[Mristudio-users] Alternative way

[susumu]

Dear Takahiro,

 

There are two options, as you already know. One is to report the average FA
of the entire reconstructed fiber. After reconstruction, you get only one FA
number. If you use CUT, that is the averaged FA of all pixels in between the
two ROIs. 

 

The second option is to report FA of pixels at each axial, sagittal, or
coronal slice. This is a good method for something like the corticospinal
tract, which is rather linear. Unfortunately, for something like the UF and
corpus callosum, with U-shape trajectory, this approach is not optimum.

 

At this point, there is not a good solution for that. There may be some time
consuming way to separate the U-shape trajectory to two I-shape
trajectories. For example, you can save the tracking results as a 1/0 binary
image and read it by RoiEditor. Using the threshold tool, you can re-define
the pixels within the UF in RoiEditor. With a bit of trick like manually
introduce a gap within the trajectory, you can separate the one U-shape
trajectory to two regions like upper UF and lower UF. Then RoiEditor can
report FA values along coronal planes.

 

Well, maybe this is too complicated. Alternatively, you can use Landmarker
to normalize the binarized UF images and create a pixel-by-pixel
population-averaged map, although, you introduce a new nuisance factor (=
registration quality).

 

Susumu

 

  _____  

From: mristudio-users-bounces at mristudio.org
[mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Takahiko
Kawashima
Sent: Sunday, November 02, 2008 11:25 AM
To: mristudio-users at mristudio.org
Subject: [Mristudio-users] Alternative way

 

Dear users,

 

Hi,

 

I'm trying to calculate FA of tracts not running along only one axis, such
as uncinate fasciculus (UF).

 

At first I planned to combine CUT with other operations to calculate FA only
between the CUT ROIs (in the case of UF, one one coronal and one on axial
slice).

But recently I've found it was a fundamental misunderstanding. (by reading
Dr 

 

If possible, I'd like to get a mean FA of summed "each fiber" FA in depicted
fibers within a defined region.

Could anybody tell me some alternative ways to do this, please?

Or, if I want to calculate FA within a defined region, can't I do anything
but to consider a mean FA of "all the voxels" on which the fibers run?

 

Because I am totally a beginner and poor in English, this question might
look quite embarrassing and illegible.

I hope your kind answer, and I'll really appreciate it.

 

 

Best Regards, 

 

Takahiko Kawashima @ Kyoto university

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