[Insight-users] Inconsistent registration result.
lien lee
lienlee at gmail.com
Thu Feb 28 17:52:56 EST 2013
Hi itk-users,
I took a further step today. I derived a class
from MattesMutualInformationImageToImageMetric, and made it being the
metric, so that, I could sneak into itk and visit the protected
member ImageToImageMetric< TFixedImage, TMovingImage
>::m_FixedImageSamples. I printed out a couple of sample points (their
coordinates and image values), and I also printed out the seed value of the
random number generator, which I set as ReinitializeSeed(76926294). I get
the seed value by
calling Statistics::MersenneTwisterRandomVariateGenerator::GetInstance()->GetSeed();
In different runs, I do see same seed were used, but I also do see
different sample points. I tried this on two different computers, at both
of which I saw the inconsistent results. Seems to be the random number
generator is non-deterministic even with same seed. However, the weird
thing is if I do not use the image mask, it would be consistent.
Any thoughts?
2013/2/26 lien lee <lienlee at gmail.com>
> Hi Seth,
>
> By clicking the link you provided, the code I saw there is as partly
> attached, which is different from what I have with ITK 4.2 on my computer.
>
> I do not have experience with this code, and I am not exactly sure how it
> works. But, looks to me, optimizer would call the function during each
> iteration, and the function would rebuild all the sample points again and
> again for all the iterations. If my understanding were correct, this would
> be quite different from what I have with ITK 4.2 on my computer, where all
> the samples were created
> in MattesMutualInformationImageToImageMetric::Initialize() as *a one time
> thing*, and the counted points would be determined for each iteration
> using the current transform by checking whether the mapped points were
> inside the moving image mask. Therefore, for the code I am working on, to
> my understanding, if I called ReinitializeSeed(76926294) before generating
> all the sample points
> in MattesMutualInformationImageToImageMetric::Initialize(), the results
> should be deterministic, no matter whether I applied the image masks or
> not. But, the testing results with image mask applied does NOT support my
> understanding.
>
> BTW, to your question, my moving image mask may not be "restrictive"
> because it occupied pretty much about 80% of the whole moving image.
>
> Thanks again for your inputs.
>
>
> 106<http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/Registration/Common/include/itkMutualInformationImageToImageMetric.hxx;h=1244e5c0be768696cf042f6f39739f4b2bdcbba6;hb=HEAD#l106>template <class TFixedImage,
> class TMovingImage>
> 107<http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/Registration/Common/include/itkMutualInformationImageToImageMetric.hxx;h=1244e5c0be768696cf042f6f39739f4b2bdcbba6;hb=HEAD#l107>void
> 108<http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/Registration/Common/include/itkMutualInformationImageToImageMetric.hxx;h=1244e5c0be768696cf042f6f39739f4b2bdcbba6;hb=HEAD#l108>MutualInformationImageToImageMetric<TFixedImage, TMovingImage>
> 109<http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/Registration/Common/include/itkMutualInformationImageToImageMetric.hxx;h=1244e5c0be768696cf042f6f39739f4b2bdcbba6;hb=HEAD#l109>::SampleFixedImageDomain(
> 110<http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/Registration/Common/include/itkMutualInformationImageToImageMetric.hxx;h=1244e5c0be768696cf042f6f39739f4b2bdcbba6;hb=HEAD#l110> SpatialSampleContainer & samples) const
> 111<http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/Registration/Common/include/itkMutualInformationImageToImageMetric.hxx;h=1244e5c0be768696cf042f6f39739f4b2bdcbba6;hb=HEAD#l111>{
