[Insight-users] VectorImage Registration Metric

Tue Feb 23 16:09:53 EST 2010

Luke,

Thanks for letting us know.

   Luis

---------------------------------------
On Tue, Feb 23, 2010 at 10:06 AM, Luke Bloy <luke.bloy at gmail.com> wrote:
> I realized in putting my code together to upload the sandbox that it
> depended on some local modifications to itk. I'm in the process of
> addressing these and will upload the code as soon as I can.
>
> Just wanted to let you know that I haven't forgotten about this :)
>
> -Luke
>
> Luis Ibanez wrote:
>>
>> Luke,
>>
>> Excellent,
>>
>> Thanks for letting us know.
>>
>> It will be great to to put the code in the Sandbox,
>> so Lisa and other interested developers can
>> collaborate to build a complete solution for
>> vector and tensor images.
>>
>> Let me know if there is anything I can do to help,
>>
>>
>>     Thanks
>>
>>
>>           Luis
>>
>>
>> ------------------------------------
>> On Wed, Feb 10, 2010 at 7:58 AM, Luke Bloy <luke.bloy at gmail.com> wrote:
>>
>>>
>>> Hi Lisa and Luis,
>>>
>>> I have extensions to ResampleImageFileter and WarpImageFilter that
>>> perform
>>> reorientation of the data model. I have to check some licensing things
>>> but I
>>> can probably put it up into the sandbox shortly.
>>>
>>> Luis, I took your suggestion of using a templated reorienter class. so
>>> these
>>> classes work with scalar data as well as tensor and qball data. Lisa, the
>>> reorientation method at the moment only does Finite-strain, although
>>> adding
>>> an option to use PPD is somewhere on my list of things to do :)
>>>
>>> There is also an interpolator for DTI which does both euclidean and
>>> log-euclidean interpolation.
>>>
>>> -Luke
>>>
>>> Luis Ibanez wrote:
>>>
>>>>
>>>> Hi Lisa,
>>>>
>>>> You are right,
>>>> Thanks for pointing this out.
>>>>
>>>>
>>>> Yes, we should move the code into the Sandbox.
>>>> (please check first if Jeffrey has defined any License
>>>> for his version of the code, if so, we have to verify if
>>>> that the license is BSD compatible, before we adopt
>>>> the code).
>>>>
>>>>
>>>> Do you have a NAMICSandbox  write account ?
>>>>
>>>> If not, please request one at:
>>>> https://www.kitware.com/Admin/SendPassword.cgi
>>>>
>>>>
>>>> Also, about your question:
>>>>
>>>> Yes, if you want to extend registration to tensor images,
>>>> a similar extension will have to be made. You will also
>>>> need a TensorResampleFilter based on the itkVector
>>>> ResampleFilter.
>>>>
>>>> Please note however that Interpolations for Tensors
>>>> may require different strategies, depending on what
>>>> the Tensor is representing.  For example, when the
>>>> Tensor represents some physical property, it may
>>>> be subject to some constrains.
>>>>
>>>> In the NAMIC group there has been some work related
>>>> to Tensor interpolation.
>>>>
>>>> Regarding the actual Metric, the adaptation of the
>>>> GetValue() method is rather easy. You simply
>>>> need to introduce a measure of distance between
>>>> two Tensors (again, probably based on what the
>>>> Tensors are representing).
>>>>
>>>> The more involved piece of work is the computation
>>>> of derivatives.
>>>>
>>>> The Derivative of the metric will involve the computation
>>>> of a third-rank Tensor, which is the result of deriving
>>>> the image Tensors with respect to space.
