[Mristudio-users] Alternative way

[susumu]

Hi all,

 

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Susumu

 

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From: mristudio-users-bounces at mristudio.org
[mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Lou muscarella
Sent: Monday, November 03, 2008 4:29 PM
To: DTI Studio, ROI Editor, Landmarker Questions/Support
Subject: Re: [Mristudio-users] Alternative way

 

How do I get off this list serve?   Please take me off
> Date: Mon, 3 Nov 2008 21:09:17 +0900
> From: dearfreud at gmail.com
> To: mristudio-users at mristudio.org
> Subject: Re: [Mristudio-users] Alternative way
> 
> 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
> >
> > _______________________________________________
> > Mristudio-users mailing list
> > Mristudio-users at mristudio.org
> > http://lists.mristudio.org/mailman/listinfo/mristudio-users
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