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<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Hi Paul,<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'>I'm not sure if I understood your question
correctly, but let me try.<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'>There are two types of file formats to
save tracking results; one is streamline and the other is binary image.<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 streamline contains the most
information. You can superimpose on images and edit (add more ROIs to choose a
part of it) them using DtiStudio.<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 downside of the streamline information
is that now we don't provide a way to transform the coordinate such as
reorientation. You need to do fiber tracking again after you reorient your
tensor.<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 binary image contain 1/0 information;
pixels with "1" contain the tract. This contains less information
(some information is degenerated) because you don't know which pixels are
connected to which pixels. This you can consider as a binary mask.<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'>This one can be easily transformed, just
like an image. To superimpose the transformed fiber coordinates, you can use
RoiEditor. For example, you can load transformed (and coregistered) FA map to
RoiEditor and also the transformed binary map. Make sure that the 1/0 binary
map was transformed by nearest neighbor (1/0 is preserved and you don't get
pixels with "0.5"). Then you can define pixels with "1"
using a threshold tool and register these pixels as an Object. Then change the
active image from the binary map to the FA map. You can see the outline for Object
is superimposed on the FA map.<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>
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face="Times New Roman"><span style='font-size:12.0pt'>
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<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>Paul Beach<br>
<b><span style='font-weight:bold'>Sent:</span></b> Thursday, May 07, 2009 3:26
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]
overlaying analyze anatomical and fiber tract data in DTI studio</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 style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 face="Times New Roman"><span style='font-size:12.0pt'>To Whom It May
Concern:<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 face="Times New Roman"><span style='font-size:12.0pt'> <o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 face="Times New Roman"><span style='font-size:12.0pt'>We were hoping for
some input regarding viewing Fiber tracts and DTI images concurrently. Due to
limitations in our data, we have been forced to reorient our DTI images and our
Fiber tracks accordingly using the Landmarker program. Unfortunately we have
not been able to decipher a way to view these two images overlayed
simultaneously which is needed as part of our delimitation methods. We
previously have done this by saving our Fiber ROI’s, then placing them on a DTI
(through DTIstudio) when needed. Since this step is not a part of the
reorientation process we do not have this data to use. Essentially we are
limited to trying to work with ANALYZE files and were wondering if DTIstudio or
its sister programs had the ability to load these in to be viewed
simultaneously. <o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 face="Times New Roman"><span style='font-size:12.0pt'> <o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 face="Times New Roman"><span style='font-size:12.0pt'>The work we’re
currently attempting to do is to list certain boundaries based on anatomical
and select fiber tract data (for example the coronal boundary of the
crura/fornical junction) and this requires having the fiber tract data mapped
onto the anatomical DTIs.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><br>
Thanks,<br>
<br>
Paul<o:p></o:p></span></font></p>
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