> 112<http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/Registration/Common/include/itkMutualInformationImageToImageMetric.hxx;h=1244e5c0be768696cf042f6f39739f4b2bdcbba6;hb=HEAD#l112> typedef ImageRandomConstIteratorWithIndex<FixedImageType> RandomIterator;
> 113<http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/Registration/Common/include/itkMutualInformationImageToImageMetric.hxx;h=1244e5c0be768696cf042f6f39739f4b2bdcbba6;hb=HEAD#l113> RandomIterator randIter( this->m_FixedImage, this->GetFixedImageRegion() );
> 114<http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/Registration/Common/include/itkMutualInformationImageToImageMetric.hxx;h=1244e5c0be768696cf042f6f39739f4b2bdcbba6;hb=HEAD#l114>
> 115<http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/Registration/Common/include/itkMutualInformationImageToImageMetric.hxx;h=1244e5c0be768696cf042f6f39739f4b2bdcbba6;hb=HEAD#l115> randIter.SetNumberOfSamples(m_NumberOfSpatialSamples);
> 116<http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/Registration/Common/include/itkMutualInformationImageToImageMetric.hxx;h=1244e5c0be768696cf042f6f39739f4b2bdcbba6;hb=HEAD#l116> randIter.GoToBegin();
> 117<http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/Registration/Common/include/itkMutualInformationImageToImageMetric.hxx;h=1244e5c0be768696cf042f6f39739f4b2bdcbba6;hb=HEAD#l117>
> 118<http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/Registration/Common/include/itkMutualInformationImageToImageMetric.hxx;h=1244e5c0be768696cf042f6f39739f4b2bdcbba6;hb=HEAD#l118> typename SpatialSampleContainer::iterator iter;
> 119<http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/Registration/Common/include/itkMutualInformationImageToImageMetric.hxx;h=1244e5c0be768696cf042f6f39739f4b2bdcbba6;hb=HEAD#l119> typename SpatialSampleContainer::const_iterator end = samples.end();
> 120<http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/Registration/Common/include/itkMutualInformationImageToImageMetric.hxx;h=1244e5c0be768696cf042f6f39739f4b2bdcbba6;hb=HEAD#l120>
> 121<http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/Registration/Common/include/itkMutualInformationImageToImageMetric.hxx;h=1244e5c0be768696cf042f6f39739f4b2bdcbba6;hb=HEAD#l121> bool allOutside = true;
> 122<http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/Registration/Common/include/itkMutualInformationImageToImageMetric.hxx;h=1244e5c0be768696cf042f6f39739f4b2bdcbba6;hb=HEAD#l122>
> 123<http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/Registration/Common/include/itkMutualInformationImageToImageMetric.hxx;h=1244e5c0be768696cf042f6f39739f4b2bdcbba6;hb=HEAD#l123> this->m_NumberOfPixelsCounted = 0; // Number of pixels that map into the
> 124<http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/Registration/Common/include/itkMutualInformationImageToImageMetric.hxx;h=1244e5c0be768696cf042f6f39739f4b2bdcbba6;hb=HEAD#l124> // fixed and moving image mask, if
> 125<http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/Registration/Common/include/itkMutualInformationImageToImageMetric.hxx;h=1244e5c0be768696cf042f6f39739f4b2bdcbba6;hb=HEAD#l125> // specified
> 126<http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/Registration/Common/include/itkMutualInformationImageToImageMetric.hxx;h=1244e5c0be768696cf042f6f39739f4b2bdcbba6;hb=HEAD#l126> // and the resampled fixed grid after
> 127<http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/Registration/Common/include/itkMutualInformationImageToImageMetric.hxx;h=1244e5c0be768696cf042f6f39739f4b2bdcbba6;hb=HEAD#l127> // transformation.
