:36.701806: 2DIAGNOSTIC, 10, -7.323920678650e-01, 1.797693134862e+308, 2.0055e+00, 1.5897e-02,
161012-21:03:36,719 interface INFO:
stdout 2016-10-12T21:03:36.701806:DIAGNOSTIC,Iteration,metricValue,convergenceValue,ITERATION_TIME_INDEX,SINCE_LAST
161012-21:03:36,730 interface INFO:
stdout 2016-10-12T21:03:36.701806: 2DIAGNOSTIC, 1, -5.569365205870e-01, 1.797693134862e+308, 2.5963e+00, 5.9080e-01,
161012-21:03:36,732 interface INFO:
stdout 2016-10-12T21:03:36.701806: 2DIAGNOSTIC, 2, -5.575384028341e-01, 1.797693134862e+308, 2.7374e+00, 1.4111e-01,
161012-21:03:37,233 interface INFO:
stdout 2016-10-12T21:03:37.233795: 2DIAGNOSTIC, 3, -5.587298836102e-01, 1.797693134862e+308, 2.8473e+00, 1.0984e-01,
161012-21:03:37,240 interface INFO:
stdout 2016-10-12T21:03:37.233795: 2DIAGNOSTIC, 4, -5.610590587281e-01, 1.797693134862e+308, 2.9701e+00, 1.2283e-01,
161012-21:03:37,242 interface INFO:
stdout 2016-10-12T21:03:37.233795: 2DIAGNOSTIC, 5, -5.614992022099e-01, 1.797693134862e+308, 3.0777e+00, 1.0764e-01,
161012-21:03:37,243 interface INFO:
stdout 2016-10-12T21:03:37.233795: 2DIAGNOSTIC, 6, -5.619310691008e-01, 1.797693134862e+308, 3.2204e+00, 1.4269e-01,
161012-21:03:37,749 interface INFO:
stdout 2016-10-12T21:03:37.749023: 2DIAGNOSTIC, 7, -5.621784231108e-01, 1.797693134862e+308, 3.3765e+00, 1.5610e-01,
161012-21:03:37,751 interface INFO:
stdout 2016-10-12T21:03:37.749023: 2DIAGNOSTIC, 8, -5.622683950831e-01, 1.797693134862e+308, 3.5631e+00, 1.8664e-01,
161012-21:03:38,253 interface INFO:
stdout 2016-10-12T21:03:38.253510: 2DIAGNOSTIC, 9, -5.622509542745e-01, 1.797693134862e+308, 4.1056e+00, 5.4248e-01,
161012-21:03:38,255 interface INFO:
stdout 2016-10-12T21:03:38.253510: 2DIAGNOSTIC, 10, -5.622509509597e-01, 1.797693134862e+308, 4.2479e+00, 1.4228e-01,
161012-21:03:38,256 interface INFO:
stdout 2016-10-12T21:03:38.253510: Elapsed time (stage 0): 4.4743e+00
161012-21:03:38,257 interface INFO:
stdout 2016-10-12T21:03:38.253510:
161012-21:03:38,258 interface INFO:
stdout 2016-10-12T21:03:38.253510:
161012-21:03:38,259 interface INFO:
stdout 2016-10-12T21:03:38.253510:Stage 1
161012-21:03:38,261 interface INFO:
stdout 2016-10-12T21:03:38.253510: iterations = 10x10x10
161012-21:03:38,263 interface INFO:
stdout 2016-10-12T21:03:38.253510: convergence threshold = 1.0000e-08
161012-21:03:38,271 interface INFO:
stdout 2016-10-12T21:03:38.253510: convergence window size = 20
161012-21:03:38,273 interface INFO:
stdout 2016-10-12T21:03:38.253510: number of levels = 3
161012-21:03:38,274 interface INFO:
stdout 2016-10-12T21:03:38.253510: using the Mattes MI metric (number of bins = 32, weight = 1.0000e+00)
161012-21:03:38,777 interface INFO:
stdout 2016-10-12T21:03:38.777221: preprocessing: winsorizing the image intensities
161012-21:03:38,779 interface INFO:
stdout 2016-10-12T21:03:38.777221: preprocessing: histogram matching the images
161012-21:03:38,780 interface INFO:
stdout 2016-10-12T21:03:38.777221: Shrink factors (level 1 out of 3): [3, 3, 3]
161012-21:03:38,781 interface INFO:
stdout 2016-10-12T21:03:38.777221: Shrink factors (level 2 out of 3): [2, 2, 2]
161012-21:03:38,782 interface INFO:
stdout 2016-10-12T21:03:38.777221: Shrink factors (level 3 out of 3): [1, 1, 1]
161012-21:03:38,783 interface INFO:
stdout 2016-10-12T21:03:38.777221: smoothing sigmas per level: [4, 2, 1]
161012-21:03:38,784 interface INFO:
stdout 2016-10-12T21:03:38.777221: regular sampling (percentage = 3.0000e-01)
161012-21:03:38,785 interface INFO:
stdout 2016-10-12T21:03:38.777221:
161012-21:03:38,786 interface INFO:
stdout 2016-10-12T21:03:38.777221:*** Running rigid registration ***
161012-21:03:38,787 interface INFO:
stdout 2016-10-12T21:03:38.777221:
161012-21:03:39,801 interface INFO:
stdout 2016-10-12T21:03:39.801052:DIAGNOSTIC,Iteration,metricValue,convergenceValue,ITERATION_TIME_INDEX,SINCE_LAST
