FSL
From hpcwiki
FSL is a collection of tools to brain analysis based in a different kinds of images:
Structural Analysis
Made in MRI which exhibits anatomical and structural elements; in the structural MRI measurement three quantities are mainly involved:
- Density of water & fat (Proton density)
- T1 relaxation time
- T2 relaxation time
The relaxation times depend on many things, but are sensitive to micro-environment and hence tissue types. Also, the intensity is usually a complicated weighting of different factors.
MRI exhibits:
- Tissue types: GM (Gray Matter) / WM (White Matter) / CSF (Cerebro-Spinal Fluid)
- Cortical surfaces
- Subcortical Structures
FSL provides a set of tools to analysis brain structure:
| BET | Brain extraction |
|---|---|
| FAST | Tissue segmentation |
| FIRST | Subcortical segmentation |
| FLIRT | Linear registration |
| FNIRT | Non-linear registration |
| FUGUE | EPI unwarping |
| SIENA | Atrophy analysis |
| VMB | grey matter density |
other FSL tools
| FSLView | simple viewer for 3D and 4D data |
|---|---|
| FSLUtils | Set of small applications to analyze and get information of images |