>>>>
>>>> This could be represented in 3D matrix of N components,
>>>> where N is the dimension of the image Space.
>>>>
>>>> It will be nice to develop this code also in a NAMICSandbox
>>>> directory, so you can benefit from the feedback of
>>>> other groups in the community.
>>>>
>>>>
>>>> Let us know if you need any help,
>>>> we will be happy to assist you.
>>>>
>>>>
>>>>        Luis
>>>>
>>>>
>>>>
>>>> -----------------------------------------------------------------------
>>>> On Tue, Feb 9, 2010 at 2:21 PM, Lisa Tang <lisat at sfu.ca> wrote:
>>>>
>>>>
>>>>>
>>>>> Hello Luis,
>>>>>
>>>>> Thanks for your reply.
>>>>>
>>>>> On closer look, I think these items have already been fixed by Jeffrey
>>>>> Dudas, whose work was discussed in Oct 2009
>>>>>
>>>>>
>>>>> http://old.nabble.com/Question-about-multiResolutionPyramidImageFilter-class-to25839179.html#a25862138
>>>>>
>>>>> For example, the code for gradient calculation has been added here:
>>>>> http://www.seas.upenn.edu/~jtduda/code/itkVectorImageToImageMetric.txx
>>>>>
>>>>>
>>>>> http://www.seas.upenn.edu/~jtduda/code/itkVectorMeanSquaresImageToImageMetric.txx
>>>>>
>>>>> Perhaps the sandbox needs to be updated with his work?
>>>>>
>>>>> A related question is its extension to Tensor images. A needed
>>>>> class/filter that comes to mind is for the purpose of reorienting
>>>>> tensors
>>>>> after the tensor image is transformed. Could you please point us to how
>>>>> we
>>>>> can proceed with this?
>>>>>
>>>>> e.g. should it follow construct of itkVectorResampleImageFilter, but
>>>>> using itkDiffusionTensor3D as input?
>>>>>
>>>>> Thanks again,
>>>>> Lisa
>>>>>
>>>>>
>>>>> ----- "Luis Ibanez" <luis.ibanez at kitware.com> wrote:
>>>>>
>>>>>
>>>>>
>>>>>>
>>>>>> From: "Luis Ibanez" <luis.ibanez at kitware.com>
>>>>>> To: "Lisa Tang" <lisat at sfu.ca>
>>>>>> Cc: "Ghassan Hamarneh" <hamarneh at cs.sfu.ca>, "itk"
>>>>>> <Insight-users at itk.org>
>>>>>> Sent: Tuesday, 9 February, 2010 10:46:19 GMT -08:00 US/Canada Pacific
>>>>>> Subject: Re: VectorImage Registration Metric
>>>>>>
>>>>>> Hi Lisa,
>>>>>>
>>>>>> Please look at the file:
>>>>>>
>>>>>> NAMICSandBox/VectorImageRegistrationMethod/Source/
>>>>>>                   itkVectorMeanSquaresImageToImageMetric.txx
>>>>>>
>>>>>> and the lines that have "FIXME" messages as comments.
>>>>>>
>>>>>>
>>>>>> These are the lines where a change from "Scalar", to "Vector"
>>>>>> computation remains to be introduced.
>>>>>>
>>>>>> For example, the "gradient", used to be a Vector in the
>>>>>> computation of a Metric for a Scalar image, but when
>>>>>> doing that computation for  a Vector image, the gradient
>>>>>> must be a Matrix, which is composed of the gradients
>>>>>> of each individual component of the vector image.
>>>>>>
>>>>>>
>>>>>> Please let us know if you see any problems with
>>>>>> the suggested implementation,
>>>>>>
>>>>>>
>>>>>>     Thanks
>>>>>>
>>>>>>
>>>>>>           Luis
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> ------------------------------------------------------------------------------------------
>>>>>> On Fri, Feb 5, 2010 at 2:30 PM, Lisa Tang <lisat at sfu.ca> wrote:
>>>>>>
>>>>>>
>>>>>>>
>>>>>>> Hi Luis,
>>>>>>>
>>>>>>> You mentioned that the version in NAMIC sandbox need "massaging":
>>>>>>>
