[Mristudio-users] A few questions about LDDMM transformations

[susumu mori]

I want to add some to Xin's reply.

On Thu, Apr 5, 2012 at 2:55 PM, Peterson, Daniel <
petersond at kennedykrieger.org> wrote:

>  Hi All,
>
>     I've got a couple of questions:
>
>  1) What kind of re-orientation strategy does DTI Studio use when
> reorienting tensors for an LDDMM transformation of tensor data. Is there a
> reference available somewhere? As I understand, this is a non-trivial
> problem.
>
>  2) What do the experts here feel about the feasibility of fiber-tracking
> in atlas-space? I know that this is traditionally considered undesireable,
> but do people think that perhaps with these more advanced methods,
> standard-space tractography could be feasable?
>
> If you want to transfer tractography results to an atlas space, you have
several options;
a) perform tractogrpahy in the native space, convert the trajectory
information into a binary masking information, and transform the binary
information into the atlas space. Repeat it for multiple subjects and
create population data.
b) Transform the image into the atlas space and perform tractography.
Repeat it for multiple subjects and create poulation data.
c) Transform the image in to the atlas space. Repeat it to for multiple
subjects and create population-averaged tensor map. Then perform
tractography.

#b and #c requires normalization of the tensor fields as described in your
question #1. I think all approaches are valid.



>  3) Are there any command-line tools available for working with LDDMM
> transformations in a scriptable, automated manner? It would help our
> productivity immensely if we could apply Hmaps and Kimaps from the
> command-line, without clicking on buttons. Being able to combine
> transformation matrices programmatically would be great as well.
>

We have not been very enthusiastic about automated pipelines both for
DtiStudio and MriStudio. This is because of quality control. We thought it
is very important to check each step of image processing and this is the
very reason we developed these programs, which are built for visual
inspection. The heart of the problem is, it is very difficult to come up
with quantitative QC report. We have been investing a lot of effort on the
automated pipeline with a good QC report. So far, it has been difficult to
get one which is as good as visual inspection. However, we are getting
there. I hope we can provide a good automated and quantitative QC for
DtiStudio this year and hopefully a first version for MriStudio. Then
automation itself would be an easy task for us.


>
>  Thanks so much,
> -Dan
>
>
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