PyMRStrain is a open source generator of synthetic Complementary SPAMM and DENSE images.
To generate CSPAMM images, in Python simply do
from PyMRStrain import *
import numpy as np
# Parameters
p = Parameters(time_steps=18)
# Encoding frequency
ke = 0.07 # encoding frequency [cycles/mm]
ke = 1000*2*np.pi*ke # encoding frequency [rad/m]
# Create complimentary image
I = CSPAMMImage(FOV=np.array([0.2, 0.2, 0.04]),
center=np.array([0.0,0.0,0.03]),
resolution=np.array([100, 100, 1]),
encoding_frequency=np.array([ke,ke,0]),
T1=0.85,
flip_angle=15*np.pi/180,
encoding_angle=90*np.pi/180,
off_resonance=phi,
kspace_factor=15,
slice_thickness=0.008,
oversampling_factor=2,
phase_profiles=50)
# Spins
spins = Spins(Nb_samples=1000000, parameters=p)
# Create phantom object
phantom = Phantom(spins, p, patient=False, write_vtk=False)
# EPI acquisiton object
artifact = EPI(receiver_bw=128*1000,
echo_train_length=10,
off_resonance=200,
acq_matrix=I.acq_matrix,
spatial_shift='top-down')
# Generate images
kspace_0, kspace_1, kspace_in, mask = I.generate(artifact, phantom, p)
# Complementary images
u = u0 - u1
# Plots
if MPI_rank==0:
multi_slice_viewer(np.abs(u[:,:,0,0,:]))
multi_slice_viewer(np.abs(u[:,:,0,1,:]))
multi_slice_viewer(np.abs(kspace_0.k[:,:,0,0,:]))
multi_slice_viewer(np.abs(kspace_0.k[:,:,0,1,:]))and run from a terminal with
mpirun -n nb_proc python3 foo.pyResulting images look like this:
| CSPAMM image with epi-like artifacts | CSPAMM kspace with epi-like artifacts |
|---|---|
 |
 |
git clone https://github.com/hernanmella/pymrstrain
cd pymrstrain
python3 setup.py installTo build the docker image run the following instruction in the command line:
docker build --rm . -t pymrstrainOnce the building process has finished, run the following to start the PyMRStrain Docker container:
docker run -ti -v "path/to/folder":"/home/pymrstrain" pymrstrainIf you wish to run the container with plotting support, i.e., allowing to the container to show images, first run:
sudo apt-get install x11-xserver-utils && xhost +and finally, use the following instruction to start the container:
docker run --rm -it \
--user="pymrstrain" \
--env="DISPLAY" \
--volume="/etc/group:/etc/group:ro" \
--volume="/etc/passwd:/etc/passwd:ro" \
--volume="/etc/shadow:/etc/shadow:ro" \
--volume="/etc/sudoers.d:/etc/sudoers.d:ro" \
--volume="/tmp/.X11-unix:/tmp/.X11-unix:rw" \
-v "/home/hernan/Git/pymrstrain/demo":"/home/pymrstrain" pymrstrainThe dependencies of the project are listed in the files install_dependencies.sh and Dockerfile.
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