Bedpost stands for Bayesian Estimation of Diffusion Parameters obtained using sampling
techniques. Bedpost runs Markov Chain Monte Carlo sampling to build up distributions on diffusion parameters at each voxel. It creates all the
files neccessary for running probabilistic tractography. For an overview of
the modelling carried out within Bedpost see the appendix.

Bedpost takes about 24 hours to run but can easily be parallelised if multiple
processors are available.

To call the FDT GUI, either run **Fdt**, or run **fsl** and press the
**FDT** button. Use the top left drop down menu to select **Bedpost**.

**Input directory:** Use the browse button to select and input directory.
That directory must contain the following files:

**data**: A 4-dimensional series of data volumes. This will include diffusion-weighted volumes and volume(s) with no diffusion weighting.**nodif**: 3D volume with no diffusion weighting**nodif_brain_mask**: 3D binary brain mask volume derived from running**bet**on nodif**bvecs**A text file containing a list of gradient directions applied during diffusion weighted volumes. The order of entries in this file must match the order of volumes in**data**.

The format is

x_1 x_2 x_3 ... x_n

y_1 y_2 y_3 ... y_n

z_1 z_2 z_3 ... z_n

Vectors should be normalised. For volumes in which there was no diffusion weighting, the entry should still be present, although the direction of the vector does not matter!**bvals**A text file containing a list of bvalues applied during each volume acquisition. The order of entries in this file must match the order of volumes in the input data and entries in the gradient directions text file.

The format is

b_1 b_2 b_3 ... b_n

The order of**bvals**must match the order of**data.**

**merged_thsamples**- 4D volume - Samples from the distribution on theta**merged_phsamples**- Samples from the distribution on phi- theta and phi together represent the principal diffusion direction in spherical polar co-ordinates
**merged_fsamples**- 4D volume - Samples from the distribution on anisotropic volume fraction (see here).**mean_thsamples**- 3D Volume - Mean of distribution on theta**mean_phsamples**- 3D Volume - Mean of distribution on phi**mean_fsamples**- 3D Volume - Mean of distribution on*f*anisotropy**dyadic_vectors**- Mean of PDD distribution in vector form. Note that this file can be loaded into fslview for easy viewing of diffusion directions**nodif**- Single volume with no diffusion weighting - copied from input directory**nodif_brain**- brain extracted version of nodif - copied from input directory**nodif_brain_mask**- binary mask created from nodif_brain - copied from input directory

**command line utility**