[Mristudio-users] Landmarker - Reorientation questions

[Paul Beach]

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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