161012-21:03:39,802 interface INFO:
stdout 2016-10-12T21:03:39.801052: 2DIAGNOSTIC, 1, -9.063143578946e-01, 1.797693134862e+308, 1.0274e+00, 1.0274e+00,
161012-21:03:39,804 interface INFO:
stdout 2016-10-12T21:03:39.801052: 2DIAGNOSTIC, 2, -9.072850343831e-01, 1.797693134862e+308, 1.0676e+00, 4.0214e-02,
161012-21:03:39,805 interface INFO:
stdout 2016-10-12T21:03:39.801052: 2DIAGNOSTIC, 3, -9.089150638492e-01, 1.797693134862e+308, 1.1146e+00, 4.7039e-02,
161012-21:03:39,806 interface INFO:
stdout 2016-10-12T21:03:39.801052: 2DIAGNOSTIC, 4, -9.115418970183e-01, 1.797693134862e+308, 1.1549e+00, 4.0292e-02,
161012-21:03:39,807 interface INFO:
stdout 2016-10-12T21:03:39.801052: 2DIAGNOSTIC, 5, -9.155859447763e-01, 1.797693134862e+308, 1.1938e+00, 3.8842e-02,
161012-21:03:39,808 interface INFO:
stdout 2016-10-12T21:03:39.801052: 2DIAGNOSTIC, 6, -9.220792081798e-01, 1.797693134862e+308, 1.2348e+00, 4.1019e-02,
161012-21:03:39,809 interface INFO:
stdout 2016-10-12T21:03:39.801052: 2DIAGNOSTIC, 7, -9.321823926579e-01, 1.797693134862e+308, 1.2752e+00, 4.0432e-02,
161012-21:03:39,810 interface INFO:
stdout 2016-10-12T21:03:39.801052: 2DIAGNOSTIC, 8, -9.500984262190e-01, 1.797693134862e+308, 1.3226e+00, 4.7386e-02,
161012-21:03:39,810 interface INFO:
stdout 2016-10-12T21:03:39.801052: 2DIAGNOSTIC, 9, -9.812796819064e-01, 1.797693134862e+308, 1.3685e+00, 4.5907e-02,
161012-21:03:40,313 interface INFO:
stdout 2016-10-12T21:03:40.313144: 2DIAGNOSTIC, 10, -1.063305422632e+00, 1.797693134862e+308, 1.4653e+00, 9.6800e-02,
161012-21:03:40,815 interface INFO:
stdout 2016-10-12T21:03:40.815427:DIAGNOSTIC,Iteration,metricValue,convergenceValue,ITERATION_TIME_INDEX,SINCE_LAST
161012-21:03:40,817 interface INFO:
stdout 2016-10-12T21:03:40.815427: 2DIAGNOSTIC, 1, -7.914100335562e-01, 1.797693134862e+308, 1.9185e+00, 4.5320e-01,
161012-21:03:40,818 interface INFO:
stdout 2016-10-12T21:03:40.815427: 2DIAGNOSTIC, 2, -7.923070601279e-01, 1.797693134862e+308, 2.0417e+00, 1.2323e-01,
161012-21:03:40,820 interface INFO:
stdout 2016-10-12T21:03:40.815427: 2DIAGNOSTIC, 3, -7.934023973276e-01, 1.797693134862e+308, 2.1464e+00, 1.0462e-01,
161012-21:03:40,826 interface INFO:
stdout 2016-10-12T21:03:40.815427: 2DIAGNOSTIC, 4, -7.950618499594e-01, 1.797693134862e+308, 2.2510e+00, 1.0462e-01,
161012-21:03:40,827 interface INFO:
stdout 2016-10-12T21:03:40.815427: 2DIAGNOSTIC, 5, -7.972927460681e-01, 1.797693134862e+308, 2.3543e+00, 1.0332e-01,
161012-21:03:41,329 interface INFO:
stdout 2016-10-12T21:03:41.329415: 2DIAGNOSTIC, 6, -8.003016117177e-01, 1.797693134862e+308, 2.4888e+00, 1.3446e-01,
161012-21:03:41,330 interface INFO:
stdout 2016-10-12T21:03:41.329415: 2DIAGNOSTIC, 7, -8.042903617484e-01, 1.797693134862e+308, 2.6082e+00, 1.1938e-01,
161012-21:03:41,331 interface INFO:
stdout 2016-10-12T21:03:41.329415: 2DIAGNOSTIC, 8, -8.182816469196e-01, 1.797693134862e+308, 2.8042e+00, 1.9601e-01,
161012-21:03:41,833 interface INFO:
stdout 2016-10-12T21:03:41.833285: 2DIAGNOSTIC, 9, -8.201318878848e-01, 1.797693134862e+308, 2.9419e+00, 1.3774e-01,
161012-21:03:41,835 interface INFO:
stdout 2016-10-12T21:03:41.833285: 2DIAGNOSTIC, 10, -8.208038062113e-01, 1.797693134862e+308, 3.0876e+00, 1.4567e-01,
161012-21:03:42,848 interface INFO:
stdout 2016-10-12T21:03:42.848579:DIAGNOSTIC,Iteration,metricValue,convergenceValue,ITERATION_TIME_INDEX,SINCE_LAST
161012-21:03:42,851 interface INFO:
stdout 2016-10-12T21:03:42.848579: 2DIAGNOSTIC, 1, -6.636611091260e-01, 1.797693134862e+308, 4.2423e+00, 1.1548e+00,
161012-21:03:43,867 interface INFO:
stdout 2016-10-12T21:03:43.866924: 2DIAGNOSTIC, 2, -6.640090978809e-01, 1.797693134862e+308, 5.1031e+00, 8.6073e-01,
161012-21:03:44,884 interface INFO:
stdout 2016-10-12T21:03:44.884373: 2DIAGNOSTIC, 3, -6.642733309388e-01, 1.797693134862e+308, 6.2475e+00, 1.1444e+00,
