Hi all,
I've just started using FSL and I have two questions with regards to the preprocessing steps in FSL.
1. Structural images:
The same set of structural images have different orientations when viewed with different programs. For example, the coronal slices are flipped 90 degrees in FSLview (i.e. neck to top of the head is left to right on the screen), while as they are upright in MRIcron. Does this matter when I'm registering functional runs to the structural images using FEAT? Will it try to register the runs to a tilted structural scan?
2. BET:
I'm also running BET on my structural scans. I remember reading somewhere that the fractional intensity threshold shouldn't be changed (default = 0.5). But I found with that threshold quite a bit of area on the edges of the brain is omitted. A 0.3 will ensure that the whole brain is included but it will also include some of the skull. Should I be prefer leaving out brain areas to including parts of the skull?
Thanks in advance!
Best,
Jane
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