[Mristudio-users] apply transformation to landmarkers & command file
Yi Jiang
yj3 at duke.edu
Wed Feb 17 14:03:49 EST 2010
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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> > > >
> >
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