<s>
Elastix	B-Algorithm
is	O
an	O
image	B-Algorithm
registration	I-Algorithm
toolbox	O
built	O
upon	O
the	O
Insight	B-Language
Segmentation	I-Language
and	I-Language
Registration	I-Language
Toolkit	I-Language
(	O
ITK	B-Language
)	O
.	O
</s>
<s>
It	O
is	O
entirely	O
open-source	B-License
and	O
provides	O
a	O
wide	O
range	O
of	O
algorithms	O
employed	O
in	O
image	B-Algorithm
registration	I-Algorithm
problems	O
.	O
</s>
<s>
Its	O
first	O
version	O
was	O
command-line	B-Application
based	I-Application
,	O
allowing	O
the	O
final	O
user	O
to	O
employ	O
scripts	O
to	O
automatically	O
process	O
big	O
data-sets	O
and	O
deploy	O
multiple	O
registration	O
pipelines	O
with	O
few	O
lines	O
of	O
code	O
.	O
</s>
<s>
Nowadays	O
,	O
to	O
further	O
widen	O
its	O
audience	O
,	O
a	O
version	O
called	O
SimpleElastix	O
is	O
also	O
available	O
,	O
developed	O
by	O
Kasper	O
Marstal	O
,	O
which	O
allows	O
the	O
integration	O
of	O
elastix	B-Algorithm
with	O
high	O
level	O
languages	O
,	O
such	O
as	O
Python	B-Language
,	O
Java	B-Language
,	O
and	O
R	B-Language
.	O
</s>
<s>
Image	B-Algorithm
registration	I-Algorithm
is	O
a	O
well-known	O
technique	O
in	O
digital	B-Algorithm
image	I-Algorithm
processing	I-Algorithm
that	O
searches	O
for	O
the	O
geometric	B-Algorithm
transformation	I-Algorithm
that	O
,	O
applied	O
to	O
a	O
moving	O
image	O
,	O
obtains	O
a	O
one-to-one	O
map	O
with	O
a	O
target	O
image	O
.	O
</s>
<s>
Even	O
though	O
there	O
are	O
a	O
plethora	O
of	O
different	O
approaches	O
to	O
image	B-Algorithm
registration	I-Algorithm
,	O
the	O
majority	O
is	O
composed	O
of	O
the	O
same	O
macro	O
building	O
blocks	O
,	O
namely	O
the	O
transformation	B-Algorithm
,	O
the	O
interpolator	B-Algorithm
,	O
the	O
metric	O
,	O
and	O
the	O
optimizer	O
.	O
</s>
<s>
Starting	O
from	O
an	O
initial	O
transformation	B-Algorithm
computed	O
from	O
the	O
image	B-Algorithm
moments	I-Algorithm
the	O
optimization	O
process	O
searches	O
for	O
the	O
best	O
transformation	B-Algorithm
parameters	O
based	O
on	O
the	O
value	O
of	O
the	O
selected	O
similarity	O
metric	O
.	O
</s>
<s>
The	O
figure	O
on	O
the	O
right	O
shows	O
the	O
high-level	O
representation	O
of	O
the	O
registration	O
of	O
two	O
images	O
,	O
where	O
the	O
reference	O
remains	O
constant	O
during	O
the	O
entire	O
process	O
,	O
while	O
the	O
moving	O
one	O
will	O
be	O
transformed	O
according	O
to	O
the	O
transformation	B-Algorithm
parameters	O
.	O
</s>
<s>
Following	O
the	O
structure	O
of	O
the	O
image	B-Algorithm
registration	I-Algorithm
workflow	O
,	O
the	O
elastix	B-Algorithm
toolbox	O
proposes	O
a	O
modular	O
solution	O
that	O
implements	O
for	O
each	O
of	O
the	O
building	O
blocks	O
different	O
algorithms	O
,	O
highly	O
employed	O
in	O
medical	O
image	B-Algorithm
registration	I-Algorithm
,	O
and	O
helps	O
the	O
final	O
users	O
to	O
build	O
their	O
specific	O
pipeline	O
by	O
selecting	O
the	O
most	O
suitable	O
algorithm	O
for	O
each	O
of	O
the	O
main	O
building	O
blocks	O
.	O
</s>
<s>
The	O
registration	O
is	O
performed	O
on	O
images	O
,	O
and	O
the	O
elastix	B-Algorithm
toolbox	O
supports	O
all	O
the	O
data	O
formats	O
supported	O
by	O
ITK	B-Language
,	O
ranging	O
from	O
JPEG	O
and	O
PNG	O
to	O
medical	O
standard	O
formats	O
such	O
as	O
DICOM	B-Algorithm
and	O
NIFTI	O
.	O
</s>
<s>
The	O
transformation	B-Algorithm
is	O
an	O
essential	O
building	O
block	O
,	O
since	O
it	O
defines	O
the	O
allowable	O
transformations	O
.	O
</s>
<s>
In	O
image	B-Algorithm
registration	I-Algorithm
,	O
the	O
main	O
distinction	O
can	O
be	O
done	O
between	O
parallel-to-parallel	O
and	O
parallel-to-non	O
parallel	O
(	O
deformable	O
)	O
line	O
mapping	O
transformations	O
.	O
</s>
<s>
In	O
the	O
elastix	B-Algorithm
toolbox	O
,	O
the	O
final	O
users	O
can	O
select	O
one	O
transformation	B-Algorithm
or	O
compose	O
more	O
transformations	O
either	O
through	O
addition	O
or	O
via	O
composition	O
.	O
</s>
<s>
Below	O
are	O
reported	O
the	O
different	O
transformation	B-Algorithm
models	O
in	O
order	O
of	O
increasing	O
