<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:m="http://schemas.microsoft.com/office/2004/12/omml" 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 14 (filtered medium)">
<style><!--
/* Font Definitions */
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
@font-face
{font-family:Tahoma;
panose-1:2 11 6 4 3 5 4 4 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0in;
margin-bottom:.0001pt;
font-size:12.0pt;
font-family:"Times New Roman","serif";}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:purple;
text-decoration:underline;}
span.EmailStyle17
{mso-style-type:personal-reply;
font-family:"Calibri","sans-serif";
color:#1F497D;}
.MsoChpDefault
{mso-style-type:export-only;
font-family:"Calibri","sans-serif";}
@page WordSection1
{size:8.5in 11.0in;
margin:1.0in 1.0in 1.0in 1.0in;}
div.WordSection1
{page:WordSection1;}
--></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="purple">
<div class="WordSection1">
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Hi Dr. Mori and MRIstudio group,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">May I follow up on the question of using T2w image for distortion correction? We have an investigator whose protocol does not include a T2 acquisition, nor
does he wish to add one. However, the protocol does include T2-FLAIR. Could the FLAIR image be used in the same way?<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><br>
Many thanks,<br>
<br>
Dave<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> mristudio-users-bounces@mristudio.org [mailto:mristudio-users-bounces@mristudio.org]
<b>On Behalf Of </b>Susumu Mori<br>
<b>Sent:</b> Sunday, December 08, 2013 3:57 PM<br>
<b>To:</b> DTI Studio, ROI Editor, DiffeoMap Questions/Support<br>
<b>Subject:</b> Re: [Mristudio-users] Applying field map to DTI ?<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<p class="MsoNormal">Unfortunately, MriStudio software doesn't offer the solution #1 (phase map based) and #3 (inverted distortion).<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style="margin-bottom:12.0pt"><o:p> </o:p></p>
<div>
<p class="MsoNormal">On Thu, Dec 5, 2013 at 10:11 AM, Dorian P. <<a href="mailto:alb.net@gmail.com" target="_blank">alb.net@gmail.com</a>> wrote:<o:p></o:p></p>
<div>
<p class="MsoNormal">Thank you Dr. Mori.<o:p></o:p></p>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">I am also looking at time concerns, both in acquisition and postprocessing. LDDMM is a bit long to run for clinical purposes. I used to do registration in Diffeomap alone (AIR linear -> AIR non-linear using white matter map segmented from
T1 as template), but this did not resolve a recent problem I had. The subject had a tiny tumor (1cm) near the insula. I could see the arcuate passing near the tumor in FA maps, but there was no way to register this onto MP-RAGE (the arcuate seemed passing
through the tumor instead). Thus I need some better solution to have millimetric precision.<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">How would I go for applying solutions 1 and 3 Dr Mori, that is applying the field map or correcting with inverted gradients (posterior-anterior rather than anterior-posterior).<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">Thank you for your quick response. <o:p></o:p></p>
</div>
</div>
<div>
<p class="MsoNormal" style="margin-bottom:12.0pt"><o:p> </o:p></p>
<div>
<p class="MsoNormal">2013/12/5 Susumu Mori <<a href="mailto:smoriw@gmail.com" target="_blank">smoriw@gmail.com</a>><o:p></o:p></p>
<div>
<p class="MsoNormal">Dorian,<o:p></o:p></p>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">DTI, which is based on single-shot echo planar imaging, is known to distort due to B0 field inhomogeneity.<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">We can map this field inhomogeneity using a separately measured field map (thus, a measurement of field is needed in addition to DTI). With this field map, we can theoretically calculate the amount of distortion and undo it.<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">However, this field map technique has some its own difficulties. From what I have heard, this method is not perfect.<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">When we judge if the distortion is well corrected, we usually compare the distortion-corrected DTI image, such as b0 image, with conventional anatomical scans, such as T2-weighted images. If the corrected b0 image matches very well with
