tknapen / pymp2rage

Lightweight Python package to process MP2RAGE and ME-MP2RAGE-data

PyMP2RAGE

This package is a lightweight python implementation of the algorithms described in Marques et al. (2010). They can be used to compute a unified T1-weighted, as well as a quantiative T1 map out of the two phase- and magnitude-images of a MP2RAGE-sequences.

Installation

To install clone this repository and install it with git:

pip install git+https://github.com/Gilles86/pymp2rage

Usage

For some examples of its usage see:

• Bias-field correction, T1 estimation and masking
• Automatic processing of data organized according to BIDS-format
• Correction for B1 transmit field inhomogenieties using a B1 fieldmap
• Estimate a T2* map for multi-echo MP2RAGE data (ME-MP2RAGE)

Readthedocs

See pymp2rage.readthedocs.io for a manual compiled using Sphinx.

References

• Marques, J. P., Kober, T., Krueger, G., van der Zwaag, W., van de Moortele, P.-F., & Gruetter, R. (2010). MP2RAGE, a self bias-field corrected sequence for improved segmentation and T1-mapping at high field. NeuroImage, 49(2), 1271–1281. http://doi.org/10.1016/j.neuroimage.2009.10.002
• The original implementations in MatLab on Github of José Marques