6.25 VA Reading - Smith 2004 Neuroimage

Smith SM, Jenkinson M, Woolrich MW, Beckmann CF, Behrens TEJ, Johansen-Berg H, Bannister PR, De Luca M, Drobnjak I, Flitney DE, Niazy RK, Saunders J, Vickers J, Zhang Y, De Stefano N, Brady JM, Matthews PM (2004). Advances in functional and structural MR image analysis and implementation as FSL. NeuroImage; 23: S208-S219.

The fundamental challenge in the analysis of functional MRI experiments is to identify voxels that show signal changes varying with changing brain states. Difficult in three ways:

1. SNR is generally poor, with the activation signal being often no larger than the noise level;
2. The neurophysiology that couples the underlying brain activity to the measured response in FMRI is complex and generally poorly understood;
3. The noise consists of a complex blend of spatiotemporal deterministic and stochastic components due to physiological and scanner-based artefacts.

Different analyses techniques for functional MRI research:

1. FILM - voxel wise series analysis
2. FLAME - multilevel modeling for group analysis
3. FEAT - a complete tool for model-based FMRI analysis
4. Bayesian inference on constrained linear basis sets for HRF models
5. MELODIC - probablistic independent component analysis for FMRI
6. Inference via spatial mixture modeling

Different analyses techniques for structural MRI research:

1. BET - brain-nonbrain segmentation
2. FAST - tissue-type segmentation and bias field correction
3. FLIRT - affine intermodal image registration
4. MCFLIRT and FORCE - head motion correction
5. SIENA - brain change analysis

FDT - diffusion and white matter connectivity analysis: the sensitivity of this "diffusion tractography" process to, for example, image noise, partial volume effects, and incomplete signal modeling, has meant that, in general, tractography has been limited to major white matter pathways that are easily found in postmortem dissection. Estimate the probablity density functions (pdfs) on fiber direction leads to being able to quantify belief in the existence of axonal connections between brain regions. By removing the need to make a deterministic decision at every step in the tractography process, we are able to trace beyond regions of low diffusion anisotropy and deep into grey matter structures.

FSL - FMRIB's software library: FMRIB's Software Library. Available as both source code and as self-contained binary distributions for many platforms. Freely available for academic (noncommercial) use. Additional help is available via the FSL email list at www.jiscmail.ac.uk/lists/fsl.html