a T2-weighted image, we say, "it is well corrected".<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">So, an alternative approach is, to nonlinearly (such as LDDMM) register DTI images to a T2-weighted anatomical scan. This approach doesn't require a separate field map data, but do requires a T2-weighted image. This approach is explained
in the #8 of Getting Started here (<a href="https://www.mristudio.org/wiki/user_manual/diffeomap" target="_blank">https://www.mristudio.org/wiki/user_manual/diffeomap</a>).<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">Another method is to acquire two sets of b0 image with different phase-encoding gradients, which generate two b0 images with a completely opposite distortion directions. From these two images, a middle image can be calculated. This approach,
however, requires such two b0 data to be acquired.<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">So, all three approaches require some extra data. Which of the three is the best? Well, all three are equally good and equally imperfect. <o:p></o:p></p>
</div>
</div>
<div>
<p class="MsoNormal" style="margin-bottom:12.0pt"><o:p> </o:p></p>
<div>
<div>
<div>
<p class="MsoNormal">On Thu, Dec 5, 2013 at 9:30 AM, Dorian Pustina <<a href="mailto:albnet@gmail.com" target="_blank">albnet@gmail.com</a>> wrote:<o:p></o:p></p>
</div>
</div>
<blockquote style="border:none;border-left:solid #CCCCCC 1.0pt;padding:0in 0in 0in 6.0pt;margin-left:4.8pt;margin-right:0in">
<div>
<div>
<div>
<p class="MsoNormal">Hello everybody at MRIstudio,<o:p></o:p></p>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">I remember reading some paper that said field maps should be applied to DWI data to correct for deformations and bring everything closer to true anatomical space. Anybody knows how to apply this field map and whether it will really correct
for the spatial distortions of DTI (thus making it easier to register DTI on MP-RAGE)?<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">Thank you<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">Dorian<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">TJU<o:p></o:p></p>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
</div>
<p class="MsoNormal" style="margin-bottom:12.0pt">_______________________________________________<br>
mristudio-users mailing list<br>
<a href="mailto:mristudio-users@mristudio.org" target="_blank">mristudio-users@mristudio.org</a><br>
<a href="http://lists.mristudio.org/mailman/listinfo/" target="_blank">http://lists.mristudio.org/mailman/listinfo/</a><br>
Unsubscribe, send a blank email to: <a href="mailto:mristudio-users-unsubscribe@mristudio.org" target="_blank">
mristudio-users-unsubscribe@mristudio.org</a><o:p></o:p></p>
</blockquote>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<p class="MsoNormal" style="margin-bottom:12.0pt"><br>
_______________________________________________<br>
mristudio-users mailing list<br>
<a href="mailto:mristudio-users@mristudio.org" target="_blank">mristudio-users@mristudio.org</a><br>
<a href="http://lists.mristudio.org/mailman/listinfo/" target="_blank">http://lists.mristudio.org/mailman/listinfo/</a><br>
Unsubscribe, send a blank email to: <a href="mailto:mristudio-users-unsubscribe@mristudio.org" target="_blank">
mristudio-users-unsubscribe@mristudio.org</a><o:p></o:p></p>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<p class="MsoNormal" style="margin-bottom:12.0pt"><br>
_______________________________________________<br>
mristudio-users mailing list<br>
<a href="mailto:mristudio-users@mristudio.org">mristudio-users@mristudio.org</a><br>
<a href="http://lists.mristudio.org/mailman/listinfo/" target="_blank">http://lists.mristudio.org/mailman/listinfo/</a><br>
Unsubscribe, send a blank email to: <a href="mailto:mristudio-users-unsubscribe@mristudio.org">
mristudio-users-unsubscribe@mristudio.org</a><o:p></o:p></p>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
</div>
<br>
<hr>
<font face="Arial" color="Gray" size="1"><br>
Confidentiality Notice: This e-mail transmission may contain confidential or legally privileged information that is intended only for the individual or entity named in the e-mail address. If you are not the intended recipient, you are hereby notified that any
disclosure, copying, distribution, or reliance upon the contents of this e-mail is strictly prohibited. If you have received this e-mail transmission in error, please reply to the sender and then delete the message from your computer. Thank you.<br>
</font>
</body>
</html>