Hi Salman,<br><br>please read <span class="src"></span><span class="src"></span><span class="src"><span class="jrnl" title="Clinical neurophysiology : official journal of the International Federation of Clinical Neurophysiology">Clin Neurophysiol</span>. 2004 Mar;115(3):589-95. to see if it is related to your question.<br>
<br>For the data used in the totorial, please follow the instruction in <a href="https://www.mristudio.org/wiki/Tutorial">https://www.mristudio.org/wiki/Tutorial</a>.<br><br>Susumu<br></span><br><div class="gmail_quote">On Thu, Feb 25, 2010 at 2:37 AM, Syed Salman Shahid <span dir="ltr"><<a href="mailto:SyedSalman.Shahid@usq.edu.au">SyedSalman.Shahid@usq.edu.au</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Hi,<br>
<br>
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.<br>
My intention is to use DTI calculated eigen values and import it in FE head model!<br>
At this stage i am not sure if this procedure is viable when DTI is involved.<br>
<br>
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.<br>
<br>
Thank you<br>
salman<br>
<br>
-----Original Message-----<br>
From: <a href="mailto:mristudio-users-bounces@mristudio.org">mristudio-users-bounces@mristudio.org</a> [mailto:<a href="mailto:mristudio-users-bounces@mristudio.org">mristudio-users-bounces@mristudio.org</a>] On Behalf Of Xin Li<br>
Sent: Thursday, 18 February 2010 5:27 AM<br>
To: Yi Jiang; DTI Studio, ROI Editor, Landmarker Questions/Support<br>
Subject: Re: [Mristudio-users] apply transformation to landmarkers & command file<br>
<br>
Hello Yi,<br>
<br>
Thank you for your information. I am going to check and give you a reply later.<br>
<br>
<br>
Xin<br>
<br>
<br>
<br>
----- Original Message -----<br>
From: Yi Jiang <<a href="mailto:yj3@duke.edu">yj3@duke.edu</a>><br>
Date: Wednesday, February 17, 2010 2:04 pm<br>
Subject: Re: [Mristudio-users] apply transformation to landmarkers & command file<br>
To: "DTI Studio, ROI Editor, Landmarker Questions/Support" <<a href="mailto:mristudio-users@mristudio.org">mristudio-users@mristudio.org</a>><br>
<br>
<br>
> Hello Xin,<br>
><br>
> It is a combined matrix.<br>
><br>
> Yi<br>
><br>
><br>
> ----- Original Message -----<br>
> From: "Xin Li" <<a href="mailto:xli16@jhmi.edu">xli16@jhmi.edu</a>><br>
> To: "Yi Jiang" <<a href="mailto:yj3@duke.edu">yj3@duke.edu</a>>; "DTI Studio, ROI Editor, Landmarker<br>
> Questions/Support" <<a href="mailto:mristudio-users@mristudio.org">mristudio-users@mristudio.org</a>><br>
> Sent: Wednesday, February 17, 2010 11:38 AM<br>
> Subject: Re: [Mristudio-users] apply transformation to landmarkers &<br>
> command<br>
> file<br>
><br>
><br>
> Hello Yi,<br>
><br>
> How did you get the matrix that you are working on? Is it a lddmm<br>
> matrix or<br>
> a combined matrix?<br>
><br>
><br>
> Xin<br>
><br>
><br>
><br>
> ----- Original Message -----<br>
> From: Yi Jiang <<a href="mailto:yj3@duke.edu">yj3@duke.edu</a>><br>
> Date: Wednesday, February 17, 2010 11:05 am<br>
> Subject: Re: [Mristudio-users] apply transformation to landmarkers &<br>
> command<br>
> file<br>
> To: "DTI Studio, ROI Editor, Landmarker Questions/Support"<br>
> <<a href="mailto:mristudio-users@mristudio.org">mristudio-users@mristudio.org</a>><br>
><br>
><br>
> > Hello Xin,<br>
> ><br>
> > Thank you! I looked at the transformation matrix. Overall it looks<br>
> > reasonable (i.e. I think my reading format of the matrix is correct.<br>
> > I was<br>
> > able to use the vector information to reasonably map land marks I<br>
> > chose).<br>
> > But I found the value of the vector somehow ranges from e.g.<br>
> > (-40~540)x(-30~270)x(-20~280) instead of (0-511)x(0-255)x(0-255) I<br>
> > would<br>
> > expect. What do those out of range (out of (0-511)x(0-255)x(0-255)<br>
