Hi,
> I used cost-function masking to normalize a lesion brain, but the normalized
> brain is not in the same dimensions as the T1.mnc file; both are 2x2x2 but
> the number of voxels and origins for the datasets are different. Is this
> normal? Why does the normalization the mni atlas not produce a normalized
> brain with the same dimensions as the template brain?
I think you want to check out the normalization defaults (defaults
button, spatial normalization). One of the defaults for writing
normalized is the bounding box, which specifies the voxel dimensions.
You can select the template dimensions there if you like. Most people
doing functional imaging use the default which cuts off things like
the brainstem on the basis that it would waste disk space to write out
those data,
Best,
Matthew
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