Dear FSL experts,
I want to register brains with lesions to a template. I understand that not
doing anything incurs in poor registration, and that using lesion-masking is
not efficient.
FSL website suggests using the "Weighting Volumes" option in FLIRT
(instuctions pasted below). I understand that I can feed a model-brain in
which each voxel is attributed a value going from zero (=non brain) to (to
how much? 1? more?), and then I can also feed a home-made lesioned-brain
with similarly valued-voxels, in which the lesion will be Zero-ed, and
therefore successfully ignored by FLIRT.
That's where my understanding stops, as I have no idea on how am I to create
such images (the weighting image and the image that is weighted).
Can you help?
thank you very much!
fabienne cazalis
[info from fsl website]
> *Weighting Volumes* - impose voxel-wise weighting to reference and/or
>input images, to affects the cost function. The weighting images must be
>the same size as the image they are weighting (e.g. refweight and reference
>images) and the voxel values of the weighting image represent how much
>weighting that particular voxel is given in the cost function. Therefore,
>by setting weights to zero, some areas of the image can be effectively
>ignored, which is useful in masking out pathologies so that they do not
>affect the registration. In this way very accurate registrations can be
>made between pathological and ``normal'' images. This cannot be achieved by
>masking the images prior to registration, as that induces artificial
>boundaries which bias the registration. Furthermore, some areas can be
>given extra weighting (such as the ventricles) so that the registration is
>most accurate near these structures, but still uses information from the
>rest of the image (e.g. the cortical surface) to improve the robustness of
>the registration.
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