Raw Data structure - josalggui/MaRGE GitHub Wiki

Sequences

A detailed explanation of the raw data stored for each sequence, including the respective variables and their initial values, can be found here.

RARE

acqTime: Acquisition time (ms)
addRdPoints: Initial rd points to avoid artifact at the begining of rd
angle: Rotation angle (º)
axesEnable: Axes enable. Use 0 for directions with matrix size 1, use 1 otherwise
axesOrientation: Axes[rd,ph,sl]
bw: Acquisition bandwidth (MHz)
dataFull: numpy array with dimensions [nScans, nSlices * partialFourierFraction, nPhases, nReadouts]. It contains acquired data.
dfov: Position of the gradient isocenter (mm), dFOV[x,y,z]
dummyData: Datas acquired along one echo train after first dummy pulse [number of batches, number of acquired points]
dummyPulses: Number of dummy pulses.
echo_shift: Echo time shift (us), Shift the gradient echo time respect to the spin echo time
echoSpacing: Echo spacing (ms)
etl: Echo train length
fileName: File name (.mat).
fov: Field of View [x,y,z] (cm)
freqCal: Calibrate frequency, 0 or 1 (useless, to be deleted)
freqOffset: Larmor frequency offset (kHz)
gradRiseTime: Gradient Rise Time (s)
gradSteps: Gradient steps
image3D: numpy array with the resulting image with dimensions [nSlices, nPhases, nReadouts]
inversionTime: Inversion time (ms)
kMax: Maximum value of aquired k coordinate [kMax_readout, kMax_phase, kMax_slice] (1/m)
kSpace3D: numpy array with the aquired k-space with dimensions [nSlices, nPhases, nReadouts]
larmorFreq: Larmor frequency (MHz)
noiseData: noise measurement obtained before the first acquisition, saved without decimation. The number of elements is nReadouts * nScans * nBatches * oversampling
nPoints: Number of points, nPoints[rd, ph, sl]
nScans: Number of scans
overData: All measurements except noise and dummpy pulses measurements prior to decimation. It contains the added readout points before and after the desired acquisition window (config/hw_config.addRdPoints)
parFourierFraction: Partial fourier fraction. Fraction of k planes aquired in slice direction
partialAcquisition: While doing partial acquisition, this is the number of extra slices acquired next to half nSlices / 2
phGradAmplitude: Máximum applied gradient along phase direction in T/m
phGradTime: Ph gradient time (ms)
phGradients: List of applied phase gradient along the sequence in T/m
preExTime: Preexitation time (ms)
randFactor: Random amplitude to add to the phase gradients (0e-3)
rdDephAmplitude: Amplitude of the dephasing gradient applied along readout direction in T/m
rdDephTime: Rd dephasing time (ms)
rdGradAmplitude: Amplitude of the readout gradient in T/m
rdGradTime: Rd gradient time (ms)
rdPreemphasis: Rd preemphasis
repetitionTime: Repetition time (ms)
resolution: Nominal pixel size along readout, phase and slice direction
rfExAmp: Amplitude of the excitation rf pulse in a.u. of red pitaya.
rfExFA: Excitation flip angle (º)
rfExTime: RF excitation time (us)
rfReAmp: Amplitude of the rf refocusing pulse in a.u. of red pitaya.
rfReFA: Refocusing flip angle (º)
rfReTime: RF refocusing time (us)
sampled numpy array with four columns for [k_readout, k_phase, k_slices, data] (1/m, 1/m, 1/m, mV).
sampledCartesian: numpy array with four columns resampled to cartesian grid.
scanTime: Approximate value of the total sequence scan time in seconds.
seqName: Sequence name. In this case: RARE which stands for Rapid Acquisition with Relaxation Enhancement.
shimming: Shimming values used along the sequence to homogenize magnetic field, val=[0.0, 0.0, 0.0]
slGradAmplitude: Máximum applied gradient along slice direction in T/m
slGradients: List of applied slice gradient along the sequence in T/m
sweepMode: Sweep mode, 0: sweep from -kmax to kmax. 1: sweep from 0 to kmax. 2: sweep from kmax to 0, val=1
sweepOrder: Array with the index representing the order of acquired phase lines.

MSE_PyPulseq

acqTime: Acquisition time (ms)
axesOrientation: Scaner axes used for [readout,phase,slice]. 0->x, 1->y, 2->z
Bandwidth_Hz: Image bandwidth in Hz
data: Data list after averaging
data_over: Data acquired directly from the red pitaya
data_full: Data after decimation of data_over
deadtime: Dead time before and after the rf pulse (us). Must be longer than the de-blanking time of the RFPA.
dfov: Field of View displacement in mm.
dummyPulses: Number of dummy pulses for batches.
echoSpacing Echo spacing in ms
etl: echo train length
fov: field of view in cm for [x-axis, y-axis and z-axis]
freqOffset: excitation and demodulation frequency offset respect to central frequency in kHz
fsp_r: multiplicative factor to crushers?
grad_rise_time: gradient rise time in us
iSpace: image space with dimension [n_echos, n_slices, n_phases, n_readouts]
kSpace: k-space with dimension [n_echos, n_slices, n_phases, n_readouts]
larmorFreq: excitation and demodulation central frequency in MHz
n_batches: number of executed batches
n_readouts: list of readouts per batch
nPoints: number of points for [readout, phase, slice]
nRD_post: number of readouts added before acquisition
nRD_pre: number of readouts added after acquisition
nScans: number of acquired scans
oversamplingFactor: oversampling applied to the acquisition to account for CIC filter issues
preemphasis: multiplicative factor applied to dephasing readout gradient
rdGradTime: readout gradient time
resolution: resolution for [readout, phase and slice]
rfExFA: rf excitation flip angle in degrees
rfExTime rf excitation time in us
rfReFA rf refocusing flip angle in degrees
rfReTime: rf refocusing flip angle in us
Sampling_Period_s: sampling period in s
Sampling_Time_s: sampling time in s
Scan_time_s: total scan time in s
shimming: shimming used in the scanner
unclock_orientation: useless

