<s>
FreeSurfer	B-Algorithm
is	O
a	O
brain	O
imaging	B-Algorithm
software	I-Algorithm
package	O
originally	O
developed	O
by	O
Bruce	O
Fischl	O
,	O
Anders	O
Dale	O
,	O
Martin	O
Sereno	O
,	O
and	O
Doug	O
Greve	O
.	O
</s>
<s>
Development	O
and	O
maintenance	O
of	O
FreeSurfer	B-Algorithm
is	O
now	O
the	O
primary	O
responsibility	O
of	O
the	O
Laboratory	O
for	O
Computational	O
Neuroimaging	O
at	O
the	O
Athinoula	O
A	O
.	O
Martinos	O
Center	O
for	O
Biomedical	O
Imaging	O
.	O
</s>
<s>
FreeSurfer	B-Algorithm
contains	O
a	O
set	O
of	O
programs	O
with	O
a	O
common	O
focus	O
of	O
analyzing	O
magnetic	O
resonance	O
imaging	O
(	O
MRI	O
)	O
scans	O
of	O
brain	O
tissue	O
.	O
</s>
<s>
FreeSurfer	B-Algorithm
includes	O
tools	O
for	O
the	O
reconstruction	O
of	O
topologically	O
correct	O
and	O
geometrically	O
accurate	O
models	O
of	O
both	O
the	O
gray/white	O
and	O
pial	O
surfaces	O
,	O
for	O
measuring	O
cortical	O
thickness	O
,	O
surface	O
area	O
and	O
folding	O
,	O
and	O
for	O
computing	O
inter-subject	O
registration	O
based	O
on	O
the	O
pattern	O
of	O
cortical	O
folds	O
.	O
</s>
<s>
57,541	O
copies	O
of	O
the	O
FreeSurfer	B-Algorithm
software	O
package	O
have	O
been	O
registered	O
for	O
use	O
as	O
of	O
April	O
2022	O
and	O
it	O
is	O
a	O
core	O
tool	O
in	O
the	O
processing	O
pipelines	O
of	O
the	O
Human	O
Connectome	O
Project	O
,	O
the	O
UK	O
Biobank	O
,	O
the	O
Adolescent	O
Brain	O
Cognitive	O
Development	O
Study	O
,	O
and	O
the	O
Alzheimer	O
's	O
Disease	O
Neuroimaging	O
Initiative	O
.	O
</s>
<s>
The	O
FreeSurfer	B-Algorithm
processing	O
stream	O
is	O
controlled	O
by	O
a	O
shell	O
script	O
called	O
recon-all	O
.	O
</s>
<s>
FreeSurfer	B-Algorithm
automatically	O
segments	O
the	O
volume	O
and	O
parcellates	O
the	O
surface	O
into	O
standardized	O
regions	B-Algorithm
of	I-Algorithm
interest	I-Algorithm
(	O
ROIs	O
)	O
.	O
</s>
<s>
Freesurfer	B-Algorithm
uses	O
a	O
morphed	O
spherical	O
method	O
to	O
average	O
across	O
subjects	O
for	O
statistical	O
(	O
general	O
linear	O
model	O
)	O
analysis	O
with	O
the	O
mri_glmfit	O
tool	O
.	O
</s>
<s>
FreeSurfer	B-Algorithm
contains	O
a	O
range	O
of	O
packages	O
allowing	O
a	O
broad	O
spectrum	O
of	O
uses	O
,	O
including	O
:	O
</s>
<s>
FreeView	O
,	O
a	O
tool	O
to	O
visualize	O
FreeSurfer	B-Algorithm
output	O
,	O
can	O
also	O
display	O
common	O
MRI	O
image	O
formats	O
.	O
</s>
<s>
FreeSurfer	B-Algorithm
interoperates	O
easily	O
with	O
the	O
FMRIB	B-Algorithm
Software	I-Algorithm
Library	I-Algorithm
(	O
FSL	O
)	O
,	O
which	O
is	O
a	O
comprehensive	O
library	O
for	O
image	O
analysis	O
,	O
written	O
by	O
the	O
Functional	B-Algorithm
MRI	I-Algorithm
of	O
the	O
Brain	O
(	O
FMRIB	O
)	O
group	O
at	O
Oxford	O
,	O
UK	O
.	O
</s>
<s>
The	O
functional	O
activation	O
results	O
obtained	O
using	O
either	O
the	O
FreeSurfer	B-Algorithm
Functional	O
Analysis	O
Stream	O
(	O
FS-FAST	B-Algorithm
)	O
or	O
the	O
FSL	O
tools	O
can	O
be	O
overlaid	O
onto	O
inflated	O
,	O
sphered	O
or	O
flattened	O
cortical	O
surfaces	O
using	O
FreeSurfer	B-Algorithm
.	O
</s>
<s>
Data	O
from	O
Statistical	O
Parametric	O
Mapping	O
(	O
SPM	O
)	O
can	O
be	O
integrated	O
into	O
FreeSurfer	B-Algorithm
data	O
sets	O
through	O
tools	O
included	O
in	O
the	O
FreeSurfer	B-Algorithm
package	O
.	O
</s>
<s>
FreeSurfer	B-Algorithm
also	O
uses	O
toolkits	O
from	O
,	O
VXL	B-Application
,	O
Tcl/Tk/Tix/BLT	O
,	O
VTK.	O
,	O
KWWidgets	O
and	O
Qt	O
,	O
which	O
are	O
all	O
available	O
with	O
the	O
distribution	O
.	O
</s>
<s>
Other	O
neuroimaging	O
programs	O
like	O
Caret	O
,	O
AFNI/SUMA	O
,	O
,	O
and	O
3D	O
Slicer	O
can	O
also	O
import	O
data	O
processed	O
by	O
FreeSurfer	B-Algorithm
.	O
</s>
<s>
FreeSurfer	B-Algorithm
runs	O
on	O
Mac	O
OS	O
and	O
Linux	B-Application
.	O
</s>
<s>
Free	O
registration	O
and	O
binary	O
installation	O
are	O
available	O
without	O
a	O
cost	O
,	O
but	O
a	O
license	O
key	O
(	O
text	O
file	O
)	O
is	O
necessary	O
to	O
run	O
the	O
FreeSurfer	B-Algorithm
binaries	O
.	O
</s>
<s>
Documentation	O
can	O
be	O
found	O
on	O
the	O
FreeSurfer	B-Algorithm
Wiki	O
and	O
limited	O
support	O
is	O
available	O
from	O
the	O
developers	O
and	O
community	O
through	O
the	O
FreeSurfer	B-Algorithm
mailing	O
list	O
.	O
</s>
<s>
The	O
following	O
is	O
a	O
sample	O
of	O
references	O
the	O
FreeSurfer	B-Algorithm
team	O
recommends	O
researchers	O
cite	O
when	O
publishing	O
findings	O
obtained	O
through	O
FreeSurfer	B-Algorithm
.	O
</s>
<s>
2004	O
2731	O
An	O
automated	O
labeling	O
system	O
for	O
subdividing	O
the	O
human	O
cerebral	O
cortex	O
on	O
MRI	O
scans	O
into	O
gyral	O
based	O
regions	B-Algorithm
of	I-Algorithm
interest	I-Algorithm
.	O
</s>
