API

x_epi data class module

class x_epi.data.XData(fov=[240, 240, 240], rbw=50, n_avg=1, n_chan=1, n_rep=1, ts=1000, ro_off=0, pe_off=0, slc_off=0, n_echo=1, delta_te=0, symm_ro=True, acq_3d=True, ramp_samp=False, alt_read=False, alt_pha=False, alt_slc=False, ori='Transverse', pe_dir='AP', **kwargs)

Data class for processing data created with an x_epi sequence

Methods

add_met([name, size, size_acq, pf_pe, ...])	Add metabolite acquisition to sequence
apply_off_res([pad])	Shifts metabolites that were acquired off-resonance
apply_phase_shift([pad])	Shifts images in phase encoding directions if image was acquired with an off center field of view.
combine_coils()	Perform sum-of-squares coil combination.
create_nii_xfm()	Creates NIfTI format affine transforms for each metabolite.
create_param_dic()	Create a dictionary for sequence parameters
fft_recon([ref_data, point, n_k])	Reconstructs metabolite data using the FFT.
flip_k_data()	Performs axis flips common to x_epi data
load_k_coords(coord_path)	Loads in k-space coordinates and adds them to each metabolite object
load_k_data(twix_path[, recon_dims])	Reads k-space data for each metabolite from Siemens twix file
regrid_k_data([method, nufft_size])	Regrid k-space in readout direction so that we have even spacing with the correct FOV
save_nii(out_root[, cmplx, mean])	Saves image data to nifti
save_param_dic(out_root)	Saves input parameters to json

__init__(fov=[240, 240, 240], rbw=50, n_avg=1, n_chan=1, n_rep=1, ts=1000, ro_off=0, pe_off=0, slc_off=0, n_echo=1, delta_te=0, symm_ro=True, acq_3d=True, ramp_samp=False, alt_read=False, alt_pha=False, alt_slc=False, ori='Transverse', pe_dir='AP', **kwargs)

Initialize X EPI data object

Attributes:

fovarray_like

Contains FOV of each dimension (mm)

rbwfloat

Readout bandwidth (kHz)

n_avgint

Number of averages

n_chanint

Number of coil channels

n_repint

Number of repeats

tsfloat

Minimum durartion of each metabolite set (ms)

ro_offfloat

Spatial offset in readout direction (mm)

pe_offfloat

Spatial offset in phase encoding direction (mm). Only for recon.

slc_off: float

Spatial offset in slice direction (mm)

n_echoint

Number of echoes following each excitation

delta_tefloat

Minimum duration between each echo (ms) #Extract sequence options

symm_robool

Uses symmetric readout if True. Otherwise uses flyback.

acq_3dbool

Uses a 3D readout if True. Otherwise uses 2D.

alt_readbool

Alternate polarity of readout every repetition

alt_phabool

Alternate polarity of phase encoding every repetition

alt_slcbool

Alternate polarity of second phase encoding every repetition

oristr

Image orientation for reconstruction.

pe_dirstr

Phase encoding direction for reconstruction

Returns:

XData object

add_met(name=None, size=[16, 16, 16], size_acq=[16, 16, 16], pf_pe=1, pf_pe2=1, freq_off=0, z_centric=False, esp=0.00048, k_acq=None, k_coord=None, k_data=None, img_data=None, **kwargs)

Add metabolite acquisition to sequence

Parameters:

namestr

Name for metabolite

sizearray_like

Grid size in x, y, and z

size_acqarray_like

Acquired dimensions in x, y, z

pf_pefloat

Partial Fourier fraction in y dimension

pf_pe2float

Partial Fourier fraction in z dimension

freq_offfloat

Frequency offset (Hz) of pulse

z_centricbool

Use centric phase encoding in z direction

espfloat

Echo spacing (s)

k_acqndarray

k-space data with dimensions size_acq, n_rep, n_echo

k_datandarrary

k-space data with dimensions size, n_rep, n_echo

img_datandarray

image data with dimensions size, n_rep, n_echo

apply_off_res(pad=8)

Shifts metabolites that were acquired off-resonance

Parameters:

padint

Size to zero pad each dimension when apply shifts

apply_phase_shift(pad=8)

Shifts images in phase encoding directions if image was acquired with an off center field of view.

Parameters:

padint

Size to zero pad each dimension when apply shifts

combine_coils()

Perform sum-of-squares coil combination.

create_nii_xfm()

Creates NIfTI format affine transforms for each metabolite. Units are in mm.

create_param_dic()

Create a dictionary for sequence parameters

Returns:

param_dicdic

Dictionary of sequence parameters

fft_recon(ref_data=None, point=True, n_k=2)

Reconstructs metabolite data using the FFT. Also can apply a phase correction for symmetrically acquired EPI data

Parameters:

ref_dataXData object

XData object containing with reference scan data (no phase encoding) for each metabolite

pointbool

Run a pointwise (True) or spline-based (False) phase correction

n_kint

Number of knots for spline-based phase correction

flip_k_data()

Performs axis flips common to x_epi data

load_k_coords(coord_path)

Loads in k-space coordinates and adds them to each metabolite object

Parameters:

coord_pathstr

Path to k-space coordinates written by x_epi apps

load_k_data(twix_path, recon_dims=True)

Reads k-space data for each metabolite from Siemens twix file

Parameters:

twix_pathstr

Path to twix data file

recon_dimsbool

If true, saves k-space data with same dimensions as eventual reconstructed image to k_data. Zero-padding is used to fill any data skipped due to partial Fourier. If False, k-space data will have dimensions matching acquisition and be saved to k_acq.

regrid_k_data(method='cubic', nufft_size=6)

Regrid k-space in readout direction so that we have even spacing with the correct FOV

Parameters:

methodstr

Cubic uses cubic spline interpolation, nufft performs a non-uniform FFT, and linear performs linear interpolation

nufft_sizeint

Size of nufft interpolator

save_nii(out_root, cmplx=False, mean=False)

Saves image data to nifti

Parameters:

out_rootstr

Root for output files. Does not include extension or cmplx/mean suffix.

cmplxbool

Saves data as complex is true

meanbool

Saves temporal mean

save_param_dic(out_root)

Saves input parameters to json

Parameters:

out_rootstr

Path to write json data to. Does not include extension