161012-21:03:45,897 interface INFO:
stdout 2016-10-12T21:03:45.897336: 2DIAGNOSTIC, 4, -6.642924286574e-01, 1.797693134862e+308, 7.4474e+00, 1.2000e+00,
161012-21:03:47,423 interface INFO:
stdout 2016-10-12T21:03:47.423197: 2DIAGNOSTIC, 5, -6.643087199500e-01, 1.797693134862e+308, 8.7566e+00, 1.3091e+00,
161012-21:03:48,439 interface INFO:
stdout 2016-10-12T21:03:48.439788: 2DIAGNOSTIC, 6, -6.643068201650e-01, 1.797693134862e+308, 9.6588e+00, 9.0219e-01,
161012-21:03:49,970 interface INFO:
stdout 2016-10-12T21:03:49.970133: 2DIAGNOSTIC, 7, -6.643067984843e-01, 1.797693134862e+308, 1.1159e+01, 1.5002e+00,
161012-21:03:50,980 interface INFO:
stdout 2016-10-12T21:03:50.979994: 2DIAGNOSTIC, 8, -6.643069191250e-01, 1.797693134862e+308, 1.2068e+01, 9.0885e-01,
161012-21:03:51,481 interface INFO:
stdout 2016-10-12T21:03:51.481868: 2DIAGNOSTIC, 9, -6.643056620223e-01, 1.797693134862e+308, 1.2862e+01, 7.9405e-01,
161012-21:03:52,501 interface INFO:
stdout 2016-10-12T21:03:52.501801: 2DIAGNOSTIC, 10, -6.643030884124e-01, 1.797693134862e+308, 1.3656e+01, 7.9436e-01,
161012-21:03:52,503 interface INFO:
stdout 2016-10-12T21:03:52.501801: Elapsed time (stage 1): 1.3863e+01
161012-21:03:52,504 interface INFO:
stdout 2016-10-12T21:03:52.501801:
161012-21:03:52,505 interface INFO:
stdout 2016-10-12T21:03:52.501801:
161012-21:03:52,506 interface INFO:
stdout 2016-10-12T21:03:52.501801:Stage 2
161012-21:03:52,507 interface INFO:
stdout 2016-10-12T21:03:52.501801: iterations = 10x10x10
161012-21:03:52,508 interface INFO:
stdout 2016-10-12T21:03:52.501801: convergence threshold = 1.0000e-08
161012-21:03:52,509 interface INFO:
stdout 2016-10-12T21:03:52.501801: convergence window size = 20
161012-21:03:52,511 interface INFO:
stdout 2016-10-12T21:03:52.501801: number of levels = 3
161012-21:03:52,512 interface INFO:
stdout 2016-10-12T21:03:52.501801: using the Mattes MI metric (number of bins = 32, weight = 1.0000e+00)
161012-21:03:52,512 interface INFO:
stdout 2016-10-12T21:03:52.501801: preprocessing: winsorizing the image intensities
161012-21:03:52,514 interface INFO:
stdout 2016-10-12T21:03:52.501801: preprocessing: histogram matching the images
161012-21:03:52,514 interface INFO:
stdout 2016-10-12T21:03:52.501801: Shrink factors (level 1 out of 3): [3, 3, 3]
161012-21:03:52,515 interface INFO:
stdout 2016-10-12T21:03:52.501801: Shrink factors (level 2 out of 3): [2, 2, 2]
161012-21:03:52,517 interface INFO:
stdout 2016-10-12T21:03:52.501801: Shrink factors (level 3 out of 3): [1, 1, 1]
161012-21:03:52,518 interface INFO:
stdout 2016-10-12T21:03:52.501801: smoothing sigmas per level: [4, 2, 1]
161012-21:03:52,523 interface INFO:
stdout 2016-10-12T21:03:52.501801: regular sampling (percentage = 3.0000e-01)
161012-21:03:52,525 interface INFO:
stdout 2016-10-12T21:03:52.501801:
161012-21:03:52,526 interface INFO:
stdout 2016-10-12T21:03:52.501801:*** Running affine registration ***
161012-21:03:52,527 interface INFO:
stdout 2016-10-12T21:03:52.501801:
161012-21:03:53,539 interface INFO:
stdout 2016-10-12T21:03:53.539819:DIAGNOSTIC,Iteration,metricValue,convergenceValue,ITERATION_TIME_INDEX,SINCE_LAST
161012-21:03:53,541 interface INFO:
stdout 2016-10-12T21:03:53.539819: 2DIAGNOSTIC, 1, -1.114714852637e+00, 1.797693134862e+308, 9.6377e-01, 9.6376e-01,
161012-21:03:53,542 interface INFO:
stdout 2016-10-12T21:03:53.539819: 2DIAGNOSTIC, 2, -1.118881718240e+00, 1.797693134862e+308, 1.0092e+00, 4.5454e-02,
161012-21:03:53,543 interface INFO:
stdout 2016-10-12T21:03:53.539819: 2DIAGNOSTIC, 3, -1.125242725580e+00, 1.797693134862e+308, 1.0573e+00, 4.8083e-02,
161012-21:03:53,544 interface INFO:
stdout 2016-10-12T21:03:53.539819: 2DIAGNOSTIC, 4, -1.135128181985e+00, 1.797693134862e+308, 1.1105e+00, 5.3149e-02,
161012-21:03:53,545 interface INFO:
stdout 2016-10-12T21:03:53.539819: 2DIAGNOSTIC, 5, -1.151487557332e+00, 1.797693134862e+308, 1.1562e+00, 4.5771e-02,
161012-21:03:53,546 interface INFO:
stdout 2016-10-12T21:03:53.539819: 2DIAGNOSTIC, 6, -1.175103179652e+00, 1.797693134862e+308, 1.2021e+00, 4.5895e-02,
161012-21:03:53,547 interface INFO:
stdout 2016-10-12T21:03:53.539819: 2DIAGNOSTIC, 7, -1.205494484658e+00, 1.797693134862e+308, 1.2575e+00, 5.5417e-02,
161012-21:03:54,49 interface INFO:
stdout 2016-10-12T21:03:54.049151: 2DIAGNOSTIC, 8, -1.235032615163e+00, 1.797693134862e+308, 1.3562e+00, 9.8638e-02,
161012-21:03:54,51 interface INFO:
stdout 2016-10-12T21:03:54.049151: 2DIAGNOSTIC, 9, -1.242592832774e+00, 1.797693134862e+308, 1.4364e+00, 8.0256e-02,
161012-21:03:54,52 interface INFO:
stdout 2016-10-12T21:03:54.049151: 2DIAGNOSTIC, 10, -1.242905885432e+00, 1.797693134862e+308, 1.4818e+00, 4.5354e-02,
161012-21:03:54,554 interface INFO:
stdout 2016-10-12T21:03:54.554296:DIAGNOSTIC,Iteration,metricValue,convergenceValue,ITERATION_TIME_INDEX,SINCE_LAST
161012-21:03:54,555 interface INFO:
stdout 2016-10-12T21:03:54.554296: 2DIAGNOSTIC, 1, -8.984922004489e-01, 1.797693134862e+308, 1.9596e+00, 4.7783e-01,
161012-21:03:54,556 interface INFO:
stdout 2016-10-12T21:03:54.554296: 2DIAGNOSTIC, 2, -8.989936143457e-01, 1.797693134862e+308, 2.0882e+00, 1.2855e-01,
161012-21:03:54,557 interface INFO:
stdout 2016-10-12T21:03:54.554296: 2DIAGNOSTIC, 3, -8.996568671261e-01, 1.797693134862e+308, 2.2292e+00, 1.4103e-01,
161012-21:03:55,59 interface INFO:
stdout 2016-10-12T21:03:55.059824: 2DIAGNOSTIC, 4, -9.004486188908e-01, 1.797693134862e+308, 2.3671e+00, 1.3786e-01,
161012-21:03:55,61 interface INFO:
stdout 2016-10-12T21:03:55.059824: 2DIAGNOSTIC, 5, -9.010519293954e-01, 1.797693134862e+308, 2.5173e+00, 1.5019e-01,
161012-21:03:55,62 interface INFO:
stdout 2016-10-12T21:03:55.059824: 2DIAGNOSTIC, 6, -9.015831192890e-01, 1.797693134862e+308, 2.7270e+00, 2.0978e-01,
161012-21:03:55,564 interface INFO:
stdout 2016-10-12T21:03:55.564219: 2DIAGNOSTIC, 7, -9.015880309387e-01, 1.797693134862e+308, 2.8728e+00, 1.4577e-01,
161012-21:03:55,565 interface INFO:
stdout 2016-10-12T21:03:55.564219: 2DIAGNOSTIC, 8, -9.017312606889e-01, 1.797693134862e+308, 3.0234e+00, 1.5057e-01,
161012-21:03:55,566 interface INFO:
stdout 2016-10-12T21:03:55.564219: 2DIAGNOSTIC, 9, -9.017821549666e-01, 1.797693134862e+308, 3.2228e+00, 1.9945e-01,
161012-21:03:56,68 interface INFO:
stdout 2016-10-12T21:03:56.068815: 2DIAGNOSTIC, 10, -9.018258335260e-01, 1.797693134862e+308, 3.3661e+00, 1.4332e-01,
161012-21:03:57,83 interface INFO:
stdout 2016-10-12T21:03:57.083694:DIAGNOSTIC,Iteration,metricValue,convergenceValue,ITERATION_TIME_INDEX,SINCE_LAST
161012-21:03:57,86 interface INFO:
stdout 2016-10-12T21:03:57.083694: 2DIAGNOSTIC, 1, -7.233980261558e-01, 1.797693134862e+308, 4.6274e+00, 1.2613e+00,
161012-21:03:58,98 interface INFO:
stdout 2016-10-12T21:03:58.098557: 2DIAGNOSTIC, 2, -7.235265457397e-01, 1.797693134862e+308, 5.7774e+00, 1.1499e+00,
161012-21:03:59,622 interface INFO:
stdout 2016-10-12T21:03:59.622600: 2DIAGNOSTIC, 3, -7.236222928251e-01, 1.797693134862e+308, 6.9360e+00, 1.1587e+00,
161012-21:04:00,636 interface INFO:
stdout 2016-10-12T21:04:00.636870: 2DIAGNOSTIC, 4, -7.236332754646e-01, 1.797693134862e+308, 8.0555e+00, 1.1194e+00,
161012-21:04:01,651 interface INFO:
stdout 2016-10-12T21:04:01.651210: 2DIAGNOSTIC, 5, -7.236476507819e-01, 1.797693134862e+308, 9.2016e+00, 1.1461e+00,
161012-21:04:02,665 interface INFO:
stdout 2016-10-12T21:04:02.665806: 2DIAGNOSTIC, 6, -7.236754211759e-01, 1.797693134862e+308, 1.0316e+01, 1.1141e+00,
161012-21:04:03,680 interface INFO:
stdout 2016-10-12T21:04:03.680217: 2DIAGNOSTIC, 7, -7.236763283501e-01, 1.797693134862e+308, 1.1426e+01, 1.1100e+00,
161012-21:04:05,206 interface INFO:
stdout 2016-10-12T21:04:05.206537: 2DIAGNOSTIC, 8, -7.236768633864e-01, 1.797693134862e+308, 1.2509e+01, 1.0837e+00,
