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Freesurfer experts,
We're attempting to get some reconstructions on MRI's for very advanced alzheimer's subjects. Many of these subjects have pretty extensive motion artifacts in their acquisitions.
There has been some work with the so-called BLADE sequences to eliminate motion. Indeed, some of the blade sequences produce fairly good contrast. But these acquisitions have slices that aren't normalized for brightness and I think this complicates the reconstruction--see ( https://imgur.com/ZWhBlcm ) for an example.
It seems like we should be able to perform some kind of slice-wise normalization to fix this, but I can't see a good way to do that with the freesurfer tools. Any advice would be greatly appreciated!
Quentin Funk, PhD Houston Methodist Research Institute 713-363-9003tel:713-363-9003
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