FSL

### Introduction

For other information on FDT and updated journal references, see the FDT web page. If you use FDT in your research, please quote the journal references listed there.

FDT (FMRIB's Diffusion Toolbox) is a software tool for analysis of diffusion weighted images. FDT is part of FSL (FMRIB's Software Library) . FDT has an easy-to-use graphical user interface (GUI) and its component programmes can also be run from the command line. FDT includes tools for data preprocessing, local diffusion modelling and tractography. Each stage in FDT is run separately. The main FDT programmes, which are accesible from the GUI are:

- eddycorrect - for correction of eddy current distortion
- bedpostx - for local modelling of diffusion parameters.
- probtrackx - for tractography and connectivity-based segmentation
- dtifit - for local fitting of diffusion tensors

The FDT GUI also includes a registration option that registers images using FLIRT.

Additional FDT utilities, that can be run only from the command line, are:

- proj_thresh - for thresholding some outputs of probtrack
- find_the_biggest - for performing hard segmentation on the outputs of connectivity-based thresholding in probtrack
- vecreg - for registering vector data
- qboot - for estimating fibre orientations and their uncertainty using ODFs and bootstrapping

The probabilistic tractography tools within FDT are very flexible and allow the user to generate connectivity distributions from single or multiple voxels, or from a FreeSurfer cortical surface; to limit these distributions based on anatomical criteria and to perform segmentation based on the probability of connection to user-defined target regions.

To call the FDT GUI, either run Fdt (Fdt_gui on Mac or Windows), or run fsl and press the FDT button.

For an overview of the local diffusion modelling and tractography used within FDT see the appendix.