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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
<title>sips</title>
<style href="">a {text-decoration: none} </style>
</head>
<body style="color: rgb(0, 0, 0); background-color: rgb(211, 227, 225);"
link="#339999" alink="#339999" vlink="#339999">
<br>
<center>
<table
style="text-align: left; width: 900px; background-color: rgb(51, 51, 153);"
border="1" cellpadding="8" cellspacing="2">
<tbody>
<tr>
<td
style="vertical-align: top; background-color: rgb(51, 51, 153);"> <img
style="width: 326px; height: 130px;" alt="" src="brains_x_3_blue.JPG"
align="right"><span
style="color: rgb(255, 255, 255); font-family: Calibri; font-weight: bold;"><font
size="7">SBIPS<br>
<font size="5"><span style="font-family: Gisha;"><br>
</span></font></font></span><span
style="color: rgb(255, 255, 255); font-family: Calibri;"><font size="7"><font
size="5"><span style="font-family: Gisha;">sips</span></font></font></span><span
style="color: rgb(255, 255, 255); font-family: Calibri; font-weight: bold;"><font
size="7"><font size="5"><br>
</font></font></span></td>
</tr>
<tr>
<td
style="background-color: rgb(255, 255, 255); text-align: center;"><a
style="font-family: Calibri;" href="index.html"><span
style="font-weight: bold;">HOME </span></a><span
style="font-family: Calibri;">- </span><a
style="font-family: Calibri;" href="https://github.com/sbips/sips"><span
style="font-weight: bold;">DOWNLOAD</span></a><span
style="font-family: Calibri;"> </span><span
style="font-weight: bold; font-family: Calibri;">-</span><span
style="font-family: Calibri;"> </span><a style="font-family: Calibri;"
href="sips_guide_v1.03.pdf"><span style="font-weight: bold;">DOCUMENTATION</span></a><span
style="font-family: Calibri;"> - </span><a
href="https://github.com/sbips/sips/issues"><span
style="font-weight: bold; font-family: Calibri;">SUPPORT</span></a><br>
</td>
</tr>
<tr>
<td style="vertical-align: top;"><big><span
style="color: rgb(255, 255, 255); font-family: Calibri; font-weight: bold;">ABOUT</span></big><br>
</td>
</tr>
<tr>
<td
style="vertical-align: top; background-color: rgb(255, 255, 255);"><br
style="font-family: Calibri;">
<span style="font-family: Calibri;">The Sunnybrook Image
Processing Software (</span><span
style="font-weight: bold; font-family: Calibri;">sips</span><span
style="font-family: Calibri;">) package consists primarily of in-house
developed programs that can be used to perform various image processing
tasks on structural magnetic resonance brain images such as tissue
segmentation (T1seg), semi-automated brain region parcellation
(SABRE), white matter hyperintensity and lesion segmentation (Lesion
Explorer/flex), and head-from-brain extraction (brain sizer).</span><br
style="font-family: Calibri;">
<br style="font-family: Calibri;">
<span style="font-family: Calibri;">Some external supporting
software is also provided in the sips package, including a subset of
programs from the FSL, MINC, and N3 packages (see <a
href="https://github.com/sbips/sips"><span style="font-weight: bold;">README
</span></a>file for details).</span><br>
<br>
</td>
</tr>
<tr>
<td style="vertical-align: top;"><big><span
style="color: rgb(255, 255, 255); font-family: Calibri; font-weight: bold;">REFERENCES</span></big><font
size="4"><br>
</font></td>
</tr>
<tr>
<td
style="vertical-align: top; background-color: rgb(255, 255, 255);"><br>
<span style="font-family: Calibri;">If the sips package is used
as part of published research, please reference the following papers
where appropriate.</span><br style="font-family: Calibri;">
<br>
<span style="font-family: Gisha; font-weight: bold;">sips Software</span><span
style="font-family: Gisha;"></span><br>
<br style="font-family: Calibri;">
<span style="font-weight: bold; font-family: Calibri;">
LESION EXPLORER / BRAIN SIZER</span><span style="font-family: Calibri;">:</span><br
style="font-family: Calibri;">
<div style="margin-left: 40px; font-family: Calibri;">Ramirez,
J., Gibson, E., Quddus, A., Lobaugh, N.J., Feinstein, A., Levine, B.
