[Mristudio-users] Re-orienting DTI data

[susumu]

Hi Igor,
 
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;
 
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.
 
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.
 
Hope this will work.
 
Susumu

  _____  

From: mristudio-users-bounces at mristudio.org
[mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Igor Korolev
Sent: Wednesday, January 21, 2009 7:05 AM
To: mristudio-users at mristudio.org
Subject: [Mristudio-users] Re-orienting DTI data


Hi Everyone,

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)?

Thank you for your help!

Best,
Igor

-- 
------------------------------------------------------------------
Igor O. Korolev
Physician-Scientist Student (Year 3)
D.O./Ph.D. Training Program
College of Osteopathic Medicine
Neuroscience Program
Michigan State University
E-mail: korolevi at msu.edu

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