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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'>The landmark-based registration simply
follows your landmarks. So, if you want to modify the outcome, you need to
modify (or add more) landmarks.<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'>You can also test automated volume
registration by AIR.<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'>Either way, you can save the
transformation matrix and apply it to fiber tracking results.<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 is one important limitation in our
current software when you normalize the tracking results.<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'>For the normalization, you have to convert
the streamline information (DtiStudio-specific fiber data format) into
pixel-by-pixel image format.<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'>For example, suppose your tracking
generated 10 fibers with average 50-pixel long. Then your native streamline
information contains [x,y,z] information for the 10 streamlines saved
sequentially.<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 streamline information is not easy to
transform. I believe Luke in my lab has an IDL code to do this, but our
MriStudio family can not do it. Please contact khua@jhu.edu if you want the IDL
code.<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'>You can convert this streamline
information to 1/0 pixel-by-pixel image format. For example, if your data is
256x256x50, the pixels that contain the tracking result are 1 and do not
contain are 0. You can save and load this info as an image file. Then you can
transform (normalize) this file as if one of your MRI contrasts. The problem of
this approach is, you can not retrieve streamline info once it was converted to
the 1/0 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'>You should think why you need to retain
the streamline information after brain registration (normalization). For
example, you can create all necessary information in a native space such as
connectivity maps and transform the resultant 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>
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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, March 05, 2009
10:52 AM<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]
Landmarker - Reorientation questions</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'>Greetings everyone,<br>
<br>
I have been attempting to use Landmarker to re-orient subject brains to a
template provided by the developers (we successfully changed the template to
our dimensions), and I have several questions regarding rigid transformations.<br>
<br>
I have successfully transformed subjects using several anatomical landmarks
(AC/PC, 1st and 2nd mid sagital, most anterior/posterior/superior/<o:p></o:p></span></font></p>
<div id=":8j">
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>inferior/left/right). However, subject brains are still usually a
bit slanted in certain views, post-transformation. Is there any advice as
to how to correct for this occuring? Is it likely a landmark placement
issue?<br>
<br>
Also, once the transformations are made, I have been attempting to apply the
saved landmarks for the subjects to the fiber tracking data (say for a
bilateral cingulum) that we have already produced for that subject using MRI
studio. However, we are a bit stumped in attempting to find a way to take
that reoriented fiber tract data and view it 3D on MRI studio without having to
redo all the ROI placement, etc. Any advice for this?<br>
<br>
I have also been experimenting with using the rotation/shift image buttons to
change subject images (I actually used this to fix a problem with the template,
as when we re-sliced it to our dimensions it was shifted off-center
axially/coronally to the user-right). Would using these buttons affect
the results of a rigid transformation?<br>
<br>
Also, I was curious regarding the general algorithm for the rigid
transformation. Is it a similar one to AFNI's manual Talairaching(?) or
does Landmarker simply re-orient the brain in a way such as to minimize the
variance in distance between all the placed landmarks?<br>
<br>
Many thanks for your assistance,<br>
<font color="#888888"><span style='color:#888888'><br>
Paul</span></font><o:p></o:p></span></font></p>
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12.0pt'><br clear=all>
<o:p></o:p></span></font></p>
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