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