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)

• 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

Another Look at Multi-Channel Segmentation with FSL FAST

MPRAGE

• Same slices as shown in the z-score slides• Lesions of interest circled

SPGR 3 class-CSF

• Generally good CSF segmentation• Does not capture most lesions

SPGR 3 class-GM

• Includes some or all of lesions

SPGR 3 class-WM

• Matches nicely with the MPRAGE scan• Partially includes lesions

SPGR 4 class-CSF

• Generally worse than 3 class CSF

SPGR 4 class-GM

• More conservative estimate of GM, much fewer lesions included

SPGR 4 class-More GM

• Deep GM• Includes many of the lesions

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

• Grabs most lesions• Unfortunately mis-classifies GM too

SPGR-FLAIR 3 class-GM

• Includes many regions previously seen as 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

• Generally worse than 3 class CSF also• Chokes back mask too far

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

• Again mis-includes a lot of 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

• Decent at outside brain CSF, though catches some WM

• Does not get any CSF inside brain

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

• Overly greedy WM• Misses focal lesions but gets GM

SPGR-T2-PD 4 class-CSF

• Same problems as with SPGR-T2-PD CSF segmentation

SPGR-T2-PD 4 class-GM

• GM + inner CSF• Catches darker lesions• Pretty poor, also gets WM

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

• A conservative estimate• Circled region shows possible inclusion of GM

and missing of brain stem

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

• SPGR 3 class (best anatomically)• SPGR 4 class (conservative)• SPGR-FLAIR 4 class (more lesion exclusion)

Best GM

• SPGR 3 class (GM+lesions)

• SPGR 4 class (deep GM+lesions)

Best Lesion

• SPGR 3 class (GM+lesions)

• SPGR-FLAIR 3 class (CSF missing some lesions)

Coming Soon

• Segmentation with a priori maps

• Ideas about how to combine maps to produce NAWM, NAGM, and lesion only masks