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BART and BartIO.jl ​

BART (Berkeley Advanced Reconstruction Toolbox) is a C-based MRI reconstruction toolbox with command-line and Python integration paths. It provides a large set of MRI reconstruction utilities used in research workflows.

Important note:

  • The toolbox is for research use (not diagnostic use).

Minimal BART pipeline example ​

A minimal phantom -> nufft -i example is shown below.

bash
bart phantom -k -t traj kspace
bart nufft -i traj kspace image

BartIO.jl from Julia ​

BartIO.jl is used in this workflow as a Julia-side interface to BART commands and BART file I/O patterns. Common usage examples include:

  • set_bart_path("/path/to/bart")

  • read_cfl(...)

  • write_cfl(...)

  • bart(nargout, "cmd", ...)

Example usage in Julia ​

julia
using BartIO

set_bart_path("/path/to/bart")

traj = bart(1, "traj -x 128 -y 256 -r")
k_phant = bart(1, "phantom -k -t", traj)
im_phant = bart(1, "nufft -i", traj, k_phant)

write_cfl("k_phant", k_phant)
k2 = read_cfl("k_phant")

This is functionally equivalent to CLI calls and keeps the experiment orchestrated inside Julia.

It also keeps file exchange explicit, because BART data can be written and read through .cfl/.hdr in the same script that performs reconstruction calls.

Why BartIO is valuable in this workflow ​

  • run BART without leaving Julia orchestration

  • compare BART output with MRIReco output in one script/notebook

  • preserve reproducibility using Julia-side metadata and plotting

Official sources ​