[Mristudio-users] basic information
susumu mori
susumu at mri.jhu.edu
Thu Feb 25 08:14:36 EST 2010
Hi Salman,
please read Clin Neurophysiol. 2004 Mar;115(3):589-95. to see if it is
related to your question.
For the data used in the totorial, please follow the instruction in
https://www.mristudio.org/wiki/Tutorial.
Susumu
On Thu, Feb 25, 2010 at 2:37 AM, Syed Salman Shahid <
SyedSalman.Shahid at usq.edu.au> wrote:
> Hi,
>
> I would like to use DTI for White matter (anisotropic) conductivity tensor
> calculation for my project. I was wondering if i am at the correct path.
> My intention is to use DTI calculated eigen values and import it in FE head
> model!
> At this stage i am not sure if this procedure is viable when DTI is
> involved.
>
> BUT most importantly, i was watching the tutorial videos and i came across
> the major issue i.e. where to get the required data. If you look into the
> data archives there is a huge amount of data and deciding which one is the
> required one is impossible.
>
> Thank you
> salman
>
> -----Original Message-----
> From: mristudio-users-bounces at mristudio.org [mailto:
> mristudio-users-bounces at mristudio.org] On Behalf Of Xin Li
> Sent: Thursday, 18 February 2010 5:27 AM
> To: Yi Jiang; DTI Studio, ROI Editor, Landmarker Questions/Support
> Subject: Re: [Mristudio-users] apply transformation to landmarkers &
> command file
>
> Hello Yi,
>
> Thank you for your information. I am going to check and give you a reply
> later.
>
>
> 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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