MSmcDESPOT: Baseline vs. 1- year Diagnosis. N008 Baseline SPGR

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– 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

Bias Map for Normals

Bias Map for Normals

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?

SPGR Parallel Coordinate Plot

SPGR Histograms in Whole Brain

SPGR Box Plot

SPGR Interquartile Band Plot

SSFP Parallel Coordinate Plot

SSFP Histograms in Whole Brain

SSFP Box Plot

SSFP Interquartile Band Plot

N008 Baseline/1yr SPGR

N008 Baseline/1-yr SSFP

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

N004 Baseline MWF – All FAs

N004 Baseline MWF – FA18 Dropped

N004 1yr MWF – All FAs

N004 1yr MWF – FA18 Dropped

N004 Baseline/1yr Ratio Map

N008 Baseline MWF – All FAs

N008 1yr MWF – All FAs

N008 Baseline/1yr Ratio Map

0m – Mean MWF in Normals

1yr – Mean MWF in Normals

MPRAGE

IRSPGR

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