[Mristudio-users] problem with re-oriented fiber tracts

[susumu]

Hi Paul,

 

Several questions:

 

1) Did you do tracking before the rotation, converted to 1/0 binary image,
and rotate with the image?

2) Or did you rotate the image and then do the tracking? If so, did you
rotate the tensor using the "Open *.d" button so that you can get correct
tensor re-orientation?

3) You mentioned, "upside-down". Does it mean you did #1 above? If you did
tracking after image rotation (#2 approach), I guess you won't get the fiber
upside-down with respect to the image.

4) What do you mean by (-) sign of the raw image? In general, if you get
your image upside-down, the culprit is the mixture of our raw format
(Radiology convention) and the Analyze format (Neurology convention as the
default).

 

Please clarify.

 

Susumu

  _____  

From: mristudio-users-bounces at mristudio.org
[mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Paul Beach
Sent: Tuesday, March 31, 2009 2:53 PM
To: Mristudio-users at mristudio.org
Subject: [Mristudio-users] problem with re-oriented fiber tracts

 

Hi everyone,

I'm in the process of reorienting subjects to a more standard space using 7
landmarks across subjects.  For the most part the transformation matrix
saved post rigid/affine transformation is reorienting fiber tracts perfectly
(we're confirming this using FSL).  However some subject's fiber tracts are
going way off when we apply their respective transformation matrices.
They'll be slanted in the axial view, etc.  Something I've noticed is that
the subjects whose tracts are mis-rotated are loading into landmarker upside
down and require me to remove a (-) sign from their raw image information.
However, not all subjects that load upside down are resulting in fiber
tracts that are mis-oriented.

Any suggestions as to why this might be occurring?

Thanks,

Paul

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