MPRAGEpre – Image Quality

1. MPRAGEpre – Image Quality • Quality is fairly consistent throughout subjects but there are a couple notable outliers: P003 & P025

2. Lesion Segmentation

3. Process • Z-score-based (> 4) one-sided thresholding method on FLAIR registered to MNI 1mm3 • > “raw MNI FLAIR z-score masks” • Similar to tissue segmentation, this seemed to contain speckling that was not clearly associated with lesions to me • Median filtering • > “filtered MNI FLAIR z-score masks” • Used median filtering with a kernel of (3mm)3 to reduce speckle • I presented Hagen with the choice of editing either the raw filtered masks

4. Process • Manual editing • Hagen decided to go work from the raw MNI FLAIR z-score masks • He found the median filtering to be overly aggressive and saw what I had considered as speckling as legitimate lesions • Basic workflow was two passes: remove non-lesion matter such as misclassified skull, add back and correct any lesion boundaries • Hagen focused heavily on the first step and after consideration, felt that most of the pre-lesion boundaries were adequate and actually advantageous because they were not generated by subjective human eyes

5. Post-Process • Warping back to patient space, SPGR target • Thresholding to recover a binary lesion mask • Further editing?

6. P015 – Low CIS – MNI

7. P015 – Low CIS – MNI

8. P015 – Low CIS – FLAIR Space

9. P015 – Low CIS – FLAIR Space

10. P027 – High CIS – MNI

11. P027 – High CIS – MNI

12. P027 – High CIS – FLAIR Space

13. P027 – High CIS – FLAIR Space

14. P001 – RR – MNI

15. P001 – RR – MNI

16. P001 – RR – FLAIR Space

17. P001 – RR – FLAIR Space

18. P016 – SP – MNI

19. P016 – SP – MNI

20. P016 – SP – FLAIR Space

21. P016 – SP – FLAIR Space

22. P021 – PP – MNI

23. P021 – PP – MNI

24. P021 – PP – FLAIR Space

25. P021 – PP – FLAIR Space

26. Quality of Edits • Free of any obvious skull defects • Many lesions remain on sulci, suspicious given limits of standard space registration

27. Thresholding • Relapsing case, P001: • Some lesions are very close to 0 in value, hard to tell if they should be thrown out • Progressive case, P021: • Thresholds of 0.4-0.6 preserve the sometimes smooth transition into surrounding normal tissue • For conservative lesion boundaries, 0.95 or higher • After we settle on a value, compute the volume of “lost” voxels as a measure of how significant the reduction was

28. Remaining Work • Tissue segmentation correction • Reiss group multi-spectral segmentation as an alternative to our lesion masks