<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="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]-->
<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:purple;
text-decoration:underline;}
span.EmailStyle17
{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;}
/* List Definitions */
@list l0
{mso-list-id:513883293;
mso-list-type:hybrid;
mso-list-template-ids:-1194827936 67698705 67698713 67698715 67698703 67698713 67698715 67698703 67698713 67698715;}
@list l0:level1
{mso-level-text:"%1\)";
mso-level-tab-stop:.5in;
mso-level-number-position:left;
text-indent:-.25in;}
@list l1
{mso-list-id:1822306296;
mso-list-type:hybrid;
mso-list-template-ids:-598558380 67698705 67698713 67698715 67698703 67698713 67698715 67698703 67698713 67698715;}
@list l1:level1
{mso-level-text:"%1\)";
mso-level-tab-stop:.5in;
mso-level-number-position:left;
text-indent:-.25in;}
ol
{margin-bottom:0in;}
ul
{margin-bottom:0in;}
-->
</style>
</head>
<body lang=EN-US link=blue vlink=purple>
<div class=Section1>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Hi Christian<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'>The optic radiation is a difficult tract
to reconstruct. Maybe you can get a good result in one subject but you may find
a poor result in the other. That’s why we didn’t include it in our
protocol paper in Neuroimage 30, 630, 2007. The reasons are following;<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 style='margin-left:.5in;text-indent:-.25in;mso-list:l1 level1 lfo1'><![if !supportLists]><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'><span style='mso-list:Ignore'>1)<font size=1 face="Times New Roman"><span
style='font:7.0pt "Times New Roman"'> </span></font></span></span></font><![endif]><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'>It has quite a sharp turn where it exits the LGN and merges into the
sagittal stratum (a huge sheet-like bundle running sagittally, which includes
the inferior fronto-occipital fasciculu, inferior longitudinal fasciculus,
projections from the splenium of the corpus callosum, and posterior thalamic
radiation). With 2-2.5 mm resolution, the turn is quite sharp.<o:p></o:p></span></font></p>
<p class=MsoNormal style='margin-left:.5in;text-indent:-.25in;mso-list:l1 level1 lfo1'><![if !supportLists]><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'><span style='mso-list:Ignore'>2)<font size=1 face="Times New Roman"><span
style='font:7.0pt "Times New Roman"'> </span></font></span></span></font><![endif]><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'>The way it exits the thalamus is oblique with respect to the
coronal, sagittal, and axial slices and it is difficult to get the
cross-section within one plane in a very selective manner.<o:p></o:p></span></font></p>
<p class=MsoNormal style='margin-left:.5in;text-indent:-.25in;mso-list:l1 level1 lfo1'><![if !supportLists]><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'><span style='mso-list:Ignore'>3)<font size=1 face="Times New Roman"><span
style='font:7.0pt "Times New Roman"'> </span></font></span></span></font><![endif]><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'>As also pointed in #1, it merges to the sagittal stratum and
therefore it is difficult to extract it selectively.<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'>To solve the #2 issue, you may need to
define the LGN or the posterior thalamus three-dimensionally as one of the
ROIs.<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'>Sorry if this is not really a solution. It
is one of the limitations of the DTI-based tractography. You are interested in
connection between A – B and between A and B there is a non-specific
large bundle (A – large bundle – B). In this kind of situation,
depending on how the A and B branches come out from the large bundle, you may
get only a portion of the fiber you want. The size of the reconstruction may
also be influenced by status of unrelated fibers in the large bundle. In
general, there are several approached you may take; <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 style='margin-left:.5in;text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'><span style='mso-list:Ignore'>1)<font size=1 face="Times New Roman"><span
style='font:7.0pt "Times New Roman"'> </span></font></span></span></font><![endif]><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'>If there is an existing knowledge that the A-B connection is the
majority of the large bundle, you may just have to measure the size of the
large bundle using the ROI delineation or the tractography of the bundle itself
(not using ROIs in A and B, because there is no guarantee that it actually increases
the specificity in this situation). In your case, this means measurement of the
sagittal stratum or the posterior thalamic radiation.<o:p></o:p></span></font></p>
