Neuroimaging Data Processing/Processing/Tools/FSL

Overview of FSL
FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data. It could be used either by FSL main GUI or the commond-lines. The advantage of the GUI lies in its simplicity but the drawback is the less flexibility comparing to the command-lines. FSLView as the display tool could be completely separate use from processing and analysis. Currently FSL only accepts the input files in NIFTI format, and the DICOM files need to be converted to NIFTI after acquisition and before processing. The convertion from DICOM to NIFIT could be fulfilled by several methods, such as dcm2nii from mricron or dcmstack. In the GUI there are nine popular modules are defined, and depending on the input file types, they fall into functional-oriented, structural-oriented or diffusion-oriented modules. The structural-oriented functions include "BET brain extraction", "FAST segmentation", "FLIRT: linear registration"; the functional-oriented functions invole "SUSAN noise reduction","FEAT FMRI analysis" and "MELODIC ICA"; the DTI-oriented functions incorporate "FDT diffusion". Besides these functional modules, there is a simulator called "POSSIUM MRI simulator", which is a software tool to produce realistic simulated MRI and FMRI images or time series. POSSUM (Physics-Oriented Simulated Scanner for Understanding MRI) includes tools for the pulse sequence generation, signal generation, noise addition and image reconstruction.



How to launch FSL
Suppose all the environmental vairables are settled well for FSL, there are two ways to launch FSL, either from the user GUI or command-line.

User GUI
Just type fsl in the console and get access to the main GUI, from where you could reach to the modules by clicking on the options. fsl

Depending on your operating system, you might need to do some additional steps prior to type in this starting command into your console/terminal

If you want to jump to specific modules directly, then just type in the name starting with a capital letter, e.g. Melodic for Melodic ICA Melodic

Command-line
If you want to launch a function from the command line, just type the function name in lowercase, along with the necessary arguments to the function. melodic -i inputfile

Functional MRI data analysis
In FSL, the functional images could be analyzed in two integration workflows, rather than step-by-step as in SPM and AFNI. Analysis for an experiment can be set up in less than 1 minute and finished in 5-20 minutes for the first-level session, producing a web page analysis report, including colour activation images and time-course plots of data vs model.

FEAT is based on general linear modelling (GLM). It allows to describe the experimental design; then a model is created that should fit the data, telling you where the brain has activated in response to the stimuli. In FEAT, the GLM method used on first-level (time-series) data is known as FILM. FILM uses a robust and accurate nonparametric estimation of time series autocorrelation to prewhiten each voxel's time series; this gives improved estimation efficiency compared with methods that do not pre-whiten.



MELODIC is model-free analysis which uses Independent Component Analysis (ICA) to decompose a single or multiple 4D data sets into different spatial and temporal components. MELODIC can pick out different activation and artefactual components without any explicit time series model being specified.

FSLUTILS
FSLUTILS is a set of useful command-line utilities which allow the conversion, processing etc. of Analyze and Nifti format data sets. Many of them work on both 3D and 4D data. For each of these programs, type just the program name to get the usage help. Those commands could be broadly divided into four categories depending on their aims.

1. Mathematical manipulation of images

2. File combination and splitting

3. Header-related utilities

4. Orientation-related Utilities

FSLView
The FSLView could be launched from terminal by typingː fslview --help

1.Cursor view



Box-1 ː show and control the cursor position in voxels

Box-2 ː show and control the cursor position in mm

Box-3 ː shows and controls the current volume in a 4D dataset

Box-4 ː shows the value in the voxel at the current cursor position

2.FSL image overlay



Box-1 ː The layer marked with chevrons to the right of it is the "main layer". This layer is the first one loaded during any given session and cannot be removed from the list as much of the viewer's display capabilities are determined from this layer's attributes.

Box-2 ː Visibilty" checkbox controls whether or not a given layer is visible; "Lock" checkbox determines if a given layer can be edited or not; "Transparency" slider determines how the selected layer blends with the layers below it