ricardorios46 / mde_auxtools

Auxiliary functions for a MDE acquisition pipeline.

MDE_auxTools (Beta)

MDE_auxTools contains some useful functions that help to implement B-tensor Encoding sequences on a Bruker scanner. The functions here are intended to use as connectors for other repositories developed by the DW-MRI scientific community to have a complete acquisition pipeline:

Use help in Matlab command window to learn how to use the functions and the inputs needed.

Repositories used in the pipeline:

• NOW
• MCW sequences
• BrkRaw
• MD-dMRI

Requirements

nowToSequence needs that NOW toolbox is already on matlab path.

Notes

brukerRawToImages is still a prototype. Ideally takes raw bruker data and outputs a nifti file with its xps for processing. It uses the pvmatlab toolbox from Bruker (To get this toolbox you need to contact Bruker support). For now it only works with one shape and one gradient amplitude for each acquisition (it works with multiple gradient rotations).

Roadmap for future implementations:

• brukerRawToImages should work with multiple shapes and amplitudes in each acquisition and use open source software.
• Erase pvtools dependency from extractDataFromBrukerRaw.
• Optional basic preprocessing steps.
• Tools for basic visualization/evaluation of data and waveforms.