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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 Jason,<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'>It seems that you had a common problem of
Radiology-Neurology display difference, which becomes an issue when you mix raw
and Analyze formats.<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'>As you can see, the axial image of
"reloaded" is inverted. This happens when you try to read images in the
Neurology convention (left is left) to DtiStudio that follows the Radiology
convention (left is right). As long as you stay with "raw" format
within DtiStudio, this problem should not happen. However, if you try to load
and save Analyze format, it may happen because the Analyze default is the
Neurology convention. If you save image data by the Analyze format through
DtiStudio, make sure to reload the image (not the fiber), by Analyze format so
that DtiStudio knows what is happening and correct it to Radiology. The fiber
information in *.dat is always the Radiology convention. <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'>So, first thing you have to do is to
figure out the way to load your image upright in axial slice.<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>
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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>Jason Stein<br>
<b><span style='font-weight:bold'>Sent:</span></b> Wednesday, May 21, 2008
12:25 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'>Cc:</span></b> Ilya Eckstein<br>
<b><span style='font-weight:bold'>Subject:</span></b> [Mristudio-users] Fiber
Tracking Saving Data Question</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=3 face="Times New Roman"><span style='font-size:
12.0pt'>Hello,<br>
<br>
I ran some fibertracking on a DTI set and am trying to get the corticospinal
tract. As per "Automated Fibertracking of Human Brain White Matter
Using Diffusion Tensor Imaging", I placed seeds as follows, an cerebral
peduncle AND motor cortex NOT contralateral hemisphere NOT cerebellum.
After that I got a bundle which corresponds very well to the corticospinal
tract. <br>
<br>
Now, I saved this dataset in both the Amira's format and the .dat format.
When I reload the dataset into DTIstudio or using other code, it shows up in
the wrong place (a few voxels off from where it originally started). I
attached a screenshot of this problem where you can see that in
OriginalFiberTract.jpg, the tract originates in the cerebral peduncle and in
the ReloadedFiberTract.jpg, the tract originates in a place slightly posterior
to the peduncle. <br>
<br>
Do you know why this happens and/or how we could fix it?<br>
<br>
Thanks in advance for any help!<br>
Jason<o:p></o:p></span></font></p>
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