[Mristudio-users] apply transformation to landmarkers & command file
Xin Li
xli16 at jhmi.edu
Mon Feb 1 10:22:37 EST 2010
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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> >
> >
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