Smoothing multi-label brain segmentations

Input: a multi-label map to be smoothed

• WM label 3
• CSF label 1
• GM(without the following specified sub-cortical structures) label 2,
• GM sub-cortical structures
  • RCaudate label 13
  • LCaudate label 14
  • RPutamen label 15
  • LPutamen label 16
  • RGlobusPallidus label 17
  • LGlobusPallidus label 18
  • RThalamus label 11
  • LThalamus label 12
  • RHippocampus label 19
  • LHippocampus label 20
• Other
  • Cerebellum Label 6
  • BrainStem Label 5

1. Segmentation using one of the approaches below
2. Up to Affine registration of the subject to bias-corrected, skull-stripped Baseline scan
3. Map the Baseline ICC mask to the State 1 space
4. Skull stripping State 1 scan
5. Bias-correction of State 1 scan
6. Repeat up to affine registration of skull-stripped, bias-corrected State 1 scan to Baseline