flexibility	O
,	O
along	O
with	O
the	O
corresponding	O
elastix	B-Algorithm
class	O
names	O
between	O
brackets	O
.	O
</s>
<s>
Below	O
are	O
reported	O
the	O
available	O
metrics	O
computed	O
employing	O
the	O
reference	O
and	O
the	O
transformed	O
images	O
and	O
the	O
corresponding	O
elastix	B-Algorithm
class	O
names	O
between	O
brackets	O
.	O
</s>
<s>
For	O
the	O
computation	O
of	O
the	O
similarity	O
metrics	O
,	O
it	O
is	O
not	O
always	O
necessary	O
to	O
consider	O
all	O
the	O
voxels	B-Algorithm
and	O
,	O
sometimes	O
,	O
it	O
can	O
be	O
useful	O
to	O
use	O
only	O
a	O
fraction	O
of	O
the	O
voxels	B-Algorithm
of	O
the	O
images	O
,	O
i.e.	O
</s>
<s>
Below	O
are	O
reported	O
the	O
available	O
criteria	O
for	O
selecting	O
a	O
fraction	O
of	O
the	O
voxels	B-Algorithm
for	O
the	O
similarity	O
metric	O
computation	O
and	O
the	O
corresponding	O
elastix	B-Algorithm
class	O
names	O
between	O
brackets	O
.	O
</s>
<s>
After	O
the	O
application	O
of	O
the	O
transformation	B-Algorithm
,	O
it	O
may	O
occur	O
that	O
the	O
voxels	B-Algorithm
used	O
for	O
the	O
similarity	O
metric	O
computation	O
are	O
at	O
non-voxel	O
positions	O
,	O
so	O
intensity	O
interpolation	B-Algorithm
should	O
be	O
performed	O
to	O
ensure	O
the	O
correctness	O
of	O
the	O
computed	O
values	O
.	O
</s>
<s>
Below	O
are	O
reported	O
the	O
implemented	O
interpolators	O
and	O
the	O
corresponding	O
elastix	B-Algorithm
class	O
names	O
between	O
brackets	O
.	O
</s>
<s>
N-th	B-Algorithm
order	I-Algorithm
B-spline	I-Algorithm
(	O
BSplineInterpolator	O
)	O
can	O
be	O
used	O
to	O
increase	O
the	O
order	O
N	O
,	O
increasing	O
quality	O
and	O
computation	O
time	O
.	O
</s>
<s>
The	O
optimizer	O
defines	O
the	O
strategy	O
employed	O
for	O
searching	O
the	O
best	O
transformation	B-Algorithm
parameter	O
to	O
reach	O
the	O
correct	O
registration	O
,	O
and	O
it	O
is	O
commonly	O
an	O
iterative	O
strategy	O
.	O
</s>
<s>
A	O
wider	O
range	O
of	O
optimizers	O
is	O
also	O
available	O
,	O
such	O
as	O
Quasi-Newton	B-Algorithm
or	O
evolutionary	B-Algorithm
strategies	I-Algorithm
.	O
</s>
<s>
The	O
elastix	B-Algorithm
software	O
also	O
offers	O
other	O
features	O
that	O
can	O
be	O
employed	O
to	O
speed	O
up	O
the	O
registration	O
procedure	O
and	O
to	O
provide	O
more	O
advanced	O
algorithms	O
to	O
the	O
end-users	O
.	O
</s>
<s>
Some	O
examples	O
are	O
the	O
introduction	O
of	O
blur	B-Error_Name
and	O
Gaussian	O
pyramid	O
to	O
reduce	O
data	O
complexity	O
,	O
and	O
multi-image	O
and	O
multi-metric	O
framework	O
to	O
deal	O
with	O
more	O
complex	O
applications	O
.	O
</s>
<s>
Elastix	B-Algorithm
has	O
applications	O
mainly	O
in	O
the	O
medical	O
field	O
,	O
where	O
image	B-Algorithm
registration	I-Algorithm
is	O
fundamental	O
to	O
get	O
comprehensive	O
information	O
regarding	O
the	O
analysed	O
anatomical	O
region	O
.	O
</s>
<s>
For	O
example	O
,	O
in	O
radiotherapy	O
planning	O
,	O
image	B-Algorithm
registration	I-Algorithm
allows	O
to	O
correctly	O
deliver	O
the	O
treatment	O
and	O
evaluate	O
the	O
obtained	O
results	O
.	O
</s>
<s>
Thanks	O
to	O
the	O
wide	O
range	O
of	O
implemented	O
algorithms	O
,	O
the	O
use	O
of	O
the	O
elastix	B-Algorithm
software	O
allows	O
physicians	O
and	O
researchers	O
to	O
test	O
different	O
registration	O
pipelines	O
from	O
the	O
simplest	O
to	O
more	O
complex	O
ones	O
,	O
and	O
to	O
save	O
the	O
best	O
one	O
as	O
a	O
configuration	O
file	O
.	O
</s>
<s>
This	O
file	O
and	O
the	O
fact	O
that	O
the	O
software	O
is	O
completely	O
open-source	B-License
makes	O
it	O
easy	O
to	O
reproduce	O
the	O
work	O
,	O
that	O
can	O
help	O
supporting	O
the	O
open	O
science	O
paradigm	O
,	O
and	O
allows	O
fast	O
reuse	O
on	O
different	O
patients	O
data	O
.	O
</s>
<s>
In	O
this	O
field	O
,	O
the	O
possibility	O
to	O
exploit	O
elastix	B-Algorithm
with	O
high-level	O
languages	O
,	O
such	O
as	O
OpenCL	B-Application
,	O
opens	O
to	O
research	O
in	O
the	O
usage	O
of	O
GPUs	B-Architecture
and	O
other	O
hardware	B-General_Concept
accelerators	I-General_Concept
.	O
</s>
