[Insight-users] Continuous Index

[Luis Ibanez]

Hi Xiangn,


In order to write the track out into a binary image,
you will have to discretize the continous index.


As described in my previous email,
you can do this with the following code:

    ImageType::IndexType index;

    index.CopyWithRound( continousIndex );

    image->SetPixel( index, tractValue );


Note that,
by doing this, you are losing information
on the actual position of the tract.



   Regards,


         Luis


---------------------------------------------
On Wed, Jul 1, 2009 at 3:53 PM, Xiang Hao <haoxiang at yahoo.cn> wrote:

> Hi Luis,
>
> I can compute the features at the continuous index by following your
> suggestion. Thank you again. Now I want to save the tract(path) in an binary
> image, but I have a problem about how to write an value in a continuous
> index.
>
> Cheers,
> Xiang
>
>
> On Tue, Jun 30, 2009 at 12:41 PM, Xiang Hao <haoxiang at yahoo.cn> wrote:
>
>> Great, Luis. Thank you again. I appreciate it very much.
>>
>> Cheers,
>> Xiang
>>
>>
>> On Tue, Jun 30, 2009 at 11:30 AM, Luis Ibanez <luis.ibanez at kitware.com>wrote:
>>
>>>
>>> Hi Xiang,
>>>
>>> If you need to evaluat the image at ContinousIndex positions,
>>> or at Point positions you will need to use an Interpolator.
>>>
>>> Something like
>>>
>>>    interpolator->SetImage( image );
>>>    interpolator->Evaluate( point );
>>>    interpolator->Evaluate( continuousIndex );
>>>
>>> For a list of ITK Interpolators, please look at:
>>>
>>> http://public.kitware.com/Insight/Doxygen/html/group__ImageInterpolators.html
>>>
>>>
>>> Note however, that, depending on how you track
>>> fibers, what you may actually need is to compute
>>> features at those points (or continuous indices)
>>> and therefore you may have to use ImageFunctions
>>> there.
>>>
>>> For example:
>>>
>>> itkGaussianBlurImageFunction.h
>>> itkGaussianDerivativeImageFunction.h
>>>
>>>
>>>
>>>        Regards,
>>>
>>>
>>>                 Luis
>>>
>>>
>>>
>>> ----------------------------------------------------------------------
>>>
>>> On Tue, Jun 30, 2009 at 1:22 PM, Xiang Hao <haoxiang at yahoo.cn> wrote:
>>>
>>>> Hi Luis,
>>>>
>>>> Thank you so much, Luis. I will try it, and BTW, as I remember, there is
>>>> a problem about setPixel() and getPixel() method while I am using the
>>>> ContinuousIndex. It said it cannot find the corresponding method. Anyway, I
>>>> will try your method and try to make it work.
>>>>
>>>> Thank you again,
>>>> Xiang
>>>>
>>>>
>>>> On Tue, Jun 30, 2009 at 10:29 AM, Luis Ibanez <luis.ibanez at kitware.com>wrote:
>>>>
>>>>>
>>>>>
>>>>> Hi Xian,
>>>>>
>>>>> If you need sub-pixel locations for the points of the fibers,
>>>>> yes, it makes sense to use ContinuousIndex instead of
>>>>> Indexes for representing the location of fibers centers.
>>>>>
>>>>> That said, it may be preferable to use itk::Point<> since
>>>>> that will take into account also the pixel spacing, image
>>>>> origin, and image orientation, and you will be able to
>>>>> do things like overlapping a visualization of the fibers
>>>>> with the original image.
>>>>>
>>>>> A) If you need to convert Index to ContinousIndex you
>>>>>      can use the method:
>>>>>
>>>>>     Constructor
>>>>>
>>>>>      IndexType  index;
>>>>>      ContinuousIndexType  cindex( index );
>>>>>
>>>>> B) In order to convert Continuous index to Index you
>>>>>      can use the method CopyWithRound()
>>>>>
>>>>>     index.CopyWithRound( continousIndex )
>>>>>
>>>>> C) In order to convert an index into a physical point
>>>>>      and back you can use the image methods
>>>>>
>>>>>       TransformIndexToPhysicalPoint( index, point );
>>>>>       TransformPhysicalPointToIndex(point, index );
>>>>>
>>>>>
>>>>>
>>>>>   Regards,
>>>>>
>>>>>
>>>>>
>>>>>         Luis
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> ----------------------------------------------------------------------------------------------
>>>>> On Sun, Jun 28, 2009 at 2:42 PM, Xiang Hao <haoxiang at yahoo.cn> wrote:
>>>>>
>>>>>> Hi,
>>>>>>
>>>>>> I am trying to write a tractography program.
>>>>>> Now I use discrete index:
>>>>>>
>>>>>> Dimension =3;
>>>>>> typedef int OutputPixelType;
>>>>>> typedef itk::Image< OutputPixelType, Dimension > OutputImageType;
>>>>>> OutputImageType::IndexType pixelIndex;
>>>>>>
>>>>>> So now the pixelIndex is discrete index and I want to change it to
>>>>>> continuous index. I know there is an ContinuousIndex class in ITK. I wonder
>>>>>> whether I should use this class and how to use it in order to change the
>>>>>> index to continuous index.
>>>>>>
>>>>>>
>>>>>> --
>>>>>> Cheers,
>>>>>> Xiang
>>>>>>
>>>>>>
>>>>>> --
>>>>>> Cheers,
>>>>>> Xiang
>>>>>>
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>>>>>>
>>>>>
>>>>
>>>>
>>>> --
>>>> Cheers,
>>>> Xiang
>>>>
>>>
>>>
>>
>>
>> --
>> Cheers,
>> Xiang
>>
>
>
>
> --
> Cheers,
> Xiang
>
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