MPRAGE Segmentation

Segmentation with Corrected MPRAGE Scans and FSL Jason Su

Homogeneity Correction • Reiss’s CIBSR group noticed a significant bias non-uniformity in the MPRAGE images, described as a “bullseye artifact” • They suggested a few tools correction: homocor3d, N3, and SPM8 • I was not able to obtain a copy of N3, their homepage is currently being transferred elsewhere

Correction Comparison - Original

Correction Comparison – homocor3d

Correction Comparison – SPM8

Correction Comparison • Visually, SPM8 seems to eliminate the bullseye artifact better than homocor3d • SPM8 does over brighten areas outside of the brain, in the neck, which has made brain extraction not as clean • Let’s see how this affects the segmentation, which is what we’re ultimately interested in

FAST Estimated Bias Fields Original

homocor3d

SPM8 • Produces the most uniform field. • This is clearly the better method as was also qualitatively discerned.

N010 – Original – WM

N010 – homocor3d – WM

N010 – SPM8 – WM

Results • The corrected versions show an improved ability to differentiate fine WM structures such as in the cerebellum • The SPM8 segmentation has slightly less speckling • Tissue near the ventricles still classified as GM • Speckling from noise in the scan is a hurdle – Potential fixes: anisotropic diffusion filter, median filter

Median Filtered SPM8 WM Segmentation

Notes and Future Work • I did segmentations for our 6 sample subjects but only showed the normal since that should be our “best case” with no lesions • Try correction with N3 • Multispectral segmentation (Fumiko is doing something along these lines as well) • Segmentation with SPM8 • Segmentation with Freesurfer