[Mristudio-users] Landmarker: Multichannel Volume LDDMM

[susumu mori]

Please see below;

On Tue, Jun 30, 2009 at 11:49 AM, Fijoy Vadakkumpadan <fijoy at jhu.edu> wrote:

> Hi all,
>
> I have a template image and a subject image, each containing 5
> intensities, including the 0 intensity for the background. I would
> like to use the Landmarker to perform multichannel LDDMM to register
> the two images. I looked at the window that pops up after I press the
> "Multichannel" button in the Landmarker, and I was wondering if
> someone could please clarify the following:
>
> 1. How many channels should I use? Should I use 4 channels, one for
> each nonzero intensity that the images have?


> If I understand it correctly, you have segmented data. For example, if we
do gray matter - white matter segmentation, you may get ONE IMAGE in which
outside is 0, gray matter is 1, white matter is 2, and ventricle 3. For a
template and a subject, you have two of these images. You can submit these
two images to the "single-channel" LDDMM.

>
>
> 2. The pop up window asks for a list of template images and a list of
> subject images. How many template and subject images should I create?
> How do I create them?


> You can use the multi-channel if you have the following situation;
> Suppose you have the above segmented image based on T1-weighted image.
> Then you create SECOND segmentation map using a FA map. For example, use
FA>0.25 and create another map in which white matter is 1 and outside is 0.
> Now you have TWO segmentation maps for the template and for the subject
(total 4 images).
> In this case, you use the "multi-channel" LDDMM. For the template, you
choose T1-based and FA-based segmentation maps and for the subject, you
choose T1-based and FA-based segmentation maps.
> Then LDDMM will do; Template T1 - Subject T1 mapping as well as Template
FA - Subject FA to get one solution that satisfies the two matching
simultaneously.

>
>
> 3. If I should have more than 1 template image, how do I load multiple
> template images into the Landmarker?


> First, open the template T1 using the Open icon in the top menu.
> Once you get a viewing window, use the Open icon in the right column of
the viewing window to open template FA.
> Go back to the Open icon in the top menu and open the subject T1
> Once you get another viewing window for the subject, use the Open icon in
the right column of the subject viewing window to open subject FA.
> Go to "multi-channel" LDDMM. You can find T1 and FA are listed for
Template and also for the subject.

Hope this clarifies your question.

Susumu
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