[Insight-users] Masks & registration

[Karthik Krishnan]

See this post
http://public.kitware.com/pipermail/insight-users/2005-April/012650.html

HTH
-karthik

Laurent PAUL wrote:

>Hi Luis,
>
>If I want to use masks, I can first apply a AND filter on Image and Mask
>and use the result as fixed and moving Image.
>If I really need masks, I'll try.
>
>Another question on masks: if I use mask, Do I have to initially transform
>the mask with the same InitialTransform applied on the MovingImage? I
>think my problem could come from there, mask hasn't the same absolute
>coordinates as Initially transformed MovingImage.
>
>Thanks for your help.
>
>Laurent.
>
>
>  
>
>>Hi Laurent,
>>
>>The Transform Initializers do not take into account the Masks.
>>
>>They compute the Moments/Geometry on the entire images.
>>
>>Note that a better way to initialize your registration is to
>>use the LandmarkBasedTransformInitializer.
>>
>>http://www.itk.org/Insight/Doxygen/html/classitk_1_1LandmarkBasedTransformInitializer.html
>>
>>It requires the user to provide at couple of homologous points
>>in both images, but it will increase a lot the quality of your
>>initialization.
>>
>>
>>
>>   Regards,
>>
>>
>>      Luis
>>
>>
>>
>>======================
>>Laurent PAUL wrote:
>>    
>>
>>> Hi users,
>>>I've got a problem with masks & registration.
>>>I use MeanSquaresImageToImageMetric and VersorRigid3DTransform for the
>>>      
>>>
>registration process.
>  
>
>>>Since I have regions of interest, I tried to pass at least 1 mask to
>>>      
>>>
>the
>  
>
>>>metric. It seems to be ok as I test it with IsInside() method with two
>>>      
>>>
>points (one in and one out).
>  
>
>>>My first question is if I use SetDefaultOutsideValue(0) for the mask,
>>>      
>>>
>any value different from 0 will be considered as Inside, right?
>  
>
>>>Then, I read a message which deals with nearly the same problem:
>>>      
>>>
>http://public.kitware.com/pipermail/insight-users/2005-September/014948.html
>This is an (interesting) extract:
>  
>
>>>>"Sure, as you pointed out, if you start off with a horrible initial
>>>>        
>>>>
>misalignment, in the worst case, the regions don't overlap and the
>  
>
>>>>metric
>>>>never gets computed.  Usually, in a registration application, if you've
>>>>        
>>>>
>gone through the trouble of specifying relevant regions in both the
>  
>
>>>fixed >and moving image regions, you already have some idea of the
>>>      
>>>
>initial >transform and there is no excuse for not specifying an initial
>transform >that guarantees significant overlap between the two masks.
>  
>
>>>>(This will of course only happen if you've specified *both* a fixed and
>>>>        
>>>>
>moving image mask, and not if just specify one of them. )"
>  
>
>>>I am in this case, where I know regions of interest.
>>>I understand the intialization problem but how initialize the
>>>registration?
>>>So far, I used the CenteredVersorTransformInitializer:
>>>   initializer->SetTransform (transform);
>>>   initializer->SetFixedImage (FixedImage);
>>>   initializer->SetMovingImage (MovingImage);
>>>   initializer->MomentsOn();
>>>What I understood is that initialisation is made upon Mass center. Is
>>>      
>>>
>mass center calculation takes account of the mask, I mean only region
>contained in the mask?
>  
>
>>>I tried too with initializer->GeometryOn();
>>>but I've got an error at runtime. Is it safe to use "GeometryOn"? More,
>>>      
>>>
>I know initialisation is quite ok. There is just a translation error.
>  
>
>>>I tried (without using Initializer):
>>>  TransformType::OutputVectorType InitialTranslation;
>>>  InitialTranslation[0] = 80;
>>>  InitialTranslation[1] = 0;
>>>  InitialTranslation[2] = 0;
>>>  transform->SetTranslation( InitialTranslation );
>>>Registration's result is bad and stops. I saw that transform center is
>>>      
>>>
>[0,0,0].
>  
>
>>>So, I first use intializer (to compute transform center) and
>>>OverrideTranslation with mine.
>>>Is there a better way to initialise the registration?
>>>If I specify a MovingMask, even with good initialization, registration
>>>      
>>>
>stops with this error message: All the points mapped to outside of the
>moving volume.
>  
>
>>>So, my last question is: Is mask initialized with the initialtransform?
>>>      
>>>
>Sorry for the long message but I had to be clear.
>  
>
>>>Laurent.
>>>_______________________________________________
>>>Insight-users mailing list
>>>Insight-users at itk.org
>>>http://www.itk.org/mailman/listinfo/insight-users
>>>      
>>>
>>
>>    
>>
>
>
>
>
>
>
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>  
>