[Insight-users] Masks & registration

[Laurent PAUL]

Hi Karthik,

If I understand what it means (sorry I'm french! I'm not english fluent
speaking), MovingMask is tranformed with the initialTransform provided by
te initializer.
If so, I don't understand why metric is never computed when I use
MovingMask...

Laurent.


> 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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>>
>