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Lesion Segmentation Methodology

Lesion Segmentation Methodology. Purpose. Currently in a dilemma as Hagen did a substantial amount of work editing the z -score FLAIR masks in MNI space, but realize that it is more standard to do such work in patient space

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Lesion Segmentation Methodology

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  1. Lesion Segmentation Methodology

  2. Purpose • Currently in a dilemma as Hagen did a substantial amount of work editing the z-score FLAIR masks in MNI space, but realize that it is more standard to do such work in patient space • Goal of this presentation is to determine how much of Hagen’s work can be salvaged and how much editing needs to be redone with the new patient space method • Secondary goal is to determine if zscore > 2 is a good method for selecting DAWM

  3. 3 Methods to Choose From • Z-score in MNI -> threshold (4, 2) -> patient space -> threshold (.95, .5, 0) • The original method, Hagen edited these • Z-score in MNI -> patient space -> threshold (4, 2) • “z-score in MNI” • Mean and std. dev. in MNI -> patient space -> z-score -> threshold (4, 2) • “z-score in patient space”

  4. P015 – Low CIS – FLAIR

  5. P015 – Low CIS – Original Method, Lesion Cores, Threshold .95

  6. P015 – Low CIS – Original Method, Lesion Cores, Threshold .5

  7. P015 – Low CIS – Original Method, Lesion Cores, Threshold 0

  8. P015 – Low CIS –z-score in MNI, Lesion Cores

  9. P015 – Low CIS –z-score in patient space, Lesion Cores

  10. P015 – Low CIS –z-score in MNI, Lesion Penumbra

  11. P015 – Low CIS –z-score in patient space, Lesion Penumbra

  12. P009– Low CIS – FLAIR

  13. P009– Low CIS – Original Method, Lesion Cores, Threshold .95

  14. P009– Low CIS – Original Method, Lesion Cores, Threshold .5

  15. P009– Low CIS – Original Method, Lesion Cores, Threshold 0

  16. P009– Low CIS –z-score in MNI, Lesion Cores

  17. P009– Low CIS –z-score in patient space, Lesion Cores

  18. P009– Low CIS –z-score in MNI, Lesion Penumbra

  19. P009– Low CIS –z-score in patient space, Lesion Penumbra

  20. Observations • z-score in MNI and in patient space give very similar results, I would argue for z-score in MNI as the better choice for simplicity • The Original Method with threshold 0 is reasonable balance between lesion cores and penumbra, needs a look at by expert eyes • Threshold z-score > 2 fills in obvious DAWM around lesion cores nicely • Not so great job with areas that did not contain a core

  21. Proposed Options • Lesion cores • Keep Hagen’s masks and threshold at .5 after warping to patient space • Alternatively, carry through z-score in MNI method and apply penumbra selection method to them using Hagen’s masks • Lesion penumbra (DAWM) • Z-score in MNI method thresholded at 2 then penumbra selection

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