Scott, C.J., Levy-Cooperman, N., Gao, F.Q., Black S.E.
(2010.) Lesion Explorer: A comprehensive segmentation and
parcellation package to obtain regional volumetrics for subcortical
hyperintensities and intracranial tissue. <span
style="font-style: italic;">Neuroimage</span>, Sep. 19 [Epub ahead of
print].<br>
</div>
<br style="font-family: Calibri;">
<span style="font-weight: bold; font-family: Calibri;">
FLEX:</span><br style="font-family: Calibri;">
<div style="margin-left: 40px; font-family: Calibri;">Gibson E.,
Gao F., Black S.E., Lobaugh N.J. (2010). Automatic
segmentation of white matter hyperintensities in the elderly using
FLAIR images at 3T.<span style="font-style: italic;"> Journal of
Magnetic Resonance Imaging</span>, 31, 1311-22.<br>
</div>
<br style="font-family: Calibri;">
<span style="font-weight: bold; font-family: Calibri;">
SABRE</span><span style="font-family: Calibri;">:</span><br
style="font-family: Calibri;">
<div style="margin-left: 40px; font-family: Calibri;">Dade L.A.,
Gao F.Q., Kovacevic N., Roy P., Rockel C., O'Toole C.M., Lobaugh N.J.,
Feinstein A., Levine B., Black S.E. (2004). Semiautomatic
brain region extraction: A method of parcellating brain regions
from structural magnetic resonance images. <span
style="font-style: italic;">Neuroimage</span>, 22, 1492-502.<br>
</div>
<br style="font-family: Calibri;">
<span style="font-weight: bold; font-family: Calibri;">
T1SEG / AUTO_HFB</span><span style="font-family: Calibri;">:</span><br
style="font-family: Calibri;">
<div style="margin-left: 40px; font-family: Calibri;"><span
style="font-family: Calibri;">Kovacevic
N, Lobaugh NJ, Bronskill MJ, Levine B, Feinstein A, Black SE.
(2002). A robust method for extraction and automatic segmentation
of brain images. </span><span
style="font-style: italic; font-family: Calibri;">Neuroimage</span><span
style="font-family: Calibri;">,
17, 1087-100.</span><br>
</div>
<br style="font-family: Gisha;">
<span style="font-family: Gisha; font-weight: bold;">sips
External Supporting Software </span><br style="font-family: Calibri;">
<br style="font-family: Calibri;">
<span style="font-family: Calibri;"> </span><span
style="font-weight: bold; font-family: Calibri;"><a
href="http://www.fmrib.ox.ac.uk/fsl/">FSL</a> </span><span
style="font-family: Calibri;">- (avwmaths, bet, fast, flirt)</span><br
style="font-family: Calibri;">
<span style="font-family: Calibri;"> </span><br
style="font-family: Calibri;">
<span style="font-family: Calibri;"> </span><a
style="font-family: Calibri;"
href="http://www.bic.mni.mcgill.ca/%7Ejgsled/"><span
style="font-weight: bold;">N3</span></a><span
style="font-family: Calibri;"> - (nu_correct)</span><br
style="font-family: Calibri;">
<br style="font-family: Calibri;">
<span style="font-family: Calibri;"> </span><span
style="font-family: Calibri; font-weight: bold;"><a
href="http://www.bic.mni.mcgill.ca/ServicesSoftware/HomePage">MINC</a></span><span
style="font-family: Calibri;"> - ( nii2mnc,
mincmath, mnc2nii)</span><br style="font-family: Calibri;">
<br>
</td>
</tr>
</tbody>
</table>
</center>
<br>
<br>
</body>
</html>