[Mristudio-users] Landmarker: Multichannel Volume LDDMM

[Fijoy Vadakkumpadan]

Hi Dr. Mori,

Thank you so much for your prompt reply. It clarifies my questions.

I was thinking of generating multiple (four in my case) binary images
from my segmented template image, by creating one binary image for
each tissue type. Similarly, I create multiple binary images from the
segmented subject image as well. Then, I wanted to use multichannel
LDDMM to register the subject binary images with template binary
images, all at once. I felt that I might obtain better registration by
using the multichannel LDDMM on these binary images, rather than using
the single channel LDDMM on the segmented images.

Fijoy

On Tue, Jun 30, 2009 at 9:17 PM, susumu mori<susumu at mri.jhu.edu> wrote:
> 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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