FSL

### Processing pipeline

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

A typical processing pipeline (and approximate time required for each stage, based on an Intel 2.4GHz processor, and a 60-direction whole brain dataset of dimensions 128x128x64, at 2.5 mm isotropic resolution) would consist of:

1. Any study or scanner-specific pre-processing (e.g., conversion from DICOM to NIFTI, removal of images affected by large artifacts). This would be done manually by the user.
2. Eddy current correction using FDT (around 3 minutes per volume).
3. Brain extraction using BET.
4. dtifit - Fitting of diffusion tensors on corrected data using dtifit within FDT to check data quality (1 minute)
5. bedpostx - Fitting of the probabilistic diffusion model on corrected data (20 hours, or less if parallelised)
6. registration - (3-6 minutes)
7. probtrackx - Probabilistic tractography run on the output of bedpostx (endless.. - depends very much on what the user wishes to do. Generating a connectivity distribution from a single voxel of interest takes about 10 seconds)
8. Further post-processing of probtrackx outputs can be carried out if required using the command-line utilities