mriphysio

Utility classes and functions for handling the following:

• Respiration waveform reconstruction from complex-valued or phase-only EPI timeseries
• Siemens/CMRR MRI physiological DICOM
• Siemens MPCU logs

Respiratory waveform from complex or phase-only EPI timeseries

The installed python package provides a command line function epi2resp that generates a BIDS-format respiratory TSV file from a complex-valued EPI timeseries.

Usage

usage: epi2resp [-h] -p PHASEDIFF -w WEIGHTMASK [-m METHOD] [-n NPCA] -o OUTFILE

Estimate respiratory waveform from complex EPI and save as BIDS-compliant TSV

options: -h, --help show this help message and exit -p PHASEDIFF, --phasediff PHASEDIFF Nifti 3D x time phase difference timeseries -w WEIGHTMASK, --weightmask WEIGHTMASK Nifti weighting mask image -m METHOD, --method METHOD Spatially weighted mean method -n NPCA, --npca NPCA Number of PCA components to retain -o OUTFILE, --outfile OUTFILE BIDS format repiratory waveform TSV

PhaseRespWave Class

The PhaseRespWave class is defined in mriphysio/phaseresp.py and mriphysio/epi2resp.py shows example use of the class for pipeline integration.

Notes on Siemens physiology log parsing

VE11C CMRR Multiband DICOM Physiological Logs

R016a of the Prisma version of CMRR multiband EPI sequences supports output of physiological logging as a DICOM file. The waveforms are encoded in the Siemens Spectroscopy tag (0x7fe1, 0x1010) and match the acquisition period of the series accurately. A jupyter notebook demonstrating handling of an example physio DICOM is provided in data/notebooks/

VB17A MPCU Matlab Functions

Legacy MPCU text log handling functions for Matlab (mpcu*.m) are provided in matlab/