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.

The GUI of FSL with nine modules

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

operating system	preparing steps
Linux/Unix	to tell your terminal, that the following commands are referred to the fsl-toolbox, your need to type in FSL in capital letters. Afterwards you will get a message, that your terminal will accept fsl-commands.
Windows	FSL is not running under Windows. Therefore you will need additional software, to emulate another operating system. FSL will run perfectly under a virtual machine like VMware Player or VirtualBox
Mac OS X	no prior steps needed

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

FSL function overviews

Structural image processing

Function	GUI/command	Aim	Online document
BET	Both	Brain extraction	http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/BET
FAST	Both	Tissue segmentation	http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FAST
FIRST	Command	Subcortical segmentation	http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FIRST
FLIRT	Both	Linear registration	http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FLIRT
FNIRT	Command	Nonlinear registration	http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FNIRT
FUGUE	Command	EPI distortion correction	http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FUGUE
SIENA	Command	Atrophy analysis	http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/SIENA
FSL-VBM	Command	Grey matter density	http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FSLVBM

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.

GUI for FEAT with six tabs

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.

GUI for MELODIC with six tabs

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

Function	Aim	Examplary command
fslcc	Run cross-correlations between every volume in one 4D data set with every volume in another	fslcc input1.nii input2.nii (measure similarities in ICA outputs)
fslfft	Outputs the Fast-Fourier Transform (or inverse) for a complex input volume	fslfft input.vol output.vol
fslmaths	Simple but powerful program to allow mathematical manipulation of images	fslmaths func_data.nii -bptf 25.0 -1 func_data_tempfilt.nii (bandpass temporal filtering)
fslmeants	Output the average timeseries of a set of voxels	fslmeants -i input.nii -o mean.txt -m mask (preliminary step for seed-based correlelation)
fslroi	Extract region of interest (ROI) from an image	fslroi input.nii output_roi.nii 0 1 (extract the first volume)

2. File combination and splitting

Function	Aim	Examplary command
fslcomplex	Allow 3D or 4D complex image files to be split or constructed from corresponding real components	fslcomplex -complexsplit source dest 1 3
fslinterleave	Interleave two inputs to form a combined image, and this combination is in Z axis only	fslinterleave input1 input2 output
fslmerge	Concatenate image files into a single output. This concatenation can be in time, X, Y or Z axis	fslmerge -t outfile infile1 infile2 (concatenate files in time series)
fslslice	Split a 3D file into lots of 2D files along Z-axis.	fslslice volfile slicefile
fslsplit	Split a 4D file into lots of 3D files in either time, X,Y,or Z axis	fslsplit -t input outfileprefix (split volumes along time series)

3. Header-related utilities

Function	Aim	Examplary command
fslcpgeom	Copy certain parts of the header information from one image to another with identical file type.	fslcpgeom source dest
fslcreatehd	Creates a new image header along with a zero intensity data image.	fslcreatehd
fslhd	Report every field of an Analyze or Nifti header	fslhd input.nii
fslinfo	Report a basic subset of an Analyze or Nifti header.	fslinfo input.nii
fslval	Report a particular parameter from an image header	fslval input.nii

4. Orientation-related Utilities

Function	Aim	Examplary command
fslreorient2std	Reorient an image to match the orientation of the standard template images (MNI152), but this only rotated to 90, 180 or 270 degree and can't substitute coregistration	fslreorient2std input output
fslorient	Advanced tool that reports or sets the orientation information in a file	fslorient -forceradiological input
fslswapdim	Advanced tool that re-orders the data storage to permit changes between axial, sagittal and coronal slicing	fslswapdim

FSLView

The FSLView could be launched from terminal by typingː

 fslview --help

1.Cursor view

FSL cursorview

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

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

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

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

2.FSL image overlay

FSL image overlay

Box-1ː 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-2ː 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