1. P025 MPRAGE Pre-Contrast

2. P025 MPRAGE w/ Z-Score < -4

3. Notes This was accomplished by doing an inverse nonlinear warp from MNI to the SPGR FA 18, then to the MPRAGE space with a linear transform (ideally these transforms should be combined) Images are larger than shown, zoom in for more detail Not all lesions are found by the z-score thresholding but a significant amount are Large volumes of white matter are found to be significantly demyelinated: perhaps DAWM or actually revealing the “invisible disease”? This was one the patients with a larger amount of low MWF volume, EDSS 5.0 SPMS

4. Another Look at Multi-Channel Segmentation with FSL FAST

5. MPRAGE Same slices as shown in the z-score slides Lesions of interest circled

6. SPGR 3 class-CSF Generally good CSF segmentation Does not capture most lesions

7. SPGR 3 class-GM Includes some or all of lesions

8. SPGR 3 class-WM Matches nicely with the MPRAGE scan Partially includes lesions

9. SPGR 4 class-CSF Generally worse than 3 class CSF

10. SPGR 4 class-GM More conservative estimate of GM, much fewer lesions included

11. SPGR 4 class-More GM Deep GM Includes many of the lesions

12. SPGR 4 class-WM Does well at excluding most focal lesions but appears to be some partially including some More conservative

13. SPGR-FLAIR 3 class-CSF Grabs most lesions Unfortunately mis-classifies GM too

14. SPGR-FLAIR 3 class-GM Includes many regions previously seen as WM

15. SPGR-FLAIR 3 class-WM Good exclusion of lesions identified by z-score Does poorly at WM and GM segmentation, misses some WM

16. SPGR-FLAIR 4 class-CSF Generally worse than 3 class CSF also Chokes back mask too far

17. SPGR-FLAIR 4 class-GM Still misidentifies a lot of WM as GM Catches edges of our lesions of interest

18. SPGR-FLAIR 4 class-More GM Again mis-includes a lot of WM

19. SPGR-FLAIR 4 class-WM Avoids lesions but also misses a lot of regular WM since those are misidentified as GM

20. SPGR-T2-PD 3 class-CSF Decent at outside brain CSF, though catches some WM Does not get any CSF inside brain

21. SPGR-T2-PD 3 class-GM Captures our lesions of interest Gets ventricle CSF Not as good as SPGR 3 class

22. SPGR-T2-PD 3 class-WM Overly greedy WM Misses focal lesions but gets GM

23. SPGR-T2-PD 4 class-CSF Same problems as with SPGR-T2-PD CSF segmentation

24. SPGR-T2-PD 4 class-GM GM + inner CSF Catches darker lesions Pretty poor, also gets WM

25. SPGR-T2-PD 4 class-More GM Catches some lesions but overall pretty garbagey Doesn’t really correspond to a distinct tissue class

26. SPGR-T2-PD 4 class-WM A conservative estimate Circled region shows possible inclusion of GM and missing of brain stem

27. Best CSF SPGR 3 class (includes some lesions) SPGR-FLAIR 3 class (includes all lesions) SPGR-T2-PD 3 class (useful for out of brain CSF, does not include lesions)

28. Best WM SPGR 3 class (best anatomically) SPGR 4 class (conservative) SPGR-FLAIR 4 class (more lesion exclusion)

29. Best GM SPGR 3 class (GM+lesions) SPGR 4 class (deep GM+lesions)

30. Best Lesion SPGR 3 class (GM+lesions) SPGR-FLAIR 3 class (CSF missing some lesions)

31. Coming Soon Segmentation with a priori maps Ideas about how to combine maps to produce NAWM, NAGM, and lesion only masks