Registration in EMSegmenter Module

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Registration in EMSegmenter Module

Nicos Markides
Hello,

My question is on the EMSegmenter Module with atlas, where we have to specify the atlas to
dataset registration parametres. I want to register the atlas_t1 which is given by the Slicer with
the T2 MR Image of my patient. Actually I don't understand why the type of registration is Affine, and
how can i change it if I want to ? Can i use the General Registration to do it ? 
Also, in what Module can I perform the BiasFieldCorrection in Slicer 4.1 ?

Thank you, Nikos

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Re: Registration in EMSegmenter Module

Kilian Pohl
On 08/19/2012 11:27 AM, Nicos Markides wrote:
Hello,

My question is on the EMSegmenter Module with atlas, where we have to specify the atlas to
dataset registration parametres. I want to register the atlas_t1 which is given by the Slicer with
the T2 MR Image of my patient.
If you want to then I can make the T2 image of the atlas accessible and then you could perform atlas T2 to subject T2 registration. You could then load it in Slicer, Rename in Step 2 T1 to T2,  and assign it in Step 5
Actually I don't understand why the type of registration is Affine, and
how can i change it if I want to ?
By default it is non-rigid - look at stpe 5

Can i use the General Registration to do it ? 
You can choose the packages listed in Step5 as long as they are installed on your machine
Also, in what Module can I perform the BiasFieldCorrection in Slicer 4.1 ?
EM does the Biasfield correction for you - it uses N4 ITK Bias Field Correction - you can also run it separately as a module

Kilian
 

Thank you, Nikos


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