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MSmcDESPOT : Baseline vs. 1-year Diagnosis

MSmcDESPOT : Baseline vs. 1-year Diagnosis. N008 Baseline SPGR. N008 1-year SPGR. SPGR WM ROI Signal Curves. SSFP 180 WM ROI Signal Curves. SPGR Signal Cures in GM. SSFP Signal Cures in GM. Signal Values. As noted before, they are quite low 50-80 range across the brain for spgr_fa11

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MSmcDESPOT : Baseline vs. 1-year Diagnosis

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  1. MSmcDESPOT: Baseline vs. 1-year Diagnosis

  2. N008 Baseline SPGR

  3. N008 1-year SPGR

  4. SPGR WM ROI Signal Curves

  5. SSFP 180 WM ROI Signal Curves

  6. SPGR Signal Cures in GM

  7. SSFP Signal Cures in GM

  8. Signal Values • As noted before, they are quite low • 50-80 range across the brain for spgr_fa11 • Similar range for ssfp180_fa41, excluding CSF (in 200-300 range) • We notice a mean shift in the signal curve, which is compensated for in the fitting algorithm (though still unexplained) • I also generated these same plots for N004 and found the same problem with spgr_fa18

  9. Bias Map for Normals

  10. Bias Map for Normals

  11. Thoughts • Collection seems good after normalization with the exception of fa18 • Need to determine IRSPGR parameters then Cyndi can probably go ahead with new scans? • Correction of fa18 or MWF bias correction?

  12. SPGR Parallel Coordinate Plot

  13. SPGR Histograms in Whole Brain

  14. SPGR Box Plot

  15. SPGR Interquartile Band Plot

  16. SSFP Parallel Coordinate Plot

  17. SSFP Histograms in Whole Brain

  18. SSFP Box Plot

  19. SSFP Interquartile Band Plot

  20. N008 Baseline/1yr SPGR

  21. N008 Baseline/1-yr SSFP

  22. More Thoughts • spgr_fa18 seems quite different between baseline and 1yr • Affects mcDESPOT mapping • Perhaps also leads to registration error though it’s not clear to me why • Poor sampling of SSFP curve for cortical GM, need to go back to signal eqns. to figure out why curve would look like this

  23. N004 Baseline MWF – All FAs

  24. N004 Baseline MWF – FA18 Dropped

  25. N004 1yr MWF – All FAs

  26. N004 1yr MWF – FA18 Dropped

  27. N004 Baseline/1yr Ratio Map

  28. N008 Baseline MWF – All FAs

  29. N008 1yr MWF – All FAs

  30. N008 Baseline/1yr Ratio Map

  31. 0m – Mean MWF in Normals

  32. 1yr – Mean MWF in Normals

  33. MPRAGE

  34. IRSPGR

  35. Conclusions • Should focus on WM comparisons between baseline and 1yr • Avoid whole brain to prevent errors due bias in GM (was used in the regression model) • Restrict ourselves one step further, focus on WM and regions where there was not much change in normals between baseline and 1yr • Trying to avoid potential criticism of applying a bias correction • How to define WM? • Intersection of baseline and 1yr segmentations? • Only use edited baseline WM? This would be like asking, how has this region changed, ignoring possible changes in the shape of the WM boundary • Tissue volume measures are no longer easy for us to obtain in a manner that’s meaningful to compare to baseline due to MPRAGE->IRSPGR change • Requires extensive editing to get similar tissue volumes which introduces a lot of noise due to human intervention

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