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

[susumu mori]

I talked with Xin and confirmed that the LDDMM-AIR combined transformation
matrix has the same format as K/H maps. They are raw files of Vector x X x Y
x Z.

On Mon, Feb 1, 2010 at 10:22 AM, Xin Li <xli16 at jhmi.edu> wrote:

> 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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> >  > Mristudio-users at mristudio.org
> >  >
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> >  > Mristudio-users-unsubscribe at mristudio.org
> >  >
> >  >
>
>
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