>>>>>>> "The Gradient of the vector image must be computed as a matrix
>>>>>>> and multiplied with the Transform jacobian in order to produce
>>>>>>> another matrix, that then will be collapsed into a gradient
>>>>>>> vector. (to be done)"
>>>>>>>
>>>>>>> However, I find that both the Sandbox's
>>>>>>>
>>>>>>>
>>>>>>
>>>>>> itkVectorMeanSquaresImageToImageMetric and
>>>>>> itkMeanSquaresImageToImageMetric calculate the metric's derivative
>>>>>> similarly, and so are the calculations of the gradient image in
>>>>>> itkVectormageToImageMetric.
>>>>>>
>>>>>>
>>>>>>>
>>>>>>> Could you please clarify which class were you referring to that
>>>>>>>
>>>>>>>
>>>>>>
>>>>>> requires the above change?
>>>>>>
>>>>>>
>>>>>>>
>>>>>>> Thanks in advance,
>>>>>>> Lisa
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> ----- "Luis Ibanez" <luis.ibanez at kitware.com> wrote:
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>>
>>>>>>>> From: "Luis Ibanez" <luis.ibanez at kitware.com>
>>>>>>>> To: "Ghassan Hamarneh" <hamarneh at cs.sfu.ca>
>>>>>>>> Cc: "Lisa Tang" <lisat at sfu.ca>
>>>>>>>> Sent: Friday, 5 February, 2010 07:04:30 GMT -08:00 US/Canada
>>>>>>>>
>>>>>>>>
>>>>>>
>>>>>> Pacific
>>>>>>
>>>>>>
>>>>>>>>
>>>>>>>> Subject: Re: VectorImage Registration Metric
>>>>>>>>
>>>>>>>> Hi Ghassan,
>>>>>>>>
>>>>>>>> I haven't seen much activity in this project for a while,
>>>>>>>> but sometimes research groups make progress without
>>>>>>>> necessarily sharing their day-to-day updates with the
>>>>>>>> community.
>>>>>>>>
>>>>>>>> I would suggest to bring up the topic to the ITK users
>>>>>>>> and developers list.
>>>>>>>>
>>>>>>>> I will be happy to ask the question in the lists if you
>>>>>>>> prefer me to do it.
>>>>>>>>
>>>>>>>>
>>>>>>>>    Regards,
>>>>>>>>
>>>>>>>>
>>>>>>>>         Luis
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> ---------------------------------------------------------
>>>>>>>> On Fri, Feb 5, 2010 at 12:55 AM, Ghassan Hamarneh
>>>>>>>>
>>>>>>>>
>>>>>>
>>>>>> <hamarneh at cs.sfu.ca>
>>>>>>
>>>>>>
>>>>>>>>
>>>>>>>> wrote:
>>>>>>>>
>>>>>>>>
>>>>>>>>>
>>>>>>>>> Hello Luis
>>>>>>>>>
>>>>>>>>> Hope all is well!
>>>>>>>>>
>>>>>>>>> I came across this thread:
>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>>  http://www.cmake.org/pipermail/insight-users/2008-May/025746.html
>>>>>>>>
>>>>>>>>
>>>>>>>>>
>>>>>>>>> We were thinking of contributing something similar (vector
>>>>>>>>>
>>>>>>>>>
>>>>>>
>>>>>> valued
>>>>>>
>>>>>>
>>>>>>>>
>>>>>>>> image registration) to the insight journal as was developed for
>>>>>>>>
>>>>>>>>
>>>>>>
>>>>>> our
>>>>>>
>>>>>>
>>>>>>>>
>>>>>>>> paper:
>>>>>>>>
>>>>>>>>
>>>>>>>>>
>>>>>>>>> [ SMRFI: Shape Matching via ] Registration of Vector-Valued
>>>>>>>>>
>>>>>>>>>
>>>>>>
>>>>>> Feature
>>>>>>
>>>>>>
>>>>>>>>
>>>>>>>> Images
>>>>>>>>
>>>>>>>>
>>>>>>>>>
>>>>>>>>> http://www.cs.sfu.ca/~hamarneh/ecopy/cvpr2008.pdf
>>>>>>>>>
>>>>>>>>> Before investing more time on this, we appreciate if you could
>>>>>>>>>
>>>>>>>>>
>>>>>>
>>>>>> let
>>>>>>
>>>>>>
>>>>>>>>
>>>>>>>> us know the status of this effort, is any one working on this,
>>>>>>>>
>>>>>>>>
>>>>>>
>>>>>> etc?
>>>>>>
>>>>>>
>>>>>>>>>
>>>>>>>>> Thanks,
>>>>>>>>>
>>>>>>>>> /Ghassan
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>
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>