Smoothing multi-label brain segmentations

smoothing workflow

1. input: a multi-label map to be smoothed. With structures:

• 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
    ** RCaudate       label 17
    ** RCaudate       label 18
    ** RCaudate       label 11
    ** RCaudate       label 12
    ** RCaudate       label 19
    ** RCaudate       label 20

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