6.19 FSL and TBSS

FSL is a comprehensive library of analysis tools for FMRI, MRI, and DTI brain imaging data.

Steps in TBSS:

1. Use medium-DoF nonlinear reg (FNIRT) to pre-align all subjects' FA;
2. "Skeletonise" Mean FA;
3. Threshold Mean FA Skeleton, giving "objective" tract map;
4. For each subject's warped FA, fill each point on the mean-space skeleton with nearest maximum FA value (i.e., from the centre of the subject's nearby tract);
5. Do cross-subject voxelwise stats on skeleton-projected FA and Threshold, (e.g., permutation testing, invluding multiple comparison correction).

TBSS Conclusion: Attempting to solve correspondence/smoothing problems; less ambiguity of interpretation / spurious results than VBM; easier to test whole brain than ROI / tractography. Limitations and Dangers: interpretation of partial volume tracts still an issue. (What is partial volume's definition?) Interpretation of crossing tracts. Future work: use full tensor (for registration and test statistics); use other test statistics (MD, PDD, width); multivariate stats (across voxels and/or different diffusion measures) & discriminant (ICA, SVM).
*Partial volume (Wiki): the loss of apparent activity in small objects or regions because of the limited resolution of the imaging system. e.g. If the object or region to be imaged is less than twice the full width at half maximum resolution in x, y, and z dimension of the imaging system, the resultant activity in the object or region is underestimated. A higher resolution decreases this effect, as it better resolves the tissue. Partial volume loss alone occurs only when the surrounding activity of the object or region is zero (Remember the example Roland Henry mentioned in the research defense). And the loss of activity in the object generally involves an increase in activity in adjacent regions, which are considered outside the object (i.e. spillover). For a small object (e.g. a voxel) or an object of size comparable to the spatial resolution of the imaging system, the observed activity is the sum of activity due to partial volume loss plus spillover from adjacent regions. The method to correct for the partial volume effect is referred to as partial volume correction.
Spillover (increase in activity) is the opposite of partial volume loss.