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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'>Several questions:<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) Did you do tracking before the
rotation, converted to 1/0 binary image, and rotate with the 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'>2) Or did you rotate the image and then do
the tracking? If so, did you rotate the tensor using the "Open *.d"
button so that you can get correct tensor re-orientation?<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) You mentioned, "upside-down".
Does it mean you did #1 above? If you did tracking after image rotation (#2
approach), I guess you won't get the fiber upside-down with respect to the
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'>4) What do you mean by (-) sign of the raw
image? In general, if you get your image upside-down, the culprit is the
mixture of our raw format (Radiology convention) and the Analyze format
(Neurology convention as the default).<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'>Please clarify.<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>
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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> Tuesday, March 31, 2009 2:53
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] problem
with re-oriented fiber tracts</span></font><o:p></o:p></p>
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<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'>Hi everyone,<br>
<br>
I'm in the process of reorienting subjects to a more standard space using 7
landmarks across subjects. For the most part the transformation matrix
saved post rigid/affine transformation is reorienting fiber tracts perfectly
(we're confirming this using FSL). However some subject's fiber tracts
are going way off when we apply their respective transformation matrices.
They'll be slanted in the axial view, etc. Something I've noticed is that
the subjects whose tracts are mis-rotated are loading into landmarker upside
down and require me to remove a (-) sign from their raw image
information. However, not all subjects that load upside down are
resulting in fiber tracts that are mis-oriented.<br>
<br>
Any suggestions as to why this might be occurring?<br>
<br>
Thanks,<br>
<br>
Paul<o:p></o:p></span></font></p>
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