> 128<http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/Registration/Common/include/itkMutualInformationImageToImageMetric.hxx;h=1244e5c0be768696cf042f6f39739f4b2bdcbba6;hb=HEAD#l128>
> 129<http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/Registration/Common/include/itkMutualInformationImageToImageMetric.hxx;h=1244e5c0be768696cf042f6f39739f4b2bdcbba6;hb=HEAD#l129> // Number of random picks made from the portion of fixed image within the
> 130<http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/Registration/Common/include/itkMutualInformationImageToImageMetric.hxx;h=1244e5c0be768696cf042f6f39739f4b2bdcbba6;hb=HEAD#l130> // fixed mask
> 131<http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/Registration/Common/include/itkMutualInformationImageToImageMetric.hxx;h=1244e5c0be768696cf042f6f39739f4b2bdcbba6;hb=HEAD#l131> SizeValueType numberOfFixedImagePixelsVisited = 0;
> 132<http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/Registration/Common/include/itkMutualInformationImageToImageMetric.hxx;h=1244e5c0be768696cf042f6f39739f4b2bdcbba6;hb=HEAD#l132> SizeValueType dryRunTolerance = this->GetFixedImageRegion().GetNumberOfPixels();
> 133<http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/Registration/Common/include/itkMutualInformationImageToImageMetric.hxx;h=1244e5c0be768696cf042f6f39739f4b2bdcbba6;hb=HEAD#l133> for( iter = samples.begin(); iter != end; ++iter )
> 134<http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/Registration/Common/include/itkMutualInformationImageToImageMetric.hxx;h=1244e5c0be768696cf042f6f39739f4b2bdcbba6;hb=HEAD#l134> {
> 135<http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/Registration/Common/include/itkMutualInformationImageToImageMetric.hxx;h=1244e5c0be768696cf042f6f39739f4b2bdcbba6;hb=HEAD#l135> // Get sampled index
> 136<http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/Registration/Common/include/itkMutualInformationImageToImageMetric.hxx;h=1244e5c0be768696cf042f6f39739f4b2bdcbba6;hb=HEAD#l136> FixedImageIndexType index = randIter.GetIndex();
> 137<http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/Registration/Common/include/itkMutualInformationImageToImageMetric.hxx;h=1244e5c0be768696cf042f6f39739f4b2bdcbba6;hb=HEAD#l137> // Get sampled fixed image value
> 138<http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/Registration/Common/include/itkMutualInformationImageToImageMetric.hxx;h=1244e5c0be768696cf042f6f39739f4b2bdcbba6;hb=HEAD#l138> ( *iter ).FixedImageValue = randIter.Get();
> 139<http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/Registration/Common/include/itkMutualInformationImageToImageMetric.hxx;h=1244e5c0be768696cf042f6f39739f4b2bdcbba6;hb=HEAD#l139> // Translate index to point
> 140<http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/Registration/Common/include/itkMutualInformationImageToImageMetric.hxx;h=1244e5c0be768696cf042f6f39739f4b2bdcbba6;hb=HEAD#l140> this->m_FixedImage->TransformIndexToPhysicalPoint(index,
> 141<http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/Registration/Common/include/itkMutualInformationImageToImageMetric.hxx;h=1244e5c0be768696cf042f6f39739f4b2bdcbba6;hb=HEAD#l141> ( *iter ).FixedImagePointValue);
> 142<http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/Registration/Common/include/itkMutualInformationImageToImageMetric.hxx;h=1244e5c0be768696cf042f6f39739f4b2bdcbba6;hb=HEAD#l142>
> 143<http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/Registration/Common/include/itkMutualInformationImageToImageMetric.hxx;h=1244e5c0be768696cf042f6f39739f4b2bdcbba6;hb=HEAD#l143> // If not inside the fixed mask, ignore the point
> 144<http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/Registration/Common/include/itkMutualInformationImageToImageMetric.hxx;h=1244e5c0be768696cf042f6f39739f4b2bdcbba6;hb=HEAD#l144> if( this->m_FixedImageMask
> 145<http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/Registration/Common/include/itkMutualInformationImageToImageMetric.hxx;h=1244e5c0be768696cf042f6f39739f4b2bdcbba6;hb=HEAD#l145> && !this->m_FixedImageMask->IsInside( ( *iter ).FixedImagePointValue ) )
> 146<http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/Registration/Common/include/itkMutualInformationImageToImageMetric.hxx;h=1244e5c0be768696cf042f6f39739f4b2bdcbba6;hb=HEAD#l146> {