161012-21:04:06,220 interface INFO:
stdout 2016-10-12T21:04:06.220393: 2DIAGNOSTIC, 9, -7.236866473233e-01, 1.797693134862e+308, 1.3611e+01, 1.1021e+00,
161012-21:04:07,233 interface INFO:
stdout 2016-10-12T21:04:07.233273: 2DIAGNOSTIC, 10, -7.236946247300e-01, 1.797693134862e+308, 1.4616e+01, 1.0050e+00,
161012-21:04:07,236 interface INFO:
stdout 2016-10-12T21:04:07.233273: Elapsed time (stage 2): 1.4766e+01
161012-21:04:07,239 interface INFO:
stdout 2016-10-12T21:04:07.233273:
161012-21:04:07,241 interface INFO:
stdout 2016-10-12T21:04:07.233273:
161012-21:04:07,242 interface INFO:
stdout 2016-10-12T21:04:07.233273:Stage 3
161012-21:04:07,243 interface INFO:
stdout 2016-10-12T21:04:07.233273: iterations = 1x5x3
161012-21:04:07,245 interface INFO:
stdout 2016-10-12T21:04:07.233273: convergence threshold = -1.0000e-02
161012-21:04:07,247 interface INFO:
stdout 2016-10-12T21:04:07.233273: convergence window size = 5
161012-21:04:07,254 interface INFO:
stdout 2016-10-12T21:04:07.233273: number of levels = 3
161012-21:04:07,255 interface INFO:
stdout 2016-10-12T21:04:07.233273: using the Mattes MI metric (number of bins = 32, weight = 5.0000e-01)
161012-21:04:07,256 interface INFO:
stdout 2016-10-12T21:04:07.233273: preprocessing: winsorizing the image intensities
161012-21:04:07,257 interface INFO:
stdout 2016-10-12T21:04:07.233273: preprocessing: histogram matching the images
161012-21:04:07,258 interface INFO:
stdout 2016-10-12T21:04:07.233273: using the CC metric (radius = 4, weight = 5.0000e-01)
161012-21:04:07,259 interface INFO:
stdout 2016-10-12T21:04:07.233273: preprocessing: winsorizing the image intensities
161012-21:04:07,260 interface INFO:
stdout 2016-10-12T21:04:07.233273: preprocessing: histogram matching the images
161012-21:04:07,263 interface INFO:
stdout 2016-10-12T21:04:07.233273: Shrink factors (level 1 out of 3): [4, 4, 4]
161012-21:04:07,264 interface INFO:
stdout 2016-10-12T21:04:07.233273: Shrink factors (level 2 out of 3): [2, 2, 2]
161012-21:04:07,265 interface INFO:
stdout 2016-10-12T21:04:07.233273: Shrink factors (level 3 out of 3): [1, 1, 1]
161012-21:04:07,267 interface INFO:
stdout 2016-10-12T21:04:07.233273: smoothing sigmas per level: [1, 0.5, 0]
161012-21:04:07,268 interface INFO:
stdout 2016-10-12T21:04:07.233273: Using default NONE metricSamplingStrategy
161012-21:04:07,269 interface INFO:
stdout 2016-10-12T21:04:07.233273:
161012-21:04:07,270 interface INFO:
stdout 2016-10-12T21:04:07.233273:*** Running SyN registration (varianceForUpdateField = 3.0000e+00, varianceForTotalField = 0.0000e+00) ***
161012-21:04:07,276 interface INFO:
stdout 2016-10-12T21:04:07.233273:
161012-21:04:08,289 interface INFO:
stdout 2016-10-12T21:04:08.289280:XXDIAGNOSTIC,Iteration,metricValue,convergenceValue,ITERATION_TIME_INDEX,SINCE_LAST
161012-21:04:08,290 interface INFO:
stdout 2016-10-12T21:04:08.289280: 1DIAGNOSTIC, 1, -6.868408721993e-01, 1.797693134862e+308, 1.0072e+00, 1.0072e+00,
161012-21:04:13,397 interface INFO:
stdout 2016-10-12T21:04:13.397200:XXDIAGNOSTIC,Iteration,metricValue,convergenceValue,ITERATION_TIME_INDEX,SINCE_LAST
161012-21:04:13,399 interface INFO:
stdout 2016-10-12T21:04:13.397200: 1DIAGNOSTIC, 1, -6.185860451892e-01, 1.797693134862e+308, 5.7341e+00, 4.7269e+00,
161012-21:04:17,479 interface INFO:
stdout 2016-10-12T21:04:17.479131: 1DIAGNOSTIC, 2, -6.352564400482e-01, 1.797693134862e+308, 9.9875e+00, 4.2533e+00,
161012-21:04:21,556 interface INFO:
stdout 2016-10-12T21:04:21.556719: 1DIAGNOSTIC, 3, -6.474597263835e-01, 1.797693134862e+308, 1.4336e+01, 4.3486e+00,
161012-21:04:26,157 interface INFO:
stdout 2016-10-12T21:04:26.157703: 1DIAGNOSTIC, 4, -6.572582517079e-01, 1.797693134862e+308, 1.8617e+01, 4.2813e+00,
161012-21:04:30,253 interface INFO:
