Hi all!
I have a data set with lesions (diffusion weighted images and structural T1 images). I will be running through FdtRegistration to register the diffusion image to its structural image, and then registering the structural image to the MNI standard. The warp will be used for tractography purposes.
I have read that we should create a lesion mask, and properly invert this mask to be 0s where the lesion is and 1s where the lesion is not. This will be applied to the flirt (diffusion to structural, structural to standard) and to fnirt (structural to standard) as inputs. This is clear to me.
However, I am not sure if I should independently create a lesion mask in the diffusion space and separately also in the structural space. I ask this since the diffusion data shows a lesion of different shape than the structural data.
Also, I am unsure how to verify that the registration worked properly in the lesioned area. Once the structural is "fnirted" to standard space, should I expect to see the lesion with its same shape in the standard space, or should I expect this lesion to be warped as well?
Thank you so much in advance!
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Miguel
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