> 147<http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/Registration/Common/include/itkMutualInformationImageToImageMetric.hxx;h=1244e5c0be768696cf042f6f39739f4b2bdcbba6;hb=HEAD#l147> ++randIter; // jump to another random position
> 148<http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/Registration/Common/include/itkMutualInformationImageToImageMetric.hxx;h=1244e5c0be768696cf042f6f39739f4b2bdcbba6;hb=HEAD#l148> continue;
> 149<http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/Registration/Common/include/itkMutualInformationImageToImageMetric.hxx;h=1244e5c0be768696cf042f6f39739f4b2bdcbba6;hb=HEAD#l149> }
> 150<http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/Registration/Common/include/itkMutualInformationImageToImageMetric.hxx;h=1244e5c0be768696cf042f6f39739f4b2bdcbba6;hb=HEAD#l150>
> 151<http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/Registration/Common/include/itkMutualInformationImageToImageMetric.hxx;h=1244e5c0be768696cf042f6f39739f4b2bdcbba6;hb=HEAD#l151> if( allOutside )
> 152<http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/Registration/Common/include/itkMutualInformationImageToImageMetric.hxx;h=1244e5c0be768696cf042f6f39739f4b2bdcbba6;hb=HEAD#l152> {
> 153<http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/Registration/Common/include/itkMutualInformationImageToImageMetric.hxx;h=1244e5c0be768696cf042f6f39739f4b2bdcbba6;hb=HEAD#l153> ++numberOfFixedImagePixelsVisited;
> 154<http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/Registration/Common/include/itkMutualInformationImageToImageMetric.hxx;h=1244e5c0be768696cf042f6f39739f4b2bdcbba6;hb=HEAD#l154> if( numberOfFixedImagePixelsVisited > dryRunTolerance )
> 155<http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/Registration/Common/include/itkMutualInformationImageToImageMetric.hxx;h=1244e5c0be768696cf042f6f39739f4b2bdcbba6;hb=HEAD#l155> {
> 156<http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/Registration/Common/include/itkMutualInformationImageToImageMetric.hxx;h=1244e5c0be768696cf042f6f39739f4b2bdcbba6;hb=HEAD#l156> // We randomly visited as many points as is the size of the fixed image
> 157<http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/Registration/Common/include/itkMutualInformationImageToImageMetric.hxx;h=1244e5c0be768696cf042f6f39739f4b2bdcbba6;hb=HEAD#l157> // region.. Too may samples mapped ouside.. go change your transform
> 158<http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/Registration/Common/include/itkMutualInformationImageToImageMetric.hxx;h=1244e5c0be768696cf042f6f39739f4b2bdcbba6;hb=HEAD#l158> itkExceptionMacro(<< "Too many samples mapped outside the moving buffer");
> 159<http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/Registration/Common/include/itkMutualInformationImageToImageMetric.hxx;h=1244e5c0be768696cf042f6f39739f4b2bdcbba6;hb=HEAD#l159> }
> 160<http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/Registration/Common/include/itkMutualInformationImageToImageMetric.hxx;h=1244e5c0be768696cf042f6f39739f4b2bdcbba6;hb=HEAD#l160> }
> 161<http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/Registration/Common/include/itkMutualInformationImageToImageMetric.hxx;h=1244e5c0be768696cf042f6f39739f4b2bdcbba6;hb=HEAD#l161>
> 162<http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/Registration/Common/include/itkMutualInformationImageToImageMetric.hxx;h=1244e5c0be768696cf042f6f39739f4b2bdcbba6;hb=HEAD#l162> MovingImagePointType mappedPoint =
> 163<http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/Registration/Common/include/itkMutualInformationImageToImageMetric.hxx;h=1244e5c0be768696cf042f6f39739f4b2bdcbba6;hb=HEAD#l163> this->m_Transform->TransformPoint( ( *iter ).FixedImagePointValue );
> 164<http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/Registration/Common/include/itkMutualInformationImageToImageMetric.hxx;h=1244e5c0be768696cf042f6f39739f4b2bdcbba6;hb=HEAD#l164>
> 165<http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/Registration/Common/include/itkMutualInformationImageToImageMetric.hxx;h=1244e5c0be768696cf042f6f39739f4b2bdcbba6;hb=HEAD#l165> // If the transformed point after transformation does not lie within the
> 166<http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/Registration/Common/include/itkMutualInformationImageToImageMetric.hxx;h=1244e5c0be768696cf042f6f39739f4b2bdcbba6;hb=HEAD#l166> // MovingImageMask, skip it.
