[Mristudio-users] apply transformation to landmarkers & command file

[susumu mori]

Hi Yi,

On Fri, Jan 29, 2010 at 5:25 PM, Yi Jiang <yj3 at duke.edu> wrote:

>  Hello, dear all,
>
>
>
> I have two questions and am wondering if someone can help.
>
>
>
>    1. I have already had a transformation matrix to map the subject image
>    onto the template image, which was generated by combining AIR rigid, AIR
>    affine, and LDDMM matrix. I want to define some landmarkers on the subject
>    image, and apply the transformation matrix to the landmarkers (to see their
>    corresponding location on the template image). How can I do that?
>
>
I think this is exactly what the K and H maps are. I need  confirmation from
Xin, but in my understanding, these transformation matrices contain vectors
at each coordinate, indicating where is the new location. If I'm not
mistaken, it is Vector (x, y, z) x X-dimension x Y-dimension x Z-dimension.
There must be a way to extarct the "Vector" information at the specified
coordinate.

>
>
>    1. I would like to use the “load command file” function. I will do AIR
>    linear rigid transformation, AIR linear affine transformation, image format
>    change to byte, automatic intensity correction by histogram, and 2-channel
>    LDDMM. Is it possible to put all these into one command file? If yes, can
>    anyone give me an example file?
>
> I believe the command file is only for the functions within the same box,
including byte-integer-float conversion, axial-sagittal-coronal conversion,
resampling, etc. They don't include transformation functions. We are working
on automation, which will take several months. Meanwhile, I believe it is
good idea to use the current way, which forces you to check the result after
each step. Transformation sometimes does silly things. Some images may have
quality problems. You may want compare different methods (e.g. Mutual Info
linear transformation vs AIR, intensity correction methods, contrast of
choice). I think it's very important to get a feel about your data and each
transformation step. Also, depending on pathology, the transformation
strategy may change. Some disease groups have severe intensity changes (e.g.
stroke), some have severely enlarged ventricles. You may find the same
methods may work for one but not the other. Automation is still a difficult
matter for transformation-based analysis.


>
>
> Thank you very much!
>
>
>
> Have a nice weekend!
>
>
>
> Best
>
> Yi
>
>
>
>
>
> _______________________________________________
> Mristudio-users mailing list
> Mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> Mristudio-users-unsubscribe at mristudio.org
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100130/29d70997/attachment.html