MRITwixTools.jl

Native Julia package for reading Siemens MRI raw data (twix .dat files).

A port of the Python packages twixtools and pymapVBVD, and the Matlab package mapVBVD, supporting both VB and VD/VE/XA software versions.

Installation

using Pkg
Pkg.add("MRITwixTools")

Or in development mode:

Pkg.develop("MRITwixTools")

Quick Start

using MRITwixTools

# Read a twix file (returns raw data by default — no processing)
twixObj = read_twix("meas_MID00305.dat")

# For multi-raid files (VD/VE/XA), twixObj is a Vector{TwixObj}
# For single-raid files (VB), it is a single TwixObj

# Read image data
data = getdata(twixObj.image)

# Or with slicing (1-based Julia indexing)
data = twixObj.image[1:128, :, :]

# Check available scan types
MDH_flags(twixObj)  # e.g. ["image", "noise", "refscan"]

Comparison with Other Twix Readers

Several tools exist for reading Siemens twix (.dat) files:

mapVBVD — the original MATLAB tool by Philipp Ehses
pymapVBVD — Python port by Will Clarke
twixtools — Python reader/writer with low-level mdb access by Philipp Ehses

Defaults

	mapVBVD (MATLAB)	pymapVBVD (Python)	twixtools (Python)	MRITwixTools.jl
Indexing	1-based	0-based	0-based	1-based
`removeOS`	`false`	`True`	`False`	`false`
`regrid`	`false`	`True`	`False`	`false`

Syntax

	mapVBVD	pymapVBVD	twixtools	MRITwixTools.jl
Read data	`twix.image()`	`twix.image['']`	loop over `mdb` list	`getdata(twix.image)`
Slice data	`twix.image(:,:,1)`	`twix.image[:,:,0]`	—	`twix.image[:,:,1]`
Squeeze	`twix.image{''}`	`.squeeze = True`	manual	`.squeeze = true`
Set flag	`.flagRemoveOS = 1`	`.flagRemoveOS = True`	`.flags['remove_os']`	`.removeOS = true`
Header	`hdr.MeasYaps` (struct)	`hdr.MeasYaps[tuple]`	`hdr['MeasYaps']`	`hdr.MeasYaps.sKSpace...`
Search	—	`search_header_for_keys`	—	`search(hdr, terms...)`

Feature Support

	mapVBVD	pymapVBVD	twixtools	MRITwixTools.jl
Tab completion	first level	first level	first level	every level
Write support	—	—	✓	—
Low-level mdb access	—	—	✓	—
Multi-raid (VD/VE/XA)	✓	✓	✓	✓

Package Overview

read_twix("file.dat")
  │
  ├── TwixObj
  │     ├── .hdr      → TwixHdr (nested header tree with tab-completion)
  │     ├── .image    → RawData (image acquisitions)
  │     ├── .noise    → RawData (noise adjustments)
  │     ├── .refscan  → RawData (GRAPPA reference lines)
  │     ├── ...       → RawData (other scan types)
  │     └── .syncdata → Vector{Vector{UInt8}} (raw MDH_SYNCDATA payloads,
  │                                             only if present in file)
  │
  └── Vector{TwixObj}   (for multi-raid VD/VE/XA files)

User Guide

Installation — Prerequisites and install methods
Header Access — Navigating header trees with tab-completion
Data Access — Reading, slicing, and processing scan data
SYNCDATA Payloads — Accessing PMU / physio / custom binary blobs
API Reference — Complete exported function listing

Developer Guide

Contributing — Development setup and PR guidelines
Architecture — Codebase walkthrough and design notes
Tab-Completion Internals — How deep REPL completion works
Internal API — Non-exported functions reference