> 167<http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/Registration/Common/include/itkMutualInformationImageToImageMetric.hxx;h=1244e5c0be768696cf042f6f39739f4b2bdcbba6;hb=HEAD#l167> if( this->m_MovingImageMask
> 168<http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/Registration/Common/include/itkMutualInformationImageToImageMetric.hxx;h=1244e5c0be768696cf042f6f39739f4b2bdcbba6;hb=HEAD#l168> && !this->m_MovingImageMask->IsInside(mappedPoint) )
> 169<http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/Registration/Common/include/itkMutualInformationImageToImageMetric.hxx;h=1244e5c0be768696cf042f6f39739f4b2bdcbba6;hb=HEAD#l169> {
> 170<http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/Registration/Common/include/itkMutualInformationImageToImageMetric.hxx;h=1244e5c0be768696cf042f6f39739f4b2bdcbba6;hb=HEAD#l170> ++randIter;
> 171<http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/Registration/Common/include/itkMutualInformationImageToImageMetric.hxx;h=1244e5c0be768696cf042f6f39739f4b2bdcbba6;hb=HEAD#l171> continue;
> 172<http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/Registration/Common/include/itkMutualInformationImageToImageMetric.hxx;h=1244e5c0be768696cf042f6f39739f4b2bdcbba6;hb=HEAD#l172> }
> 173<http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/Registration/Common/include/itkMutualInformationImageToImageMetric.hxx;h=1244e5c0be768696cf042f6f39739f4b2bdcbba6;hb=HEAD#l173>
>
> <http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/Registration/Common/include/itkMutualInformationImageToImageMetric.hxx;h=1244e5c0be768696cf042f6f39739f4b2bdcbba6;hb=HEAD#l174>
>
> 2013/2/26 Seth Gilchrist <seth at mech.ubc.ca>
>
>> Hi Lien,
>> Unfortunately I have not used masks when performing registrations, so
>> can't help you with this specific problem.
>>
>> I took a look at the git blob for the MattesMutual...Metric and was
>> examining how the decision to keep or reject a give point is handled. If
>> you are setting a mask on both the fixed and moving images, this will
>> change what points are used because a check is done to see if a point is in
>> the fixed mask and if it is in the moving mask after applying the current
>> transform. Could your moving image mask be too restrictive for the early
>> stages of the registration?
>>
>> You can read the code at:
>>
>> http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/Registration/Common/include/itkMutualInformationImageToImageMetric.hxx;h=1244e5c0be768696cf042f6f39739f4b2bdcbba6;hb=HEAD
>>
>> Starting on line 108, specifically on line 162.
>>
>> Cheers,
>> Seth
>>
>> *Seth Gilchrist, MASc, PhD Candidate
>> +---------------------------------------+
>> Orthopaedic and Injury Biomechanics Group
>> UBC Department of Mechanical Engineering
>> 6th Floor-2635 Laurel Street
>> Vancouver, BC V5Z-1M9
>> +---------------------------------------+
>> seth at mech.ubc.ca
>> Fax 604-675-2576*
>>
>>
>
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