stdout 2016-10-12T21:04:30.253013: 1DIAGNOSTIC, 5, -6.652331672927e-01, 1.008447184278e-02, 2.2875e+01, 4.2573e+00,
161012-21:05:05,582 interface INFO:
stdout 2016-10-12T21:05:05.582055:XXDIAGNOSTIC,Iteration,metricValue,convergenceValue,ITERATION_TIME_INDEX,SINCE_LAST
161012-21:05:05,583 interface INFO:
stdout 2016-10-12T21:05:05.582055: 1DIAGNOSTIC, 1, -6.053890195011e-01, 1.797693134862e+308, 5.8249e+01, 3.5374e+01,
161012-21:05:40,407 interface INFO:
stdout 2016-10-12T21:05:40.407884: 1DIAGNOSTIC, 2, -6.091382641947e-01, 1.797693134862e+308, 9.3096e+01, 3.4848e+01,
161012-21:06:15,778 interface INFO:
stdout 2016-10-12T21:06:15.778507: 1DIAGNOSTIC, 3, -6.133245136515e-01, 1.797693134862e+308, 1.2835e+02, 3.5256e+01,
161012-21:06:15,779 interface INFO:
stdout 2016-10-12T21:06:15.778507: Elapsed time (stage 3): 1.2894e+02
161012-21:06:15,780 interface INFO:
stdout 2016-10-12T21:06:15.778507:
161012-21:06:15,780 interface INFO:
stdout 2016-10-12T21:06:15.778507:
161012-21:06:15,781 interface INFO:
stdout 2016-10-12T21:06:15.778507:Total elapsed time: 1.6205e+02
Out[14]:
composite_transform = /home/vagrant/fmri-analysis-vm/analysis/normalization/nipype_mem/nipype-interfaces-ants-registration-Registration/71cf12fd00af0abd2f55c82d0f5ee549/transformComposite.h5
forward_invert_flags = []
forward_transforms = []
inverse_composite_transform = /home/vagrant/fmri-analysis-vm/analysis/normalization/nipype_mem/nipype-interfaces-ants-registration-Registration/71cf12fd00af0abd2f55c82d0f5ee549/transformInverseComposite.h5
inverse_warped_image = <undefined>
reverse_invert_flags = []
reverse_transforms = []
save_state = <undefined>
warped_image = /home/vagrant/fmri-analysis-vm/analysis/normalization/nipype_mem/nipype-interfaces-ants-registration-Registration/71cf12fd00af0abd2f55c82d0f5ee549/transform_Warped.nii.gz
Lets plot the normalized subject brain next to the MNI template.
In [16]:
nilearn.plotting.plot_anat(os.path.join(os.getenv('FSLDIR'),'data/standard/MNI152_T1_2mm_brain.nii.gz'),
cut_coords=(-1,2,20), draw_cross=False)
nilearn.plotting.plot_anat(ants_results.outputs.warped_image,
cut_coords=(-1,2,20), draw_cross=False)
Out[16]:
<nilearn.plotting.displays.OrthoSlicer at 0x7f94e54bae80>
Again we can plot grey-white matter outline as an overlay to asses the quality of the corregistration. First we need to warp the WM segmentation file to the MNI space using just estimated transform
In [17]:
T1_to_MNI_warp = mem.cache(ants.ApplyTransforms)
T1wm_to_MNI_warp_results = T1_to_MNI_warp(input_image = epi_reg_results.outputs.wmseg,
reference_image = os.path.join(os.getenv('FSLDIR'),'data/standard/MNI152_T1_2mm_brain.nii.gz'),
interpolation = "NearestNeighbor",
transforms = ants_results.outputs.composite_transform)
fig = nilearn.plotting.plot_anat(os.path.join(os.getenv('FSLDIR'),'data/standard/MNI152_T1_2mm_brain.nii.gz'))
fig.add_contours(T1wm_to_MNI_warp_results.outputs.output_image, levels=[.5])
161012-21:07:55,814 workflow INFO:
Executing node fd430d60e7f373ed87b125e6af5166ca in dir: /home/vagrant/fmri-analysis-vm/analysis/normalization/nipype_mem/nipype-interfaces-ants-resampling-ApplyTransforms/fd430d60e7f373ed87b125e6af5166ca
161012-21:07:55,820 workflow INFO:
Running: antsApplyTransforms --default-value 0 --input /home/vagrant/fmri-analysis-vm/analysis/normalization/nipype_mem/nipype-interfaces-fsl-epi-EpiReg/8aa1a7a3a91b013599dd0026e9a31d4e/epi2struct_fast_wmseg.nii.gz --interpolation NearestNeighbor --output epi2struct_fast_wmseg_trans.nii.gz --reference-image /usr/share/fsl/5.0/data/standard/MNI152_T1_2mm_brain.nii.gz --transform /home/vagrant/fmri-analysis-vm/analysis/normalization/nipype_mem/nipype-interfaces-ants-registration-Registration/71cf12fd00af0abd2f55c82d0f5ee549/transformComposite.h5
161012-21:07:56,378 interface INFO:
stdout 2016-10-12T21:07:56.378534:Using double precision for computations.
