Brain imaging data analysis tool FSL 6.0.7.3 Windows | macOS | Linux

FSL can be used for macOS (Intel and M1/M2) and Linux, and Windows computers are supported through the Windows Linux subsystem (WSL). If you want to compile the code yourself, the source code is downloaded and installed as part of the standard installation.

What is FSL?

The full name is: F MRIB’s  S oftware  L ibrary

• FMRIB is the Brain Functional Magnetic Resonance Imaging Center of Oxford University, UK, and FSL is a software library developed by them.
• Developed by Professor Stephen Smith and released in 2000
• Applicable to all operating systems
• Used for structural MRI, functional MRI (task, resting), diffusion MRI analysis
• Preprocessing and analysis of MRI and CT data
• Review of MRI and CT data

Specifically, it can be divided into the following four types of functions

1 Structural MRI

• Registration: linear (FLIRT)&non linear (FNIRT)
• Brain segmentation/extraction (BET)
• Organization type segmentation (FAST)
• Subcortical structure segmentation (FIRST)
• Voxel GM density analysis (FSLVBM)
• Shrinkage estimation (SIENA)

2 . Functional MRI

• Motion correction (MCFLIRT)
• EPI distortion correction (FUGUE, PRELUDE)
• Model based analysis (FEAT)
• ICA analysis without model: model free ICA based analysis (MELODIC)
• Bayesian analysis of perfusion, ASL data
  (FABBER, VERBENA, BASIL)

3 Diffusion MRI

• Distortion correction (TOPUP)
• Eddy current correction (EDDY)
• Diffusion toolbox (FDT)
• Spatial statistics: tract based spatial statistics (TBSS)

4 Others
The first three functions are aimed at specific research groups, but the other gadgets are suitable for processing MRI, CT and other images, which are very practical.

Application examples of FSL

1. Segmentation - brain image extraction/decapitation

The brain image of ordinary scanning contains a lot of tissues.
In addition to brain tissue, it also includes skin, skull, eyeball, mouth, throat and other anatomical structures, which will affect our analysis of the brain. Therefore, we hope to segment brain tissue and non brain tissue automatically.
You can use it here bet Function, this process can be called [bone removal/brain tissue extraction]

Seen from the figure, the operation is also very simple. One command will do it. Orange and purple areas on the picture are the extracted brain tissue.

2. Split - Organization Split

In the above, we only segment the brain tissue from the image. Further, we can segment the brain parenchyma to separate white matter (WM), gray matter (GM) and nucleus (CSF).
This task is equivalent to three types of segmentation of brain tissue.

You can use it here FAST Function.

3. Registration

The registration function is also very powerful, with many standard spaces built in.
Functions used here FLIRT: Linear transformation ,  FNIRT: nonlinear transformation

However, both segmentation and registration have limitations: it only works on MRI brain data, because FSL itself is a brain image data processing software.

What else can we do without MRI brain data?

Some general functions are briefly introduced as follows:

4. Use FSLeyes to view images

This tool is a bit like PS tool, which can overlay several layers for display. For example, the bottom layer is the original image, and the upper layer is the segmentation result.
Recommended level of this function: ⭐ ️ ⭐ ️ ⭐ ️ ⭐ ️ ⭐ ️

5. Fslutils Toolkit

FSLUTILS It is a set of useful command line utilities that allow analysis and conversion and processing of Nifti format data sets. 3D and 4D data can be processed simultaneously. For each of these programs, just type the program name to get help.

List several common commands:

• Fslcpgeom – Copy some parts of the title information (image size, voxel size, voxel size unit string, image direction/) from one image to another
• Fslinfo – Header file information for reporting Nifti data
• Fslmaths – Simple but powerful program that allows mathematical processing of images
• Fslmerge – Merge multiple image files
• Fslroi – Extract Region of Interest (ROI) from image
• Fslslice – Split 3D files into many 2D files (along the z-axis)
• Fslsplit – Split a 4D file into many 3D files
• Fslorent – Report the acquisition direction information of the image

The above is just a brief introduction to FSL. It is easy to get started with FSL common tools. However, it will be difficult to use FSL to analyze the neuroimaging.

FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data. It runs on Apple and PCs (both Linux, and Windows via a Virtual Machine), and is very easy to install. Most of the tools can be run both from the command line and as GUIs (“point-and-click” graphical user interfaces). To quote the relevant references for FSL tools you should look in the individual tools’ manual pages, and also please reference one or more of the FSL overview papers:

1. M.W. Woolrich, S. Jbabdi, B. Patenaude, M. Chappell, S. Makni, T. Behrens, C. Beckmann, M. Jenkinson, S.M. Smith. Bayesian analysis of neuroimaging data in FSL. NeuroImage, 45:S173-86, 2009
2. S.M. Smith, M. Jenkinson, M.W. Woolrich, C.F. Beckmann, T.E.J. Behrens, H. Johansen-Berg, P.R. Bannister, M. De Luca, I. Drobnjak, D.E. Flitney, R. Niazy, J. Saunders, J. Vickers, Y. Zhang, N. De Stefano, J.M. Brady, and P.M. Matthews. Advances in functional and structural MR image analysis and implementation as FSL. NeuroImage, 23(S1):208-19, 2004
3. M. Jenkinson, C.F. Beckmann, T.E. Behrens, M.W. Woolrich, S.M. Smith. FSL. NeuroImage, 62:782-90, 2012

Overview of FSL tools

Functional MRI: FEAT, MELODIC, FABBER, BASIL, VERBENA
Structural MRI: BET, FAST, FIRST, FLIRT & FNIRT, FSLVBM, SIENA & SIENAX, MIST, BIANCA, MSM, fsl_anat
Diffusion MRI: FDT, TBSS, eddy, topup
GLM / Stats: GLM general advice, Randomise, Cluster, FDR, Dual Regression, Mm, FLOBS
Other: FSLeyes, FSLView, Fslutils, Atlases, Atlasquery, SUSAN, FUGUE, MCFLIRT, Miscvis, POSSUM, BayCEST

Official website: https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FSL

Download address

Get the official download address:
https://fsl.fmrib.ox.ac.uk/fsldownloads_registration
FSL 6.0.7.3 installation script (Win | Mac | Linux):
https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/fslinstaller.py
https://pan.quark.cn/s/d0c2014de0c8
https://www.123pan.com/s/PjcA-O9ORA.html
http://ctfile.luochenzhimu.com/d/13552432-58069401-242018
https://pan.baidu.com/s/1_CCS6-GvSL2AKC2dhd1UXA?pwd=a919

Installation Guide
Windows computers are installed through Windows Linux subsystem (WSL) Ubuntu:
https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation/Windows
Installation of macOS system
https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation/MacOsX
Linux Installation Guide:
https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation/Linux

Installation case:
[Create Brain Imaging Workstation] FSL Graphic and Text Tutorial for Windows Installation
https://zhuanlan.zhihu.com/p/618637035