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

[michiel mentink]

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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