I am preproccessing with BET to get brain masks prior to running DTIFIT. I
have one scan where the mask has a hole in it at just about any choice of the
fractional intensity threshold (FIT). By a hole I mean a volume within the mask
that is not masked - this volume is in the rough shape of a cylinder running in
the axial direction. Their are obvious non-zero voxels in this hole, so I do not
understand why the masking process avoids this region.
There are only 25 axial slices with 1.76 mm spacing, so I tried the -Z option,
but still get some holes, though I do not have to lower the FIT so far to get
most of the brain in.
Can someone suggest other options to try? Thanks.
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