[Mristudio-users] Landmarker - Reorientation questions

[XIN LI]

Dr. Beach,

You are right about the algorithm for the rigid transformation.  Landmarker re-orients the brain in a way to minimize the variance in distance between all the placed landmarks.


Xin



----- Original Message -----
From: Paul Beach <pabeach1 at gmail.com>
Date: Thursday, March 5, 2009 10:51 am
Subject: [Mristudio-users] Landmarker - Reorientation questions
To: mristudio-users at mristudio.org


> Greetings everyone,
>  
>  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.
>  
>  I have successfully transformed subjects using several anatomical landmarks
>  (AC/PC, 1st and 2nd mid sagital, most
>  anterior/posterior/superior/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?
>  
>  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?
>  
>  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?
>  
>  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?
>  
>  Many thanks for your assistance,
>  
>  Paul 
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