BedpostX

Tool for estimating multiple fibre orientations from diffussion MRI on NVIDIA GPUs

Part of FSL (FMRIB Software Library)

For information about the functionality of the tool, see the BEDPOSTX User Guide

This page provides binary downloads of the GPU version of Bedpostx.

Installation

  • Download the correct bedpostx_gpu file for your CUDA version
  • Unzip bedpostx_gpu file
  • Copy all the files from bin directory into your $FSLDIR/bin directory
  • Copy all the files from lib directory into your $FSLDIR/lib directory
  • To execute it use: $FSLDIR/bin/bedpostx_gpu

FSL 6.x FILES

CUDA 11.3 or later version binaries will be supported within FSL installer starting from FSL 6.0.6

Speedup

GPU BedpostX offers accelerations of more than 200 times using a single GPU compared to a single CPU core: 1 GPU ≈ 200 CPU cores.

Execution times in logarithmic scale of a single CPU core and a single GPU (NVIDIA K80) fitting ball & sticks model in a whole dataset. The application fits the model in a low resolution dataset with 106,910 voxels and in a high resolution dataset with 684,203 voxels. Different number of diffusion measurements (36/72/108/145/181/218/254/291) and number of fibres (1/2/3 with 6/9/12 parameters) are showed.

Measurements 36 72 108 145 181 218 254 291
Low-res 1 fibre 96× 145× 167× 175× 183× 195× 202× 196×
Low-res 2 fibres 98× 149× 174× 180× 193× 206× 217× 207×
Low-res 3 fibres 92× 144× 172× 195× 210× 225× 235× 220×
High-res 1 fibre 99× 148× 171× 180× 214× 225× 233× 227×
High-res 2 fibres 109× 168× 196× 203× 215× 232× 238× 230×
High-res 3 fibres 96× 163× 194× 201× 209× 223× 236× 221×

Citation

If you use Bedpostx GPU in publications, please cite this paper:

Hernández M, Guerrero GD, Cecilia JM, García JM, Inuggi A, Jbabdi S, Behrens TE, Sotiropoulos SN. Accelerating fibre orientation estimation from diffusion weighted magnetic resonance imaging using GPUs. PLoS One. 2013 Apr 29;8(4):e61892

Credits

  • Moises Hernandez Fernandez (FMRIB, University of Oxford, UK)
  • Stamatios N Sotiropoulos (FMRIB, University of Oxford, UK)
  • Gines D. Guerrero (University of Murcia, Spain)
  • José M. Cecilia (University of Murcia, Spain)
  • José M. García (University of Murcia, Spain)
  • Timothy E. J. Behrens (FMRIB, University of Oxford, UK)
  • Saad Jbabdi (FMRIB, University of Oxford, UK)
  • Alberto Inuggi (Basque Center on Cognition, Brain and Language, Spain)

Part of FSL (FMRIB Software Library)

License Infomation