[Mristudio-users] questions about Fiber tracking

[Kotikalapudi Raviteja]

Dear Susumu,

I have been using JHU-Parcellation atlas for DTI analysis. I want to
extract the FA maps from corticospinal tract for which I made an ROI from
the JHU-Parcellation atlas. But it is not overlapping well with the FA
images. I need to know if there is a way to shift the ROI on the FA image?

Your suggestions would be appreciated.

Many thanks,
Ravi


On Fri, Aug 16, 2013 at 11:03 PM, Susumu Mori <smoriw at gmail.com> wrote:

> Hi Ying,
>
> Here is my view of "registration".
>
> > Imaging is all about what is where.
> > When you quantify images, you have to make sure that you are measuring
> the same structures or locations across subjects. This act of identifying
> the same thing is "registration".
> > For example, you can manually define the hippocampus across subjects. By
> doing so, you identify a group of voxels that belong to the hippo and you
> "register" the hippo locations across subjects. You defined corresponding
> voxels across subjects. In this sense, manual ROI delineation is one of the
> registration methods.
> > Because the manual delineation is time consuming, people don't want to
> do it. Then what we do is to align all images and assume all voxels are
> registered automatically. This means, if I pick up an arbitrary location
> (like a single voxel), I can immediately locate the corresponding location
> (voxel) in each subject by using the same x, y, z coordinates.
> > Tractography can also be considered as a registration tool because, for
> example, we can identify a group of voxels that belong to the corticospinal
> tract across subjects. Therefore, there is nothing wrong with defining the
> cst in each subject without image-alignment.
> > However, there could be several reasons why you may want to do image
> alignment (thus voxel-by-voxel registration) first and then additional
> registration by tractography. First, tractography requires manually (or
> automatically) defined  ROIs for seed and destination. This could be done
> more reproducibly if all images are aligned. Second, after tracts are
> defined, you can easily create population-averaged probabilistic maps by
> simply adding the 3D masking files that define the tract locations. On the
> other hand, if you are just interested in voxel count (size of the tract)
> and FA values, image alignment may not be necessary.
>
> Susumu
>
>
> On Fri, Aug 16, 2013 at 2:25 AM, <wyzyf at mail.ustc.edu.cn> wrote:
>
>>
>>
>>
>>   Hello professor:
>>
>>     As I understood, fiber tracking analysis with DTI studio should be a
>> group analysis and image registration is
>>   necessary. Am I right?
>>
>>     I have finished the image registration with DiffeoMap through linear
>> and nonlinear(b0+FA) registration but I don`t
>>   know how to achieve group analysis and the registrated FA doesn`t match
>> the origin vector.
>>
>>     Thank you very much~!
>>
>>                                                     Ying Wang
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>
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