> )<br>
> > values<br>
> > mean?<br>
> ><br>
> > Best,<br>
> > Yi<br>
> ><br>
> ><br>
> > ----- Original Message -----<br>
> > From: "Xin Li" <<a href="mailto:xli16@jhmi.edu">xli16@jhmi.edu</a>><br>
> > To: "Yi Jiang" <<a href="mailto:yj3@duke.edu">yj3@duke.edu</a>>; "DTI Studio, ROI Editor, Landmarker<br>
> > Questions/Support" <<a href="mailto:mristudio-users@mristudio.org">mristudio-users@mristudio.org</a>><br>
> > Sent: Wednesday, February 17, 2010 10:01 AM<br>
> > Subject: Re: [Mristudio-users] apply transformation to landmarkers<br>
> &<br>
> > command<br>
> > file<br>
> ><br>
> ><br>
> > Hello Yi,<br>
> ><br>
> > If your image size is 512x256x256, the vector should be<br>
> > (0-511)x(0-255)x(0-255)<br>
> ><br>
> ><br>
> > Xin<br>
> ><br>
> ><br>
> ><br>
> ><br>
> > ----- Original Message -----<br>
> > From: Yi Jiang <<a href="mailto:yj3@duke.edu">yj3@duke.edu</a>><br>
> > Date: Wednesday, February 17, 2010 8:44 am<br>
> > Subject: Re: [Mristudio-users] apply transformation to landmarkers<br>
> &<br>
> > command<br>
> > file<br>
> > To: "DTI Studio, ROI Editor, Landmarker Questions/Support"<br>
> > <<a href="mailto:mristudio-users@mristudio.org">mristudio-users@mristudio.org</a>><br>
> ><br>
> ><br>
> > > Hello, Xin,<br>
> > ><br>
> > > Thank you very much for the information.<br>
> > ><br>
> > > I have one more question: does the vector indicating new location<br>
> > > start from<br>
> > > 0 or 1? That is: if my image size is 512x256x256, the vector should<br>
> > > be<br>
> > > (0-511)x(0-255)x(0-255) or (1-512)x(1-256)x(1-256)?<br>
> > ><br>
> > > Thank you!<br>
> > ><br>
> > > Best,<br>
> > > Yi<br>
> > ><br>
> > ><br>
> > > ----- Original Message -----<br>
> > > From: "Xin Li" <<a href="mailto:xli16@jhmi.edu">xli16@jhmi.edu</a>><br>
> > > To: "susumu mori" <<a href="mailto:susumu@mri.jhu.edu">susumu@mri.jhu.edu</a>>; "Yi Jiang" <<a href="mailto:yj3@duke.edu">yj3@duke.edu</a>>;<br>
> > > "DTI<br>
> > > Studio, ROI Editor, Landmarker Questions/Support"<br>
> > > <<a href="mailto:mristudio-users@mristudio.org">mristudio-users@mristudio.org</a>>; "Jiangyang Zhang" <<a href="mailto:jzhang3@jhmi.edu">jzhang3@jhmi.edu</a>><br>
> > > Sent: Monday, February 01, 2010 10:22 AM<br>
> > > Subject: Re: [Mristudio-users] apply transformation to landmarkers<br>
> > &<br>
> > > command<br>
> > > file<br>
> > ><br>
> > ><br>
> > > Hello Yi,<br>
> > ><br>
> > > As Susumu said, transformation matrices contain vectors at each<br>
> > > coordinate,<br>
> > > indicating where is the new location. The structure is Vector (x,<br>
> > y,<br>
> > > z) x<br>
> > > X-dimension x Y-dimension x Z-dimension. You may write matlab code<br>
> > to<br>
> > ><br>
> > > extract the vector information.<br>
> > ><br>
> > ><br>
> > > Xin<br>
> > ><br>
> > ><br>
> > ><br>
> > ><br>
> > ><br>
> > > ----- Original Message -----<br>
> > > From: susumu mori <<a href="mailto:susumu@mri.jhu.edu">susumu@mri.jhu.edu</a>><br>
> > > Date: Saturday, January 30, 2010 8:29 am<br>
> > > Subject: Re: [Mristudio-users] apply transformation to landmarkers<br>
> > &<br>
> > > command<br>
> > > file<br>
> > > To: Yi Jiang <<a href="mailto:yj3@duke.edu">yj3@duke.edu</a>>, "DTI Studio, ROI Editor, Landmarker<br>
> > > Questions/Support" <<a href="mailto:mristudio-users@mristudio.org">mristudio-users@mristudio.org</a>>, Xin Li<br>
> > > <<a href="mailto:xli16@jhmi.edu">xli16@jhmi.edu</a>>,<br>
> > > Jiangyang Zhang <<a href="mailto:jzhang3@jhmi.edu">jzhang3@jhmi.edu</a>><br>
> > ><br>
> > ><br>
> > > > Hi Yi,<br>
> > > ><br>
> > > > On Fri, Jan 29, 2010 at 5:25 PM, Yi Jiang <<a href="mailto:yj3@duke.edu">yj3@duke.edu</a>> wrote:<br>
> > > ><br>
> > > > > Hello, dear all,<br>
