[Mristudio-users] Re: 回复： Re： LDDMM questions

Wed Jul 15 10:07:32 EDT 2009

Hi Jinsong, click on the link I sent you. I just downloaded it and it's
fine.

Siewmin

On Wed, Jul 15, 2009 at 9:32 AM, jinsong tang <tangjinsonghn at yahoo.com.cn>wrote:

>   Dear Siewmin and venkateswaran,
>
> Thank you for your kindly help.  But I cannot download the attachments.
> Would you please sent it again.
>
> Best,
>
> Jinsong
>
>
>  ------------------------------
> *发件人：* Siewmin Gan <siewmin.gan at gmail.com>
> *收件人：* "DTI Studio, ROI Editor, Landmarker Questions/Support" <
> mristudio-users at mristudio.org>
> *已发送：* 2009/7/14(周二), 下午10:35:12
> *主题：* Re: [Mristudio-users] Re： LDDMM questions
>
> Hi, This is from Xin. It works.
>  https://www.yousendit.com/download/cmcyWUhwMGtxRTJGa1E9PQ.
>
> Siewmin
>
> On Wed, Jul 15, 2009 at 12:30 AM, jinsong tang <tangjinsonghn at yahoo.com.cn
> > wrote:
>
>>   Hello, Dear all,
>>
>> I am trying to use Landmarker with the AIR functions. I am using a 32bit
>> windows XP. According to the instruction, I need to compile the AIR
>> functions myself. However,  I was not able to build those executable
>> files. Are there anyone has those .exe files,and could share them with us.
>>
>> Best regars,
>>
>> Jinsong
>> ------------------------------
>> *发件人：* Xin Li <xli16 at jhmi.edu>
>> *收件人：* Yi Jiang <yj3 at duke.edu>
>> *抄送：* "DTI Studio, ROI Editor, Landmarker Questions/Support" <
>> mristudio-users at mristudio.org>
>> *已发送：* 2009/7/14(周二), 下午10:10:47
>> *主题：* Re: [Mristudio-users] LDDMM questions
>>
>> Yi,
>>
>> Landmarker can combine AIR matrix and LDDMM matrix. The button for this
>> function is right below the button for multichannel remote LDDMM.
>>
>>
>> Xin
>>
>>
>>
>> ----- Original Message -----
>> From: susumu mori <susumu at mri.jhu.edu>
>> Date: Tuesday, July 14, 2009 2:21 am
>> Subject: Re: [Mristudio-users] LDDMM questions
>> 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>
>>
>>
>> > Hi Yi,
>> >
>> >  1) I recommend you to do AIR first from two reasons. First one is a
>> >  practical reason. Our LDDMM requires that the matrix and pixel sizes
>> > of the
>> >  two images are identical. After AIR, even if the input images have
>> different
>> >  dimensions, the output will have the same dimension. This is handy.
>> Second
>> >  one is more important. Let me use fitting of a X-Y plot for analogy.
>> > When
>> >  you use linear fitting, no matter which software you use, the results
>> > are
>> >  almost identical. This is because the energy landscape of linear
>> fitting
>> >  usually has a very simple "one-valley" shape, meaning the results
>> always
>> >  converge at the same solution. On the other hand, when you are using
>> >  non-linear fitting, you are required to provide initial values, which
>> > are
>> >  close to the real solution. Usually you first do linear solution and
>> > then
>> >  use the result as the initial value for the subsequent non-linear
>> fitting.
>> >  This is because the energy landscape of non-linear fitting has a
>> complicated
>> >  "multi-valley" shape. If your initial values are far away from the real
>> >  solution, the fitting is trapped by a local minima.
>> >
>> >  Non-linear warping is very similar. You are required to bring two
>> > brains as
>> >  close as possible before you start non-linear warping.
>> >
>> >  When you adopt AIR+LDDMM, you have to transform the image twice,
>> including
>> >  tensor reorientation. Landmarker can combine transformation matrices
>> > so that
>> >  you can do multiple transformation at once to avoid multiple
>> interpolation.
>> >
>> >  Xin, can we combine AIR matrix and LDDMM matrix?
>> >
>> >  2) We usually don't use non-linear AIR. So we don't have much
>> experience
>> >  with it. Yes, it should do tensor reorientation if you apply the
>> >  transformation to a tensor file.
>> >
>> >
>> >
>> >  On Mon, Jul 13, 2009 at 4:12 PM, Yi Jiang <yj3 at duke.edu> wrote:
>> >
>> >  >  Dear All,
>> >  >
>> >  > I have two questions about LDDMM:
>> >  >
>> >  >
>> >  >
>> >  > 1. if I have a template image and a subject image and I want to
>> register
>> >  > these two by LDDMM eventually, 1). should I use LDDMM to register
>> > these two
>> >  > directly or 2). should I use AIR linear to affine transform them
>> > first, and
>> >  > then LDDMM the updated subject image? In the 2nd case, I need to
>> reorient
>> >  > tensors twice, once by the AIR transformation matrix and once by
>> > the LDDMM
>> >  > transformation matrix, right?
>> >  >
>> >  >
>> >  >
>> >  > I am asking this question because for some other registration
>> > software I
>> >  > have used, it seems the elastic transformation works better after
>> affine
>> >  > registering the images first.
>> >  >
>> >  >
>> >  >
>> >  > Or maybe LDDMM covers rigid and affine transformation well already
>> > so we
>> >  > can do #1?
>> >  >
>> >  >
>> >  >
>> >  > 2. How does the nonlinear AIR compensate/compare with LDDMM? Can the
>> >  > nonlinear AIR transformation be applied to reorient tensors?
>> >  >
>> >  >
>> >  >
>> >  > Thank you very much!
>> >  >
>> >  >
>> >  >
>> >  > Best,
>> >  >
>> >  > Yi
>> >  >
>> >  > _______________________________________________
>> >  > Mristudio-users mailing list
>> >  > Mristudio-users at mristudio.org
>> >  >
>> >  > Unsubscribe, send a blank email to:
>> >  > Mristudio-users-unsubscribe at mristudio.org
>> >  >
>> >  >
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