LARMOR

This sequence runs a single spin echo to find larmor.

acqTime: Acquisition time (s)
bw: Bandwidth (Hz), nPoints / acqTime
bw_true: bw * 1e6
data: measured voltages in mV after averaging the scans.
data_full: measured voltages in mV before averaging the scans.
dataOver: oversampled measured voltages in mV.
dF: Frequency resolution (Hz)
echoTime: 2 * acqTime
fileName: File name (.mat).
larmorFreq: Larmor frequency (Hz)
name_string: Sequence name. In this case: Noise
nPoints: Number of points, nPoints[rd, ph, sl]
nScans: Number of scans
repetitionTime: Repetition time (s)
rfExFA: Excitation flip angle (º)
rfExTime: RF excitation time (s)
rfReFA: Refocusing flip angle (º)
rfReTime: RF refocusing time (s)
sampledPoint: signal amplitude in mV at the middle of the acquisition window.
samplingPeriod: 1 / bw
seqName: Sequence name. In this case: Larmor
shimming: Shimming
signalVStime: [tVector, signal]
spectrum: [fVector, spectrum]

SHIMMING

This sequence sweep the shimming in the three axis.

acqTime: Acquisition time (s)
amplitudeVSshimming: 3xn matrix containing the amplitude of the spectrum for each shimming value of the three channels.
bw: acquisition bandwidth (Hz), nPoints/acqTime
data: acquired voltages in mV
dShimming: Shiming step
dummyPulses: Dummy pulses
echoTime: Echo time (s)
fileName: File name (.mat)
freqOffset: Larmor frequency offset (Hz)
name_string: Sequence name. In this case: Noise
nPoints: Number of points, val=60
nShimming: n Shimming steps, val=10
repetitionTime: Repetition time (s)
rfExFA: Excitation flip angle (º)'
rfExTime: RF excitation time (s)
rfReFA: Refocusing flip angle (º)'
rfReTime: RF refocusing time (s)'
samplingPeriod: 1 / bw
seqName: Sequence name. In this case: Shimming
shimming0: center values for shimming sweep
sxVector: shimming values used for x-axis
syVector: shimming values used for y-axis
szVector: shimming values used for z-axis

NOISE

bw: Acquisition bandwidth (Hz)
data: data in mV
dataOver: Oversampled data in mV
fileName: File name (.mat)
larmorFreq: RF frequency determined by the scanner hardware configuration file.
freqOffset: RF frequency offset (Hz)
name_string: String with acquisition date and time
nPoints: Number of points
rxChannel: Rx channel used in the acquisition
sampledPoint: noise rms amplitude
seqName: Sequence name. In this case: Noise

RABI FLOPS

Rabi Flops with different methods. Set RF refocusing amplitude to 0.0 to get single excitation behavior Set RF refocusing time to 0.0 to auto set the RF refocusing time:

If Rephasing method = 0, refocusing amplitude is twice the excitation amplitude
If Rephasing method = 1, refocusing time is twice the excitation time
acqTime: Acquisition time (s)
bw: nPoints / acqTime * hw.oversamplingFactor (MHz), where is defined in hw_config as oversamplingFactor = 6
cal_method: Calibration method, val='FID'. It can be either FID or ECHO.
dataEcho: measured data along the echo in mV.
dataEchoAvg: average of the measured data along the echo in mV.
dataFID: measured data after the excitation in mV.
dataFIDAvg: average of the measured data after the excitation in mV.
dataFull: all acquired data in mV.
dataOversampled: oversampled acquired data in mV.
deadTime: Dead time (s)
dummyPulses: Dummy pulses
echoTime: Echo time (s)
fileName: File name (.mat)
freqOffset: Larmor frequency offset (Hz)
method: Rephasing method: 0->Amp, 1->Time
nPoints: Number of points
nScans: Number of scans
nSteps: Number of steps
name_string: Sequence name. In this case: Noise
piHalfTime: rf excitation time to pi/2 flip angle
rabiEcho: rabi from echo amplitudes
rabiFID: rabi from fid amplitudes
repetitionTime: Repetition time (s)
rfExAmp: RF excitation amplitude (a.u.)
rfExTime0: RF pulse time, Start (s)
rfExTime1: RF pulse time, End (s)
rfReAmp: RF refocusing amplitude (a.u.)
rfReTime: RF refocusing time (s)
rfRefPhase: Refocusing phase (degrees)
rfTime: list of time durations for rf pulses
samplingPeriod: 1 / bw
seqName: Sequence name. In this case: RabiFlops
shimming: Shimming