> > > > ><br>
> > > > ><br>
> > > > ><br>
> > > > > I have two questions and am wondering if someone can help.<br>
> > > > ><br>
> > > > ><br>
> > > > ><br>
> > > > > 1. I have already had a transformation matrix to map<br>
> the<br>
> > subject<br>
> > > > image<br>
> > > > > onto the template image, which was generated by combining<br>
> > AIR<br>
> > > > rigid, AIR<br>
> > > > > affine, and LDDMM matrix. I want to define some<br>
> > landmarkers on<br>
> > > > the subject<br>
> > > > > image, and apply the transformation matrix to the landmarkers<br>
> > > > (to see their<br>
> > > > > corresponding location on the template image). How can<br>
> I<br>
> > do that?<br>
> > > > ><br>
> > > > ><br>
> > > > I think this is exactly what the K and H maps are. I need<br>
> > > > confirmation from<br>
> > > > Xin, but in my understanding, these transformation matrices<br>
> > > contain<br>
> > > > vectors<br>
> > > > at each coordinate, indicating where is the new location. If<br>
> > I'm not<br>
> > > > mistaken, it is Vector (x, y, z) x X-dimension x Y-dimension<br>
> x<br>
> > > > Z-dimension.<br>
> > > > There must be a way to extarct the "Vector" information at the<br>
> ><br>
> > > specified<br>
> > > > coordinate.<br>
> > > ><br>
> > > > ><br>
> > > > ><br>
> > > > > 1. I would like to use the "load command file"<br>
> function. I<br>
> > will<br>
> > > > do AIR<br>
> > > > > linear rigid transformation, AIR linear affine transformation,<br>
> > > > image format<br>
> > > > > change to byte, automatic intensity correction by histogram,<br>
> > > and<br>
> > > > 2-channel<br>
> > > > > LDDMM. Is it possible to put all these into one command<br>
> file?<br>
> > > If<br>
> > > > yes, can<br>
> > > > > anyone give me an example file?<br>
> > > > ><br>
> > > > > I believe the command file is only for the functions<br>
> within the<br>
> > > > same box,<br>
> > > > including byte-integer-float conversion, axial-sagittal-coronal<br>
> > > > conversion,<br>
> > > > resampling, etc. They don't include transformation functions.<br>
> > We are<br>
> > > > working<br>
> > > > on automation, which will take several months. Meanwhile, I<br>
> believe<br>
> > > > it is<br>
> > > > good idea to use the current way, which forces you to check<br>
> the<br>
> > > > result after<br>
> > > > each step. Transformation sometimes does silly things. Some<br>
> images<br>
> > > > may have<br>
> > > > quality problems. You may want compare different methods (e.g.<br>
> > Mutual<br>
> > > > Info<br>
> > > > linear transformation vs AIR, intensity correction methods,<br>
><br>
> > contrast<br>
> > > > of<br>
> > > > choice). I think it's very important to get a feel about<br>
> your data<br>
> > > > and each<br>
> > > > transformation step. Also, depending on pathology, the<br>
> > transformation<br>
> > > > strategy may change. Some disease groups have severe intensity<br>
> > > > changes (e.g.<br>
> > > > stroke), some have severely enlarged ventricles. You may<br>
> find the<br>
> > > same<br>
> > > > methods may work for one but not the other. Automation is still<br>
> > a<br>
> > ><br>
> > > > difficult<br>
> > > > matter for transformation-based analysis.<br>
> > > ><br>
> > > ><br>
> > > > ><br>
> > > > ><br>
> > > > > Thank you very much!<br>
> > > > ><br>
> > > > ><br>
> > > > ><br>
> > > > > Have a nice weekend!<br>
> > > > ><br>
> > > > ><br>
> > > > ><br>
> > > > > Best<br>
> > > > ><br>
> > > > > Yi<br>
> > > > ><br>
> > > > ><br>
> > > > ><br>
> > > > ><br>
> > > > ><br>
> > > > > _______________________________________________<br>
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> > ><br>
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</blockquote></div><br>