[Mristudio-users] apply transformation to landmarkers & command file
Xin Li
xli16 at jhmi.edu
Mon Feb 22 12:56:18 EST 2010
Hello Yi,
I have asked my colleague about your question. Actually the out of range values are normal. Even in LDDMM, you may find some out-of-range values, and affine will definitely generate more. The out-of-range values do not mean your object in the image will be transformed out-of-range, just some pixels in the background will be moved outside due to mainly affine and, to some degree, LDDMM. If you rotate a square 45 degrees, it will have some part out of the original squre.
Regards,
Xin
----- Original Message -----
From: Yi Jiang <yj3 at duke.edu>
Date: Wednesday, February 17, 2010 2:04 pm
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,
>
> It is a combined matrix.
>
> 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 11:38 AM
> Subject: Re: [Mristudio-users] apply transformation to landmarkers &
> command
> file
>
>
> Hello Yi,
>
> How did you get the matrix that you are working on? Is it a lddmm
> matrix or
> a combined matrix?
>
>
> Xin
>
>
>
> ----- Original Message -----
> From: Yi Jiang <yj3 at duke.edu>
> Date: Wednesday, February 17, 2010 11:05 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! 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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