Step By Step Guides

The step by step guides are provided here as simple recipes to introduce the use of a particular type of analysis. However, FSL is a very flexible toolset and there are many variants for each kind of analysis beyond those presented here. These outlines are therefore not universal recommendations, but intended as a first introduction for learning how to use tools in FSL.

• Initial Processing (for all modalities)

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Structural Imaging

• Brain Extraction (BET)

• Registration (FLIRT/FNIRT)

• Tissue-Type Segmentation and Bias-Field Correction (FAST)

• Subcortical Structure Segmentation (FIRST)

• Voxel-Based Morphometry (VBM)

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Diffusion Imaging

• Diffusion Tensor Fitting (DTIFIT)

• TBSS (voxel-wise analysis of local diffusion measures)

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FMRI Imaging

• First-Level Task FMRI (FEAT)

• Higher-Level Task FMRI (FEAT)

• Resting-State FMRI (dual regression)

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