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

[Yi Jiang]

Hello Xin,

Thank you! I looked at the transformation matrix. Overall it looks 
reasonable (i.e. I think my reading format of the matrix is correct. I was 
able to use the vector information to reasonably map land marks I chose). 
But I found the value of the vector somehow ranges from e.g. 
(-40~540)x(-30~270)x(-20~280) instead of (0-511)x(0-255)x(0-255) I would 
expect. What do those out of range (out of (0-511)x(0-255)x(0-255)  ) values 
mean?

Best,
Yi


----- Original Message ----- 
From: "Xin Li" <xli16 at jhmi.edu>
To: "Yi Jiang" <yj3 at duke.edu>; "DTI Studio, ROI Editor, Landmarker 
Questions/Support" <mristudio-users at mristudio.org>
Sent: Wednesday, February 17, 2010 10:01 AM
Subject: Re: [Mristudio-users] apply transformation to landmarkers & command 
file


Hello Yi,

If your image size is 512x256x256, the vector should be 
(0-511)x(0-255)x(0-255)


Xin




----- Original Message -----
From: Yi Jiang <yj3 at duke.edu>
Date: Wednesday, February 17, 2010 8:44 am
Subject: Re: [Mristudio-users] apply transformation to landmarkers & command 
file
To: "DTI Studio, ROI Editor, Landmarker Questions/Support" 
<mristudio-users at mristudio.org>


> 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
>  >  >
>  >  >
>  >  >
>  >  >
>  >  >
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