MyoQMRI

This project is an open-source effort to put together tools for quantitative MRI of the muscles. Currently, it supports fast water T2 mapping from multi echo spin echo images.

Citing

If you find this work useful, please cite the following paper:

Santini F, Deligianni X, Paoletti M, et al., Fast open-source toolkit for water T2 mapping in the presence of fat from multi-echo spin-echo acquisitions for muscle MRI, Frontiers in Neurology 2021, https://doi.org/10.3389/fneur.2021.630387.

Multi-Echo Spin Echo

The main function is used to obtain water T2 and fat fraction from multi-echo spin echo images as described in Marty et al.

This implementation uses the GPU for the generation of a dictionary of signals through Extended Phase Graph simulation.

Usage

usage: epgFit.py [-h] [--fit-type T] [--fat-t2 T2] [--noise-level N] [--nthreads T] [--plot-level L] [--t2-limits min max] [--b1-limits min max] [--use-gpu] [--ff-map dir]
                 [--register-ff] [--etl-limit N] [--out-suffix ext] [--slice-range start end] [--refocusing-width factor] [--exc-profile path] [--ref-profile path]
                 path

Fit a multiecho dataset

positional arguments:
  path                  path to the dataset

optional arguments:
  -h, --help            show this help message and exit
  --fit-type T, -y T    type of fitting: T=0: EPG, T=1: Single exponential, T=2: Double exponential (default: 0)
  --fat-t2 T2, -f T2    fat T2 (default: 151)
  --noise-level N, -n N
                        noise level for thresholding (default: 300)
  --nthreads T, -t T    number of threads to be used for fitting (default: 12)
  --plot-level L, -p L  do a live plot of the fitting (L=0: no plot, L=1: show the images, L=2: show images and signals)
  --t2-limits min max   set the limits for t2 calculation (default: 20-80)
  --b1-limits min max   set the limits for b1 calculation (default: 0.5-1.2)
  --use-gpu, -g         use GPU for fitting
  --ff-map dir, -m dir  load a fat fraction map
  --register-ff, -r     register the fat fraction dataset
  --etl-limit N, -e N   reduce the echo train length
  --out-suffix ext, -s ext
                        add a suffix to the output map directories
  --slice-range start end, -l start end
                        Restrict the fitting to a subset of slices
  --refocusing-width factor, -w factor
                        Slice width of the refocusing pulse with respect to the excitation (default 1.2) (Siemens standard)
  --exc-profile path    Path to the excitation slice profile file
  --ref-profile path    Path to the refocusing slice profile file

Dataset

The dataset must be a directory containing 2D DICOM images from a multiecho spin echo acquisition, ordered as (slice1echo1 - slice2echo1 - ... - slice1echo2 - slice2echo2 - ...)

Slice profile

An accurate slice profile is crucial to obtain accurate results. By default, a hanning-windowed sinc pulse is used, and the refocusing pulse has a 1.2x the slice width of the excitation pulses. This reflects the parameters of the standard Siemens Spin Echo sequence.

External slice profile files can be provided. They are text files with angle values (in degrees) across half the profile (i.e. starting with ~90 or ~180 and decreasing), with one value per line.

Either none or both slice profiles must be given, and both slice arrays must contain the same number of samples.

Example:

90
89.8014
89.2106
88.2423
86.9198
85.2734
83.3385
81.1537
78.7585
76.1921
...

Acknowledgments

EPG code was made possible by Matthias Weigel.

This project was supported by the SNF (grant number 320030_172876)

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