Command Line

Reconstruction for Siemens data acquired with x_epi

usage: x_epi_recon [-h] [-anat ANAT] [-complex]
                   [-freq_off FREQ_OFF [FREQ_OFF ...]] [-k_coord K_COORD]
                   [-mean] [-n_k KNOTS] [-n_avg N_AVG] [-n_rep N_REP]
                   [-n_chan N_CHAN] [-point] [-ref_info REF_INFO REF_INFO]
                   [-ts TS] [-save_k] [-combine]
                   [-regrid {cubic,nufft,linear}]
                   twix json out

Positional Arguments

twix

Twix file containing EPI data

json

Json file describing sequence from x_epi_app.py

out

Root for file outputs

Named Arguments

-anat

Anatomical reference image

-complex

Save complex image as well as magnitude.

Default: False

-freq_off

Additional off-resonance for each metabolite

-k_coord

k-space coordinates for ramp sampling recon

-mean

Output temporal means

Default: False

-n_k

Number of knots for spline. Default is 2, which is a linear fit.

Default: 2

-n_avg

Number of total averages

Default: 1

-n_rep

Number of total repetitions

Default: 1

-n_chan

Number of coil channels

Default: 1

-point

Run pointwise phaes correction. Default is spline based.

Default: False

-ref_info

Twix data and json file for reference scan

-ts

Sampling time (s)

-save_k

Saves k-space data

Default: False

-combine

Combine coils

Default: False

-regrid

Possible choices: cubic, nufft, linear

Regriding method. Default is nufft.

Default: “nufft”