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<DIV dir=ltr align=left><SPAN class=120453914-21012009><FONT face=Arial
color=#0000ff size=2>Hi Igor,</FONT></SPAN></DIV>
<DIV dir=ltr align=left><SPAN class=120453914-21012009><FONT face=Arial
color=#0000ff size=2></FONT></SPAN> </DIV>
<DIV dir=ltr align=left><SPAN class=120453914-21012009><FONT face=Arial
color=#0000ff size=2>I think the easiest way is to use "rigid" transformation in
Landmarker. Whatever the method you choose, you have to do at least the rigid
transformation (just rotation and translation) of your data to realign your data
to AC-PC. Because your data is a tensor data, you have to be careful and use a
tool that can re-orient each tensor in each pixel. Of course, if you first
calculate FA map and then do AC-PC alignment, you don't have to worry about it.
Using Landmarker, there are two ways;</FONT></SPAN></DIV>
<DIV dir=ltr align=left><SPAN class=120453914-21012009><FONT face=Arial
color=#0000ff size=2></FONT></SPAN> </DIV>
<DIV dir=ltr align=left><SPAN class=120453914-21012009><FONT face=Arial
color=#0000ff size=2>1) Use the rigid transformation option in AIR. By using
this option, it will re-sample your original data to the template of your
choice. For example, if you choose our ICBM-DTI-MNI, the output will be
181x217x181 with 1mm resolution. The brain position and orientation should be
aligned to those of the ICBM-DTI-MNI image. As long as you are using rigid, it
doesn't touch the size of your data. If you don't want the resampling to the
atlas dimensions, you can use one of your good data, say, 256x256x50, as your
template. Then you can keep the original dimensions.</FONT></SPAN></DIV>
<DIV dir=ltr align=left><SPAN class=120453914-21012009><FONT face=Arial
color=#0000ff size=2></FONT></SPAN> </DIV>
<DIV dir=ltr align=left><SPAN class=120453914-21012009><FONT face=Arial
color=#0000ff size=2>2) Use the landmarking functions. Again, you can choose one
of our atlases or one of your good data as a template. Pick AC and PC in the
template data and also in the data you want to re-align. Because your data could
have an olbique angle, you have to be precise and careful to define the AC and
the PC. Then use the landmark-driven rigid alignment, which are provided as one
of the buttons in the top menu bar.</FONT></SPAN></DIV>
<DIV dir=ltr align=left><SPAN class=120453914-21012009><FONT face=Arial
color=#0000ff size=2></FONT></SPAN> </DIV>
<DIV dir=ltr align=left><SPAN class=120453914-21012009><FONT face=Arial
color=#0000ff size=2>Hope this will work.</FONT></SPAN></DIV>
<DIV dir=ltr align=left><SPAN class=120453914-21012009><FONT face=Arial
color=#0000ff size=2></FONT></SPAN> </DIV>
<DIV dir=ltr align=left><SPAN class=120453914-21012009><FONT face=Arial
color=#0000ff size=2>Susumu</FONT></SPAN></DIV><BR>
<DIV class=OutlookMessageHeader lang=en-us dir=ltr align=left>
<HR tabIndex=-1>
<FONT face=Tahoma size=2><B>From:</B> mristudio-users-bounces@mristudio.org
[mailto:mristudio-users-bounces@mristudio.org] <B>On Behalf Of </B>Igor
Korolev<BR><B>Sent:</B> Wednesday, January 21, 2009 7:05 AM<BR><B>To:</B>
mristudio-users@mristudio.org<BR><B>Subject:</B> [Mristudio-users] Re-orienting
DTI data<BR></FONT><BR></DIV>
<DIV></DIV>Hi Everyone,<BR><BR>While in the scanner, some of our subjects had
their heads tilted, resulting in DTI volumes that are out of standard
orientation. We want to rotate the DTI volumes into standard orientation (i.e.
with AC-PC line as the horizontal). I understand this can be done by
co-registering the data to a template in Landmarker, but this requires
normalization of the original data. Is there a way to re-orient the data in MRI
Studio, for instance relative to a user-defined AC-PC line, without normalizing
data (as we want to preserve original dimensions in the data)?<BR><BR>Thank you
for your help!<BR><BR>Best,<BR>Igor<BR clear=all><BR>--
<BR>------------------------------------------------------------------<BR>Igor
O. Korolev<BR>Physician-Scientist Student (Year 3)<BR>D.O./Ph.D. Training
Program<BR>College of Osteopathic Medicine<BR>Neuroscience Program<BR>Michigan
State University<BR>E-mail: <A
href="mailto:korolevi@msu.edu">korolevi@msu.edu</A><BR></BODY></HTML>