Command-line
usage: x_epi [-out OUT] [-fov RO PE SLC] [-rbw BW] [-n_avg N] [-n_rep N] [-tr TR] [-tv TV] [-ts TS] [-ro_off OFFSET] [-pe_off OFFSET] [-slc_off OFFSET] [-n_echo N] [-delta_te DELTA]
[-ori {Sagittal,Coronal,Transverse}] [-pe_dir {AP,RL,SI}] [-symm_ro] [-acq_3d] [-no_pe] [-no_slc] [-grad_spoil] [-ramp_samp] [-ro_os FACTOR] [-slice_axis {X,Y,Z}]
[-alt_read] [-alt_pha] [-alt_slc] [-run_spec {START,END,BOTH,NO}] [-spec_size N] [-spec_bw BW] [-spec_flip ANGLE] [-spec_tr TR] [-n_spec N] [-b0 B0]
[-nuc {13C,1H,2H,15N,17O,31P,19F,23Na,129Xe}] [-max_grad GRAD] [-max_slew SLEW] [-rf_ringdown_time RF_RINGDOWN_TIME] [-rf_dead_time RF_DEAD_TIME]
Named Arguments
- -out
Root for file outputs
Default: “epi”
Image parameters
- -fov
Field of view in readout, phase, and slice dimensions [mm]
Default: [240, 240, 240]
- -rbw
Readout bandwidth [kHz]
Default: 50
- -n_avg
Number of averages
Default: 1
- -n_rep
Number of repetitions
Default: 1
- -tr
Minimum repetition time [ms]
Default: 0
- -tv
Minimum volume time [ms]
Default: 0
- -ts
Minimum set time [ms]
Default: 0
- -ro_off
Offset in readout dimension [mm]
Default: 0
- -pe_off
Offset in phase encoding dimension [mm]
Default: 0
- -slc_off
Offset in slice/second phase encoding dimension [mm]
Default: 0
- -n_echo
Number of echos
Default: 1
- -delta_te
Minimum time between echoes [ms]
Default: 0
- -ori
Possible choices: Sagittal, Coronal, Transverse
Acquistion orientation. Only used for reconstruction
Default: “Transverse”
- -pe_dir
Possible choices: AP, RL, SI
Phase encoding direction. Only used for reconstruction
Default: “AP”
Acquisition options
- -symm_ro
Replace flyback readout with a symmetric one.
Default: False
- -acq_3d
Use a 3D readout instead of 2D
Default: False
- -no_pe
Turn phase encoding on/off
Default: False
- -no_slc
Turn off slice gradients
Default: False
- -grad_spoil
Turn gradient spoiling on
Default: False
- -ramp_samp
Turn on ramp sampling
Default: False
- -ro_os
Readout oversampling factor for ramp sampling
Default: 1.0
- -slice_axis
Possible choices: X, Y, Z
Axis to play slice selection gradients
Default: “Z”
- -alt_read
Alternate polarity of readout gradient every repeition
Default: False
- -alt_pha
Alternate polarity of phase encoding gradient every repeition
Default: False
- -alt_slc
Alternate polarity of second phase encoding every repetition
Default: False
Spectra options
- -run_spec
Possible choices: START, END, BOTH, NO
Run a slice selective spectra at the start and/or end of the seqience.
Default: “NO”
- -spec_size
Number of points in spectra
Default: 2048
- -spec_bw
Spectral bandwidth [kHz]
Default: 25
- -spec_flip
Flip angle for slcie selective pulse [deg]
Default: 2.5
- -spec_tr
Minimum repetition time for spectra acquistions [ms]
Default: 1000
- -n_spec
Number of spectra acquisitions
Default: 1
Scanner Options
- -b0
B0 Field Strength [Tesla]
Default: 3
- -nuc
Possible choices: 13C, 1H, 2H, 15N, 17O, 31P, 19F, 23Na, 129Xe
Nucleus to imaage
Default: “13C”
- -max_grad
Maximum gradient strength [mT/m]
Default: 100
- -max_slew
Maximum slew rate [T/m/s]
Default: 200
- -rf_ringdown_time
RF ringdown time [us]
Default: 30
- -rf_dead_time
RF dead time [us]
Default: 100
x_epi: An EPI sequence for X-Nucleus imaging
usage: x_epi [-h] [-name NAME] [-grd_path PATH] [-rf_path PATH] [-formula FORMULA] [-use_sinc] [-flip ANGLE] [-freq_off OFFSET] [-sinc_dur DUR] [-sinc_frac FRAC] [-sinc_tbw TBW]
[-size RO PE SLC] [-pf_pe FRAC] [-pf_pe2 FRAC] [-z_centric]
Named Arguments
- -name
Metabolite name
Metabolite Specific Waveforms
- -grd_path
Path to gradient file from Spectral-Spatial RF Toolbox
Default: “/Users/blazeyt/Documents/code/x_epi/x_epi/../seq/siemens_singleband_pyr_3T.GRD”
- -rf_path
Path to RF file from Spectral-Spatial RF Toolbox
Default: “/Users/blazeyt/Documents/code/x_epi/x_epi/../seq/siemens_singleband_pyr_3T.RF”
- -formula
Formula for scaling SSRF gradient where x is slice thickness in mm
Default: “1”
Metabolite Specific Excitation
- -use_sinc
Use sinc pulse instead of an ssrf pulse
Default: False
- -flip
Flip angle [deg]
Default: 90
- -freq_off
Frequency offset [Hz]
Default: 0
- -sinc_dur
Duration of sinc pulse [ms]
Default: 4
- -sinc_frac
Center fraction of sinc pulse
Default: 0.5
- -sinc_tbw
Time-bandwidth product of sinc pulse
Default: 4
Metabolite Specific Imaging Parameters
- -size
Grid size in readout, phase, and slice dimensions
Default: [16, 16, 16]
- -pf_pe
Partial Fourier in phase encoding dimension
Default: 1
- -pf_pe2
Partial Fourier in second phase encoding dimension
Default: 1
- -z_centric
Use centric encoding instead of linear for second phase encoding dimension.
Default: False
Each metabolite must be preceded by -met.