Estimate fiber orientations

You’ll need to estimate fiber orientations for tractography. You need to run FSL’s bedpostx on your diffusion data. The input directory, e.g., diffusion_data, must contain the following files:

  • data.nii.gz - the 4D diffusion weighted data

  • bvecs - the b-vectors for the diffusion weighted data

  • bvals - the b-values for the diffusion weighted data

  • nodif_brain_mask.nii.gz - a brain mask for the diffusion weighted data

Tip: Run bedpostx_datacheck in command line to check if your input directory contains the correct files required for bedpostx. Then to run bedpostx, type in command line:

bedpostx <diffusion_data> -n 3

This will create a directory called diffusion_data.bedpostX with the following files:

  • merged_th<i>samples - 4D volume - Samples from the distribution on theta

  • merged_ph<i>samples - 4D volume - Samples from the distribution on phi (theta and phi together represent the principal diffusion direction)

  • merged_f<i>samples - 4D volume - Samples from the distribution on anisotropic volume fraction

  • mean_th<i>samples - 3D volume - Mean of the distribution on theta

  • mean_ph<i>samples - 3D volume - Mean of the distribution on phi

  • mean_f<i>samples - 3D volume - Mean of the distribution on anisotropic volume fraction

  • dyads<i> - Mean of principal diffusion direction in vector form

  • mean_S0samples - 3D volume - Mean of distribution on T2w baseline signal intensity S0

  • mean_dsamples - 3D volume - Mean of distribution on diffusivity

  • mean_d_stdsamples - 3D Volume - Mean of distribution on diffusivity variance parameter d_std (not produced if –model=1)

  • dyads<i>_dispersion` - 3D Volume - Uncertainty on the estimated fibre orientation.

  • nodif_brain_mask - binary mask created from nodif_brain - copied from input directory

For a detailed understanding and any troubleshooting, refer to the BEDPOSTX UserGuide.