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

[Yi Jiang]

Hello, Xin,

Thank you very much for the information.

I have one more question: does the vector indicating new location start from 
0 or 1? That is: if my image size is 512x256x256, the vector should be 
(0-511)x(0-255)x(0-255) or (1-512)x(1-256)x(1-256)?

Thank you!

Best,
Yi


----- Original Message ----- 
From: "Xin Li" <xli16 at jhmi.edu>
To: "susumu mori" <susumu at mri.jhu.edu>; "Yi Jiang" <yj3 at duke.edu>; "DTI 
Studio, ROI Editor, Landmarker Questions/Support" 
<mristudio-users at mristudio.org>; "Jiangyang Zhang" <jzhang3 at jhmi.edu>
Sent: Monday, February 01, 2010 10:22 AM
Subject: Re: [Mristudio-users] apply transformation to landmarkers & command 
file


Hello Yi,

As Susumu said, transformation matrices contain vectors at each coordinate, 
indicating where is the new location. The structure is Vector (x, y, z) x 
X-dimension x Y-dimension x Z-dimension. You may write matlab code to 
extract the vector information.


Xin





----- Original Message -----
From: susumu mori <susumu at mri.jhu.edu>
Date: Saturday, January 30, 2010 8:29 am
Subject: Re: [Mristudio-users] apply transformation to landmarkers & command 
file
To: Yi Jiang <yj3 at duke.edu>, "DTI Studio, ROI Editor, Landmarker 
Questions/Support" <mristudio-users at mristudio.org>, Xin Li <xli16 at jhmi.edu>, 
Jiangyang Zhang <jzhang3 at jhmi.edu>


> 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
>  >
>  > Unsubscribe, send a blank email to:
>  > Mristudio-users-unsubscribe at mristudio.org
>  >
>  >

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