Automated script for magnitude-and-phase-based T2 mapping method

Authors: Difei Wang, DZNE Bonn

Processing pipeline

Data processing is performed by the script T2T1AM.py. To call the script use

 python T2T1AM.py <magnitude> <phase> <mask> <b1map> -tr TR -fa FA -phi delta_phi -outputdir path

where

• magnitude is the filename of the magnitude image
• phase is the filename of the phase image
• mask is the filename of the mask
• b1map is the filename of the B1 map
• TR is the repetition time in ms
• FA is the flip angle in degrees
• delta_phi is the list of RF phase increments
• path is the path to the output folder.

The pipeline expects the following data:

• B₁⁺ map in percentage unit
• mask of the brain
• background-removed 4D magnitude images
• background-removed 4D phase images

The outputs are T₂, T₁, amplitude maps.

Demo Dataset

An example dataset of the phantom can be found in here.

Required package

The EPG package can be found in here.

The Python packages are:

• numpy
• nibabel
• scipy.optimize
• os
• glob
• pymp-pypi
• argparse
• sys
• time / datetime (optional)