Applications

bartorch.tools: BART’s applications, one function per command. In each section the hand-written wrappers come first; the rest are built from BART’s own declaration of the command and take its options under their long names.

Simulation

phantom	An analytical phantom, as an image or as its k-space.
bloch	simulation tool
coils	Compute coil sensitivitity maps in x-space or k-space.
epg	Simulate MR pulse sequence based on Extended Phase Graphs (EPG)
fakeksp	Recreate k-space from image and sensitivities.
mobasig	Forward calculation of physical signal models.
noise	Add noise with selected variance to input.
pulse	Pulse generation tool
seq	Computes a GRE sequence.
signal	Analytical simulation tool.
sim	simulation tool

Sampling and trajectories

traj	A k-space trajectory, in grid units.
bin	Binning
estdelay	Estimate gradient delays from radial data.
estdims	Estimate image dimension from non-Cartesian trajectory.
grid	Compute sampling grid for x-space / k-space (and time).
nufftbase	Compute the Fourier transform of a basis function to be used in the nuFFT.
pattern	Compute sampling pattern from kspace
poisson	Computes Poisson-disc sampling pattern.
psf	Calculate point-spread-function (PSF) of given trajectory.
raga	Generate file with RAGA indices for given approximated tiny golden ratio angle/raga increment and full frame spokes.
rmfreq	Remove angle-dependent frequency
ssa	Perform SSA-FARY or Singular Spectrum Analysis.
trajcor	Correct delays for a given trajectory.
upat	Create a sampling pattern.
wavepsf	Generate a wave PSF in hybrid space.

Coil calibration

ecalib	Coil sensitivities by ESPIRiT.
caldir	Coil sensitivities from the centre of k-space directly.
calmat	Compute calibration matrix.
cc	Performs coil compression.
ccapply	Apply coil compression forward/inverse operation.
ecaltwo	Second part of ESPIRiT calibration.
estscaling	Estimate scaling from k-space center.
estvar	Estimate the noise variance assuming white Gaussian noise.
ncalib	Estimate coil sensitivities using ENLIVE calibration.
phasepole	Detect and sample phase poles.
rovir	Compute coil compression matrix using ROVir.
walsh	Estimate coil sensitivities using walsh method (use with ecaltwo).
whiten	Apply multi-channel noise pre-whitening on <input> using noise data <ndata>.

Reconstruction

pics	Parallel-imaging compressed-sensing reconstruction.
nlinv	Nonlinear inversion: the image and the sensitivities together.
grog	GROG calibration and gridding of radial data.
homodyne	Perform homodyne reconstruction along dimension dim.
itsense	A simplified implementation of iterative sense reconstruction with l2-regularization.
looklocker	Compute T1 map from M_0, M_ss, and R_1*.
lrmatrix	Perform (multi-scale) low rank matrix completion
moba	Model-based nonlinear inverse reconstruction
mobafit	Pixel-wise fitting of physical signal models.
pocsense	Perform POCSENSE reconstruction.
rtnlinv	Jointly estimate a time-series of images and sensitivities with nonlinear inversion using {iter} iteration steps.
sake	Use SAKE algorithm to recover a full k-space from undersampled data using low-rank matrix completion.
sqpics	Parallel-imaging compressed-sensing reconstruction.
wave	Perform a wave-caipi reconstruction.
wshfl	Perform a wave-shuffling reconstruction.