FSL - NSBLab/MATLAB-connectome-intro GitHub Wiki

Introduction

FSL is a library of useful neuroimaging software tools that we often use in our research. To use FSL on MASSIVE, simply load the module in a terminal with the command: module load fsl

You can also specify which specific version you wish to load: module load fsl/6.04

General Use

The FSL wiki has many tutorials for all the different tools within the library

Key tools for each modality include:

• fMRI - FEAT, MELODIC, FABBER, BASIL
• sMRI - BET, FAST, FIRST, FLIRT, FNIRT
• dMRI - FDT, TBSS, EDDY, TOPUP

Specific tools

ICA and fMRI de-noising

• FIX and AROMA are two useful tools developed by the FSL team for denoising fMRI data through ICA.

• These aren’t currently included in FSL because they have other dependencies, but they are installed as modules on MASSIVE and can be loaded accordingly

e.g., module load fix

MSM

• MSM is an important tool used in cortical registration

• MSM is included in FSL, but MSM_HOCR, a revised version of MSM, needs to be loaded as a separate module

FSLeyes

• FSLeyes is a visualisation software for FSL that can also be used for other neuroimaging data

• Like all visualisation tools on MASSIVE, this will require the addition of 'vlgrun' at the start of your commands

• FSLeyes is required when inspecting FEAT/MELODIC ICA components for FSL-FIX

HCP pipelines

• A commonly used series of neuroimaging pipelines built around FSL and wb_command