Fiberfox in a container

This code uses a Docker or Singularity image to simulate diffusion weighted MRI.

The container has all the data and software needed to simulate images based on the realistic streamline set used in the ISMRM 2015 challenge. You can produce simulated dMRI using just the bvals and bvecs (in FSL format) and add additional noise.

Making images

To get the Docker image, run

  $ docker pull pennbbl/fiberfox:latest

To build a Singularity image:

  $ singularity build ~/fiberfox.simg docker://pennbbl/fiberfox:latest

Running simulations

Download and unpack this repository and change into this directory. From python

from simulate_scheme import simulate

simulate("gradients/hcp_multishell.bvec", "gradients/hcp_multishell.bval",
         output_dir="~/", singularity_image="~/fiberfox.simg")

If you're using Docker instead of Singularity, set singularity_image="". After these arguments, you can add anything that goes into the Fiberfox ffp file format. Here are the currently available options (documentation here)

# Acquisition parameters
acquisitiontype=0 # 0=EPI
coilsensitivityprofile=0
numberofcoils=1
reversephase="false" # Only does something if combined with doAddDistortions

# Pulse sequence
partialfourier=1
trep=4000
signalScale=100
tEcho=108
tLine=1
tInhom=50

# Streamline-based fiber parameters
axonRadius=0
diffusiondirectionmode=0
fiberseparationthreshold=30
doSimulateRelaxation="true"
doDisablePartialVolume="false"

# k space
simulatekspace="true"
kspaceLineOffset=0.1
addringing="false"

# Motion
doAddMotion="false"
randomMotion="false"
motionvolumes=(6, 12, 24)
# These determine the range of possible motion
translation0=2
translation1=0
translation2=0
rotation0=0
rotation1=0
rotation2=4

# Noise
addnoise="false"
noisetype="gaussian"
noisevariance=251

# ghosts/aliasing
addghosts="false"
addaliasing="false"
aliasingfactor=0

# Signal spikes
addspikes="false"
spikesnum=0
spikesscale=1

# Eddy currents
addeddycurrents="false"
eddyStrength=0
eddyTau=70

# B0 distortion
doAddDistortions="false"

# image
outputvolumefractions="false"
artifactmodelstring="_COMPLEX-GAUSSIAN-251"