erwin 1.0.0rc1

Toolbox to generate quantitative maps from MRI images

erwin — a qMRI toolbox

erwin is a Python-based toolbox dedicated to the computation of quantitative maps from MRI data. Accessible through either its Python API or its command-line interface, erwin provides a unified interface to well-known methods and toolboxes.

• Field mapping: relative B₀ and relative B₁
• Cerebral blood flow: ASL-based models (pulsed ASL, pseudo-continuous ASL)
• Diffusion: DTI and spherical harmonics, NODDI
• Motion correction
• Magnetization transfer: MTR and single-point qMT
• Magnetic susceptibility: QSM and R₂^*
• T₁ and T₂ mapping: VFA, bSSFP, pSSFP

Since quantitative MRI requires accessing acquisition parameters, often stored in vendor-specific meta-data, erwin includes tools to access meta-data in a vendor-neutral way.

Using doit and Spire, erwin allows the definition of complex pipelines with automatic dependency handling.

Installation

erwin requires Python ≥ 3.5 The easiest way to install erwin and its dependencies is through PyPi and pip (the python3 executable may need to be adjusted to fit your local installation):

python3 -m pip install erwin

Using the following methods requires additional dependencies:

• Diffusion tensor and spherical harmonics: MRtrix; conversion from Bruker or Siemens DICOM also requires Dicomifier
• Motion correction: ANTs
• NODDI: Amico
• QSM: MEDI

Command-line usage

On the command-line, the main executable is called erwin; a list of all methods can be obtained by

erwin --list

The documentation of each individual method is accessed by appending --help to its name, e.g.

erwin b0_map.double_echo --help

Due to the large number of parameters -- input and output paths, flip angles, echo times, imaging frequencies, etc. -- each command line argument is named. Parameters corresponding to physical quantities are expressed in SI units in order to avoid discrepancies between standards: DICOM uses "usual" units, e.g. milliseconds for TR or degrees for flip angles, while BIDS uses seconds for TR, but keeps degrees for flip angles.

erwin b0_map --magnitude /path/to/magnitude.nii.gz --phase /path/to/phase.nii.gz --echo-times 0.01 0.02 --target B0_map.nii.gz

erwin includes a generic meta-data reader to facilitate the conversion to SI: from either a DICOM or a JSON file, meta-data can be queried using specific units. A flip angle can be read and converted to radians using one of the two following examples, from a DICOM file or from a BIDS sidecar file:

ALPHA=$(erwin meta_data.get -p /path/to/some_file -q FlipAngle -u deg)

The same tool can be used for array-like meta-data (erwin meta_data.get -p /path/to/file.dcm -q ImageType.0) or for nested structures, including vendor-specific elements. For example, Siemens-specific meta-data from the sequence card can be queried by

erwin meta_data.get -p /path/to/some_file -q 00291020.MrPhoenixProtocol.0.sWiPMemBlock.adFree.0

Usage in a Python program

TODO Sample B0 from program

import erwin
import nibabel

magnitude = nibabel.load("/path/to/magnitude.nii.gz")
phase = nibabel.load("/path/to/phase.nii.gz")

TODO Sample T2 pipeline