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P025 MPRAGE Pre-Contrast. P025 MPRAGE w/ Z-Score < -4. 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)

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notes
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
mprage
MPRAGE
  • Same slices as shown in the z-score slides
  • Lesions of interest circled
spgr 3 class csf
SPGR 3 class-CSF
  • Generally good CSF segmentation
  • Does not capture most lesions
spgr 3 class gm
SPGR 3 class-GM
  • Includes some or all of lesions
spgr 3 class wm
SPGR 3 class-WM
  • Matches nicely with the MPRAGE scan
  • Partially includes lesions
spgr 4 class csf
SPGR 4 class-CSF
  • Generally worse than 3 class CSF
spgr 4 class gm
SPGR 4 class-GM
  • More conservative estimate of GM, much fewer lesions included
spgr 4 class more gm
SPGR 4 class-More GM
  • Deep GM
  • Includes many of the lesions
spgr 4 class wm
SPGR 4 class-WM
  • Does well at excluding most focal lesions but appears to be some partially including some
  • More conservative
spgr flair 3 class csf
SPGR-FLAIR 3 class-CSF
  • Grabs most lesions
  • Unfortunately mis-classifies GM too
spgr flair 3 class gm
SPGR-FLAIR 3 class-GM
  • Includes many regions previously seen as WM
spgr flair 3 class wm
SPGR-FLAIR 3 class-WM
  • Good exclusion of lesions identified by z-score
  • Does poorly at WM and GM segmentation, misses some WM
spgr flair 4 class csf
SPGR-FLAIR 4 class-CSF
  • Generally worse than 3 class CSF also
  • Chokes back mask too far
spgr flair 4 class gm
SPGR-FLAIR 4 class-GM
  • Still misidentifies a lot of WM as GM
  • Catches edges of our lesions of interest
spgr flair 4 class more gm
SPGR-FLAIR 4 class-More GM
  • Again mis-includes a lot of WM
spgr flair 4 class wm
SPGR-FLAIR 4 class-WM
  • Avoids lesions but also misses a lot of regular WM since those are misidentified as GM
spgr t2 pd 3 class csf
SPGR-T2-PD 3 class-CSF
  • Decent at outside brain CSF, though catches some WM
  • Does not get any CSF inside brain
spgr t2 pd 3 class gm
SPGR-T2-PD 3 class-GM
  • Captures our lesions of interest
  • Gets ventricle CSF
  • Not as good as SPGR 3 class
spgr t2 pd 3 class wm
SPGR-T2-PD 3 class-WM
  • Overly greedy WM
  • Misses focal lesions but gets GM
spgr t2 pd 4 class csf
SPGR-T2-PD 4 class-CSF
  • Same problems as with SPGR-T2-PD CSF segmentation
spgr t2 pd 4 class gm
SPGR-T2-PD 4 class-GM
  • GM + inner CSF
  • Catches darker lesions
  • Pretty poor, also gets WM
spgr t2 pd 4 class more gm
SPGR-T2-PD 4 class-More GM
  • Catches some lesions but overall pretty garbagey
  • Doesn’t really correspond to a distinct tissue class
spgr t2 pd 4 class wm
SPGR-T2-PD 4 class-WM
  • A conservative estimate
  • Circled region shows possible inclusion of GM and missing of brain stem
best csf
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)
best wm
Best WM
  • SPGR 3 class (best anatomically)
  • SPGR 4 class (conservative)
  • SPGR-FLAIR 4 class (more lesion exclusion)
best gm
Best GM
  • SPGR 3 class (GM+lesions)
  • SPGR 4 class (deep GM+lesions)
best lesion
Best Lesion
  • SPGR 3 class (GM+lesions)
  • SPGR-FLAIR 3 class (CSF missing some lesions)
coming soon
Coming Soon
  • Segmentation with a priori maps
  • Ideas about how to combine maps to produce NAWM, NAGM, and lesion only masks
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