<p class=MsoNormal style='margin-left:.5in;text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'><span style='mso-list:Ignore'>2)<font size=1 face="Times New Roman"><span
style='font:7.0pt "Times New Roman"'> </span></font></span></span></font><![endif]><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'>Identify regions where the tract is more pure before merging to the
large bundle (e.g. A – large bundle or large bundle – B regions). For
example, if you are interested in the corticospinal tract, the lower pons
region is anatomically known to be more pure CST. For the optic radiation, it
is where the OR comes out from the LGN or exits to the CF, although I’m
not sure if you can see a nicely defined tract in such regions.<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>
<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>
<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>Christian Bieck<br>
<b><span style='font-weight:bold'>Sent:</span></b> Tuesday, October 28, 2008
1:49 PM<br>
<b><span style='font-weight:bold'>To:</span></b> mristudio-users@mristudio.org<br>
<b><span style='font-weight:bold'>Subject:</span></b> [Mristudio-users] Optic
radiations</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>
<p class=MsoNormal><font size=2 color=black face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New";color:black'>Hello,</span></font><br>
<br>
<font size=2 color=black face="Courier New"><span style='font-size:10.0pt;
font-family:"Courier New";color:black'>Since my last inquiry seemed to have
escaped notice, I write you again </span></font><br>
<font size=2 color=black face="Courier New"><span style='font-size:10.0pt;
font-family:"Courier New";color:black'>in the hopes of finding a solution to my
problem. </span></font><br>
<font size=2 color=black face="Courier New"><span style='font-size:10.0pt;
font-family:"Courier New";color:black'>As I wrote in my last email, I’m
analyzing the FA values of the optic </span></font><br>
<font size=2 color=black face="Courier New"><span style='font-size:10.0pt;
font-family:"Courier New";color:black'>radiations and have, so far, extracted
them by using </span></font><br>
<font size=2 color=black face="Courier New"><span style='font-size:10.0pt;
font-family:"Courier New";color:black'>anatomical landmarks and the DTIStudio
functions AND, OR and NOT. The </span></font><br>
<font size=2 color=black face="Courier New"><span style='font-size:10.0pt;
font-family:"Courier New";color:black'>focus of my research concerns the
posterior parts of the optic </span></font><br>
<font size=2 color=black face="Courier New"><span style='font-size:10.0pt;
font-family:"Courier New";color:black'>radiations ending in the primary visual
cortex, but I find myself </span></font><br>
<font size=2 color=black face="Courier New"><span style='font-size:10.0pt;
font-family:"Courier New";color:black'>unable to extract them properly. Using
the ROI-Operations in the Fiber </span></font><br>
<font size=2 color=black face="Courier New"><span style='font-size:10.0pt;
font-family:"Courier New";color:black'>Tab during Fiber Tracking oftentimes
results in the removal of entire </span></font><br>
<font size=2 color=black face="Courier New"><span style='font-size:10.0pt;
font-family:"Courier New";color:black'>fiber tracts instead of just the
anterior parts and any attempts to </span></font><br>
<font size=2 color=black face="Courier New"><span style='font-size:10.0pt;
font-family:"Courier New";color:black'>work with ROI Editor have not been
successful so far. </span></font><br>
<font size=2 color=black face="Courier New"><span style='font-size:10.0pt;
font-family:"Courier New";color:black'>I have seen at least one paper in which
the anterior/posterior parts </span></font><br>
<font size=2 color=black face="Courier New"><span style='font-size:10.0pt;
font-family:"Courier New";color:black'>and their FA values were examined via
DTIStudio, so I know it’s </span></font><br>
<font size=2 color=black face="Courier New"><span style='font-size:10.0pt;
font-family:"Courier New";color:black'>possible, but I’m completely
puzzled as how to actually do it. </span></font><br>
<font size=2 color=black face="Courier New"><span style='font-size:10.0pt;
font-family:"Courier New";color:black'>I would appreciate it *very* much if you
could point me in the right </span></font><br>
<font size=2 color=black face="Courier New"><span style='font-size:10.0pt;
font-family:"Courier New";color:black'>direction. </span></font><br>
<font size=2 color=black face="Courier New"><span style='font-size:10.0pt;
font-family:"Courier New";color:black'>Thank you for your time. </span></font><br>
<br>
<font size=2 face="Courier New"><span style='font-size:10.0pt;font-family:"Courier New"'>Cheers,</span></font><br>
<font size=2 face="Courier New"><span style='font-size:10.0pt;font-family:"Courier New"'>Christian
Bieck</span></font><o:p></o:p></p>
</div>
</body>
</html>