161012-21:07:56,380 interface INFO:
stdout 2016-10-12T21:07:56.378534:Input scalar image: /home/vagrant/fmri-analysis-vm/analysis/normalization/nipype_mem/nipype-interfaces-fsl-epi-EpiReg/8aa1a7a3a91b013599dd0026e9a31d4e/epi2struct_fast_wmseg.nii.gz
161012-21:07:56,380 interface INFO:
stdout 2016-10-12T21:07:56.378534:Reference image: /usr/share/fsl/5.0/data/standard/MNI152_T1_2mm_brain.nii.gz
161012-21:07:56,381 interface INFO:
stdout 2016-10-12T21:07:56.378534:=============================================================================
161012-21:07:56,382 interface INFO:
stdout 2016-10-12T21:07:56.378534:The composite transform comprises the following transforms (in order):
161012-21:07:56,383 interface INFO:
stdout 2016-10-12T21:07:56.378534: 1. /home/vagrant/fmri-analysis-vm/analysis/normalization/nipype_mem/nipype-interfaces-ants-registration-Registration/71cf12fd00af0abd2f55c82d0f5ee549/transformComposite.h5[0] (type = Euler3DTransform)
161012-21:07:56,383 interface INFO:
stdout 2016-10-12T21:07:56.378534: 2. /home/vagrant/fmri-analysis-vm/analysis/normalization/nipype_mem/nipype-interfaces-ants-registration-Registration/71cf12fd00af0abd2f55c82d0f5ee549/transformComposite.h5[1] (type = TranslationTransform)
161012-21:07:56,384 interface INFO:
stdout 2016-10-12T21:07:56.378534: 3. /home/vagrant/fmri-analysis-vm/analysis/normalization/nipype_mem/nipype-interfaces-ants-registration-Registration/71cf12fd00af0abd2f55c82d0f5ee549/transformComposite.h5[2] (type = Euler3DTransform)
161012-21:07:56,385 interface INFO:
stdout 2016-10-12T21:07:56.378534: 4. /home/vagrant/fmri-analysis-vm/analysis/normalization/nipype_mem/nipype-interfaces-ants-registration-Registration/71cf12fd00af0abd2f55c82d0f5ee549/transformComposite.h5[3] (type = AffineTransform)
161012-21:07:56,386 interface INFO:
stdout 2016-10-12T21:07:56.378534: 5. /home/vagrant/fmri-analysis-vm/analysis/normalization/nipype_mem/nipype-interfaces-ants-registration-Registration/71cf12fd00af0abd2f55c82d0f5ee549/transformComposite.h5[4] (type = DisplacementFieldTransform)
161012-21:07:56,387 interface INFO:
stdout 2016-10-12T21:07:56.378534:=============================================================================
161012-21:07:56,388 interface INFO:
stdout 2016-10-12T21:07:56.378534:Default pixel value: 0
161012-21:07:56,388 interface INFO:
stdout 2016-10-12T21:07:56.378534:Interpolation type: NearestNeighborInterpolateImageFunction
161012-21:07:56,389 interface INFO:
stdout 2016-10-12T21:07:56.378534:Output warped image: epi2struct_fast_wmseg_trans.nii.gz
Note that we have not yet combined the two transformations. We will do that when it comes to group level analysis. We will apply the combined transformations to single subject (first level) contrast maps.
We can test this procedure on the mean EPI image
In [19]:
epi_to_t1 = mem.cache(fsl.ApplyWarp)
epi_to_t1_results = epi_to_t1(in_file=mcflirt_results.outputs.mean_img,
ref_file=t1file,
field_file=epi_reg_results.outputs.fullwarp,
interp="spline")
t1_to_mni = mem.cache(ants.ApplyTransforms)
t1_to_mni_results = t1_to_mni(input_image=epi_to_t1_results.outputs.out_file,
reference_image=os.path.join(os.getenv('FSLDIR'),'data/standard/MNI152_T1_2mm_brain.nii.gz'),
transforms=ants_results.outputs.composite_transform,
interpolation="BSpline")
t1_to_mni_results.outputs
161012-21:09:26,357 workflow INFO:
Executing node 4f3ff33f3c52dd0c5814b62ea35a8a94 in dir: /home/vagrant/fmri-analysis-vm/analysis/normalization/nipype_mem/nipype-interfaces-fsl-preprocess-ApplyWarp/4f3ff33f3c52dd0c5814b62ea35a8a94
161012-21:09:26,362 workflow INFO:
Running: applywarp --in=/home/vagrant/fmri-analysis-vm/analysis/normalization/nipype_mem/nipype-interfaces-fsl-preprocess-MCFLIRT/fbfa00c218746e802e49f0bde8aa0174/sub00001_ses014_task002_run001_bold_mcf.nii.gz_mean_reg.nii.gz --ref=/home/vagrant/data/ds031/sub00001/ses018/anatomy/sub00001_ses018_T1w_001.nii.gz --out=/home/vagrant/fmri-analysis-vm/analysis/normalization/nipype_mem/nipype-interfaces-fsl-preprocess-ApplyWarp/4f3ff33f3c52dd0c5814b62ea35a8a94/sub00001_ses014_task002_run001_bold_mcf.nii.gz_mean_reg_warp.nii.gz --warp=/home/vagrant/fmri-analysis-vm/analysis/normalization/nipype_mem/nipype-interfaces-fsl-epi-EpiReg/8aa1a7a3a91b013599dd0026e9a31d4e/epi2struct_warp.nii.gz --interp=spline
161012-21:09:44,810 workflow INFO:
Executing node 6d006c8fd9579ba7cd3af98ef449c1f1 in dir: /home/vagrant/fmri-analysis-vm/analysis/normalization/nipype_mem/nipype-interfaces-ants-resampling-ApplyTransforms/6d006c8fd9579ba7cd3af98ef449c1f1
161012-21:09:44,816 workflow INFO:
Running: antsApplyTransforms --default-value 0 --input /home/vagrant/fmri-analysis-vm/analysis/normalization/nipype_mem/nipype-interfaces-fsl-preprocess-ApplyWarp/4f3ff33f3c52dd0c5814b62ea35a8a94/sub00001_ses014_task002_run001_bold_mcf.nii.gz_mean_reg_warp.nii.gz --interpolation BSpline --output sub00001_ses014_task002_run001_bold_mcf.nii.gz_mean_reg_warp_trans.nii.gz --reference-image /usr/share/fsl/5.0/data/standard/MNI152_T1_2mm_brain.nii.gz --transform /home/vagrant/fmri-analysis-vm/analysis/normalization/nipype_mem/nipype-interfaces-ants-registration-Registration/71cf12fd00af0abd2f55c82d0f5ee549/transformComposite.h5
161012-21:09:45,366 interface INFO:
stdout 2016-10-12T21:09:45.366560:Using double precision for computations.
