[Insight-users] imageregistration with mask fails because of all points outside of all points mapped outside of moving image

[michiel mentink]

Dear Luis,

I have solved the problem by extending imageRegistration12 to 3 dimensions
and changing the
registration method and optimizer references to Versor3D.

cheers,

Michael

On Mon, Mar 8, 2010 at 11:04 AM, michiel mentink <
michael.mentink at st-hughs.ox.ac.uk> wrote:

>
> that should be
> The tibia is segmented and all the 'tibia' voxels have grey values (not
> binary).
>
>
>
>
>
> On Mon, Mar 8, 2010 at 11:03 AM, michiel mentink <
> michael.mentink at st-hughs.ox.ac.uk> wrote:
>
>> Dear Luis,
>>
>> Background: I have an image volume, MRI of the knee. The tibia is
>> segmented and
>> all the 'femur' voxels have grey values (not binary). All the rest is
>> black.
>> Therefore, I create a mask by applying a thresholder with a threshold of
>> 1: all the
>> voxels that have intensity>0 are given the value '1'.
>>
>>     typedef itk::ThresholdImageFilter< FixedImageType >
>> ThresholdFilterType;
>>     ThresholdFilterType::Pointer thresholder = ThresholdFilterType::New();
>>     thresholder->SetInput( fixedImage);
>>     thresholder->SetOutsideValue( 1 );
>>     thresholder->ThresholdAbove( 0 );
>>     thresholder->Update();
>>
>>   // insert caster here, casting from float to unsigned char
>>   typedef  unsigned char  MaskPixelType;
>>   typedef itk::Image< MaskPixelType, Dimension > MaskImageType;
>>   typedef itk::CastImageFilter< FixedImageType, MaskImageType >
>> CastFilterType;
>>
>>   CastFilterType::Pointer  caster =  CastFilterType::New();
>>   caster->SetInput( thresholder->GetOutput() );
>>
>>   // create a 3D mask type
>>   typedef itk::ImageMaskSpatialObject< 3 >   MaskType;
>>   // then create the mask itself
>>   MaskType::Pointer  mask = MaskType::New();
>>
>>   //connect the binary image to the mask
>>   mask->SetImage(caster->GetOutput() );
>>
>>   // pass the spatial object mask to the image metric
>>   metric->SetFixedImageMask( mask);
>> //  metric->SetMovingImageMask( mask);
>>
>>   // write the mask to a file, just to check if thresholding went alright
>>   typedef itk::ImageFileWriter< MaskImageType >  MaskImageWriter;
>>   MaskImageWriter::Pointer writerBinary = MaskImageWriter::New();
>>   writerBinary->SetInput( caster->GetOutput() );
>>   writerBinary->SetFileName("mask.mhd" );
>>   writerBinary->Update();
>>   std::cout << "mask created" << std::endl << std::endl;
>>
>> I'm afraid I can't post the mask file to the mailing list (1.7MB) but I'll
>> mail it to you.
>>
>> cheers,
>>
>> Michael
>>
>>
>>
>>
>> On Sat, Mar 6, 2010 at 11:02 PM, Luis Ibanez <luis.ibanez at kitware.com>wrote:
>>
>>> Hi Michiel,
>>>
>>> Thanks for sharing your findings in this problem.
>>>
>>> Can you tell us more about the mask (the segmentation)
>>> that you created ?
>>>
>>> Have you checked this mask with any visualization
>>> application ?
>>>
>>> What are the pixel values ?
>>>
>>> Is there a chance that you could share that binary image
>>> with us ?
>>>
>>>
>>>    Thanks
>>>
>>>
>>>          Luis
>>>
>>>
>>> ---------------------------------------------------------------------------
>>> On Fri, Mar 5, 2010 at 11:28 AM, michiel mentink
>>> <michael.mentink at st-hughs.ox.ac.uk> wrote:
>>> > Dear all,
>>> >
>>> > When running an image registration algorithm with mask, I get this
>>> error:
>>> >
>>> > File:
>>> >
>>> /MMprogs/src/ITK_src/Code/Algorithms/itkMeanSquaresImageToImageMetric.txx
>>> > Line: 364
>>> > Description: itk::ERROR: MeanSquaresImageToImageMetric(0x95f63f0): All
>>> the
>>> > points mapped to outside of the moving image
>>> >
>>> > I've traced this to the following problem:
>>> > in ImageMaskSpatialObject->IsInside(), all points are found outside of
>>> the
>>> > mask/image (?)
>>> >
>>> > and this is because the boundingbox of the mask has bounding values of
>>> 0, 0,
>>> > 0, 0, 0, 0, so indeed, there are no points that
>>> > can be found inside these values.
>>> >
>>> > I am a bit stuck now, apparently, the mask that I created from a
>>> segmented
>>> > volume is not converted into a bounding box correctly.
>>> >
>>> > Where do I check to find out why this is happening?
>>> >
>>> > cheers,
>>> >
>>> > Michael
>>> >
>>> >
>>> > ps: some more info about my data:
>>> >
>>> > new moving image origin:    [0, 0, 0]
>>> > fixed image size:      [215, 172, 48]
>>> > fixed image origin:    [44.0625, 0, 0]
>>> > fixed image spacing:   [0.3125, 0.3125, 1.9808]
>>> > fixed image direction:
>>> > 1 0 0
>>> > 0 1 0
>>> > 0 0 1
>>> >
>>> >
>>> > moving image size:      [512, 512, 52]
>>> > moving image origin:    [0, 0, 0]
>>> > moving image spacing:   [0.3125, 0.3125, 1.92911]
>>> > moving image direction:
>>> > 1 0 0
>>> > 0 1 0
>>> > 0 0 1
>>> >
>>> >
>>> > image mask size:      [215, 172, 48]
>>> > image mask origin:    [44.0625, 0, 0]
>>> > image mask spacing:   [0.3125, 0.3125, 1.9808]
>>> > image mask direction:
>>> > 1 0 0
>>> > 0 1 0
>>> > 0 0 1
>>> >
>>> >
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>>
>>
>>
>
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