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

Wed Jul 15 10:45:23 EDT 2009

sorry about that. the zip and unzip files are executable and gmail
doesn't allow me send it, for security reason
Siewmin

On Wed, Jul 15, 2009 at 10:36 AM, jinsong tang
<tangjinsonghn at yahoo.com.cn>wrote:

>   I will try it again. The internet explorer cannot display the webpage in
> the office. I will try it at home.
>
> Thanks,
>
> 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：* 2009/7/15(周三), 下午10:07:32
> *主题：* [Mristudio-users] Re: 回复： Re： LDDMM questions
>
>    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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