<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:st1="urn:schemas-microsoft-com:office:smarttags" xmlns="http://www.w3.org/TR/REC-html40">
<head>
<meta http-equiv=Content-Type content="text/html; charset=us-ascii">
<meta name=Generator content="Microsoft Word 11 (filtered medium)">
<!--[if !mso]>
<style>
v\:* {behavior:url(#default#VML);}
o\:* {behavior:url(#default#VML);}
w\:* {behavior:url(#default#VML);}
.shape {behavior:url(#default#VML);}
</style>
<![endif]--><o:SmartTagType
namespaceuri="urn:schemas-microsoft-com:office:smarttags" name="PersonName"/>
<!--[if !mso]>
<style>
st1\:*{behavior:url(#default#ieooui) }
</style>
<![endif]-->
<style>
<!--
/* Font Definitions */
@font-face
{font-family:"MS Mincho";
panose-1:2 2 6 9 4 2 5 8 3 4;}
@font-face
{font-family:Tahoma;
panose-1:2 11 6 4 3 5 4 4 2 4;}
@font-face
{font-family:"\@MS Mincho";
panose-1:2 2 6 9 4 2 5 8 3 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0in;
margin-bottom:.0001pt;
font-size:12.0pt;
font-family:"Times New Roman";}
a:link, span.MsoHyperlink
{color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{color:blue;
text-decoration:underline;}
pre
{margin:0in;
margin-bottom:.0001pt;
font-size:10.0pt;
font-family:"Courier New";}
span.EmailStyle18
{mso-style-type:personal-reply;
font-family:Arial;
color:navy;}
@page Section1
{size:8.5in 11.0in;
margin:1.0in 1.25in 1.0in 1.25in;}
div.Section1
{page:Section1;}
-->
</style>
<!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]-->
</head>
<body lang=EN-US link=blue vlink=blue>
<div class=Section1>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>There are three ways for skull stripping
in RoiEditor.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>1) Simple thresholding: This produce the
same results as the DtiStudio's masking function.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>2) Region growing: if you use this
function together with b0 or average(all DWIs), you should be able to achieve
very decent skull stripping. We use this routinely. We use average(DWIs) often.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>3) Skull-stripping button: The region
growing may leak out to some tissues outside the brain if high-intensity areas
of the brain and outside tissues are connected. This skull-stripping function
poses some restrictions in the shape of the object. Namely, the brain surface
should be smooth without anything budding out in an extreme manner. If the
region growing function consistently leaks out and defines tissues outside the
brain, you can try this function. This function also allows you to load
"second image", such as an anatomical T2. The brain contour defined
by b0 or average(DWIs) will be superimposed on the second image (please note,
the brain contour will not align perfectly because of subject motion and DTI
(EPI)-related brain distortion). This b0-defined contour then will be used as
an initial guess of the brain contour of the second image and do the skull
strip. We use this function for skull-strip of co-registered T2 (and T1). It
works decently, but not perfect (I've never seen any perfect automated
skull-strip that works for all images anyway).<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>susumu<o:p></o:p></span></font></p>
<div>
<div class=MsoNormal align=center style='text-align:center'><font size=3
face="Times New Roman"><span style='font-size:12.0pt'>
<hr size=2 width="100%" align=center tabindex=-1>
</span></font></div>
<p class=MsoNormal><b><font size=2 face=Tahoma><span style='font-size:10.0pt;
font-family:Tahoma;font-weight:bold'>From:</span></font></b><font size=2
face=Tahoma><span style='font-size:10.0pt;font-family:Tahoma'>
mristudio-users-bounces@mristudio.org
[mailto:mristudio-users-bounces@mristudio.org] <b><span style='font-weight:
bold'>On Behalf Of </span></b>Jim Li<br>
<b><span style='font-weight:bold'>Sent:</span></b> Monday, December 08, 2008
1:53 PM<br>
<b><span style='font-weight:bold'>To:</span></b> DTI Studio, ROI Editor,
Landmarker Questions/Support<br>
<b><span style='font-weight:bold'>Subject:</span></b> Re: [Mristudio-users]
about effect of masking</span></font><o:p></o:p></p>
</div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>Hi Susumu,<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'> <o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>Thanks a lot for your information. I tried the skull-stripping
of ROIEditor using the default setting. The result is not bad, but I hope
to add/remove some areas manually on top of the outcoming mask file to define a
better mask. Also I hope to better understand the default parameters in the
skull-stripping algorithm so I can tailor them to my need. I wish
there's an instruction manual for ROIEditor that can tell me all of
these...<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'> <o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>Cheers,<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'> <o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>Jim<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'> <o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>-----------------------------------------<o:p></o:p></span></font></p>
</div>
<div><pre><font size=2 face="Courier New"><span style='font-size:10.0pt'>Hi Jim,<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'><o:p> </o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>When you do tensor calculation, you want to mask out the areas outside the brain. The easiest way is to use the threshold value to mask out the noise floor. This approach however leaves a lot of extra-brain tissues. RoiEditor (and many other programs) offers much more tools to define the brain as a binary map and remove other tissues using tools such as region growing and skull-strip tools. If you have any binary masking generated by another program you can load such a file through this function. <o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'><o:p> </o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>Susumu<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'><o:p> </o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>------Original Message------<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>From: Jim Li<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>Sender: <a
href="http://lists.mristudio.org/mailman/listinfo/mristudio-users"
target="_blank">mristudio-users-bounces at mristudio.org</a><o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>To: DTI Studio, ROI Editor, Landmarker Questions/Support<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>ReplyTo: <st1:PersonName
w:st="on">DTI Studio, ROI Editor, Landmarker Questions/Support</st1:PersonName><o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>Subject: [Mristudio-users] about effect of masking<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>Sent: Dec 5, 2008 17:57<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'><o:p> </o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>Hi all, Can anybody give me a hint? In the DTIstudio software I clicked the "Tensor, Color map, etc" button in the "Calculation" section of the "DtiMap" tab. Then, from the pop-out window called "DTI-Map Options", I saw a choice called "Select a mask-image". Under what situation should we use that choice? Should it be a default choice when the brain has some lesions, given that the lesional area can be at about the same level as the background noise level and thus can be easily wiped out even if we choose a low background noise level from which to create a mask-image? Thanks a lot, Jim _______________________________________________ Mristudio-users mailing list <a
href="http://lists.mristudio.org/mailman/listinfo/mristudio-users"
target="_blank">Mristudio-users at mristudio.org</a> <a
href="http://lists.mristudio.org/mailman/listinfo/mristudio-users"
target="_blank">http://lists.mristudio.org/mailman/listinfo/mristudio-users</a> <o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>Sent via BlackBerry by AT&T<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'><o:p> </o:p></span></font></pre></div>
</div>
</body>
</html>