[Mristudio-users] Alternative way

[Kawashima Takahiko]

Dear Dr Mori,


Thank you very much for your kind, detailed explanation.

I'd like to go through each method you've shown and choose one.


Sincerely,

Takahiko Kawashima
> 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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