161012-21:09:45,367 interface INFO:
stdout 2016-10-12T21:09:45.366560:Input scalar image: /home/vagrant/fmri-analysis-vm/analysis/normalization/nipype_mem/nipype-interfaces-fsl-preprocess-ApplyWarp/4f3ff33f3c52dd0c5814b62ea35a8a94/sub00001_ses014_task002_run001_bold_mcf.nii.gz_mean_reg_warp.nii.gz
161012-21:09:45,368 interface INFO:
stdout 2016-10-12T21:09:45.366560:Reference image: /usr/share/fsl/5.0/data/standard/MNI152_T1_2mm_brain.nii.gz
161012-21:09:45,871 interface INFO:
stdout 2016-10-12T21:09:45.870915:=============================================================================
161012-21:09:45,872 interface INFO:
stdout 2016-10-12T21:09:45.870915:The composite transform comprises the following transforms (in order):
161012-21:09:45,872 interface INFO:
stdout 2016-10-12T21:09:45.870915: 1. /home/vagrant/fmri-analysis-vm/analysis/normalization/nipype_mem/nipype-interfaces-ants-registration-Registration/71cf12fd00af0abd2f55c82d0f5ee549/transformComposite.h5[0] (type = Euler3DTransform)
161012-21:09:45,873 interface INFO:
stdout 2016-10-12T21:09:45.870915: 2. /home/vagrant/fmri-analysis-vm/analysis/normalization/nipype_mem/nipype-interfaces-ants-registration-Registration/71cf12fd00af0abd2f55c82d0f5ee549/transformComposite.h5[1] (type = TranslationTransform)
161012-21:09:45,874 interface INFO:
stdout 2016-10-12T21:09:45.870915: 3. /home/vagrant/fmri-analysis-vm/analysis/normalization/nipype_mem/nipype-interfaces-ants-registration-Registration/71cf12fd00af0abd2f55c82d0f5ee549/transformComposite.h5[2] (type = Euler3DTransform)
161012-21:09:45,874 interface INFO:
stdout 2016-10-12T21:09:45.870915: 4. /home/vagrant/fmri-analysis-vm/analysis/normalization/nipype_mem/nipype-interfaces-ants-registration-Registration/71cf12fd00af0abd2f55c82d0f5ee549/transformComposite.h5[3] (type = AffineTransform)
161012-21:09:45,875 interface INFO:
stdout 2016-10-12T21:09:45.870915: 5. /home/vagrant/fmri-analysis-vm/analysis/normalization/nipype_mem/nipype-interfaces-ants-registration-Registration/71cf12fd00af0abd2f55c82d0f5ee549/transformComposite.h5[4] (type = DisplacementFieldTransform)
161012-21:09:45,876 interface INFO:
stdout 2016-10-12T21:09:45.870915:=============================================================================
161012-21:09:45,877 interface INFO:
stdout 2016-10-12T21:09:45.870915:Default pixel value: 0
161012-21:09:47,402 interface INFO:
stdout 2016-10-12T21:09:47.401945:Interpolation type: BSplineInterpolateImageFunction
161012-21:09:47,907 interface INFO:
stdout 2016-10-12T21:09:47.907341:Output warped image: sub00001_ses014_task002_run001_bold_mcf.nii.gz_mean_reg_warp_trans.nii.gz
Out[19]:
output_image = /home/vagrant/fmri-analysis-vm/analysis/normalization/nipype_mem/nipype-interfaces-ants-resampling-ApplyTransforms/6d006c8fd9579ba7cd3af98ef449c1f1/sub00001_ses014_task002_run001_bold_mcf.nii.gz_mean_reg_warp_trans.nii.gz
Now let's look at the warp field from ANTS
In [20]:
import h5py
composite_transform=h5py.File(ants_results.outputs.composite_transform, "r")
transform_group=composite_transform['TransformGroup']
warpfield=numpy.reshape(transform_group['5']['TranformParameters'],(91,109,91,3))
warped_t1=nibabel.load(ants_results.outputs.warped_image)
warped_t1_data=warped_t1.get_data()
slicenum=50
plt.figure(figsize=(12,8))
plt.imshow(warped_t1_data[:,:,slicenum],cmap='gray')
plt.quiver(warpfield[:,:,slicenum,0],warpfield[:,:,slicenum,1],linewidths=0.001,width=0.001)
Out[20]:
<matplotlib.quiver.Quiver at 0x7f94e3405198>
Exercise: Zoom into a part of the image and show a close-up of the warp field around the anterior cingulate cortex.
Finally we can interactivelly interrogate the three images (EPI, T1, MNI tempalate) in fslview
In [21]:
!fslview {t1_to_mni_results.outputs.output_image} {os.path.join(os.getenv('FSLDIR'),'data/standard/MNI152_T1_2mm_brain.nii.gz')} {ants_results.outputs.warped_image}
In [ ]:
Content source: poldrack/fmri-analysis-vm
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