Tensor Distribution Function

Diffusion magnetic resonance imaging (dMRI) is a powerful tool for studying white matter microstructure features such as white matter connectivity and integrity in the human brain. Diffusion Tensor Imaging (DTI) has been the gold standard for measuring white matter microstructure, but DTI is not sufficient to resolve fiber crossings and intermixing of tracts.

Since the tensor distribution function (TDF) represents the diffusion profile as a probabilistic mixture of tensors, it can be used to reconstruct multiple underlying fibers.

Requirements:

• MATLAB

How to use the toolbox:

1. Step_1 instructions :

sh step_1_TDF.sh --bval /path/bval.txt
                 --bvec /path/bvec.txt
                 --dwi /path/diffusion_image.nii.gz
                 --mask /path/mask.nii.gz
                 --outdir /path/output_directory
                 --tdf /path/TDF_toolbox

2. Step_2 instructions :

• Using local desktop

  SGE_TASK_ID=1
  segments_total=1
  /path/TDF/main_TDF.sh --indir /path/output_directory_step_1 
                        --node_ID ${SGE_TASK_ID} 
                        --max_node ${segments_total} 
                        --sl 1 
                        --tdf /path/TDF_toolbox 
                        --solver quadprog

• Using grid for parallelization

  #$ -N TDF
  #$ -t 1-10
  #$ -q name.q

  # SGE_TASK_ID == Job Array Index (SGE)
  # The total number of nodes/segments
  segments_total=10
  /path/TDF/main_TDF.sh --indir /path/output_directory_step_1 
                        --node_ID ${SGE_TASK_ID} 
                        --max_node ${segments_total} 
                        --sl 1 
                        --tdf /path/TDF_toolbox 
                        --solver quadprog

3. Step_3 instructions :

sh step_3_TDF.sh --indir /path/output_directory_step_2
                 --max_node total_node_used_in_step_2
                 --tdf /path/TDF_toolbox
                 --postfix name_QC_solver_in_step_2 

Use --help to see all options.

Citation

• Leow, A. D., Zhu, S., Zhan, L., McMahon, K., de Zubicaray, G. I., Meredith, M., … & Thompson, P. M. (2009). The tensor distribution function. Magnetic Resonance in Medicine: An Official Journal of the International Society for Magnetic Resonance in Medicine, 61(1), 205-214.
• Zhan, L., Leow, A. D., Jahanshad, N., Chiang, M. C., Barysheva, M., Lee, A. D., … & Thompson, P. M. (2010). How does angular resolution affect diffusion imaging measures?. Neuroimage, 49(2), 1357-1371.
• Zhan, L., Leow, A. D., Zhu, S., Barysheva, M., Toga, A. W., McMahon, K. L., … & Thompson, P. M. (2009, September). A novel measure of fractional anisotropy based on the tensor distribution function. In International Conference on Medical Image Computing and Computer-Assisted Intervention (pp. 845-852). Springer, Berlin, Heidelberg.
• Isaev, D. Y., Nir, T. M., Jahanshad, N., Villalon-Reina, J. E., Zhan, L., Leow, A. D., & Thompson, P. M. (2017, January). Improved clinical diffusion MRI reliability using a tensor distribution function compared to a single tensor. In 12th International Symposium on Medical Information Processing and Analysis (Vol. 10160, p. 101601K). International Society for Optics and Photonics.