OCTOPUS.fieldmap subpackage

OCTOPUS.fieldmap.simulate module

Methods to simulate different types of field maps

Author: Marina Manso Jimeno

Last modified: 07/16/2020

OCTOPUS.fieldmap.simulate.fieldmap_bin(field_map, bin)

Bins a given field map given a binning value

Parameters:
  • field_map (numpy.ndarray) – Field map matrix in Hz
  • bin (int) – Binning value in Hz
Returns:

binned_field_map – Binned field map matrix
Return type:

numpy.ndarray
OCTOPUS.fieldmap.simulate.hyperbolic(N, fmax, bin_opt=True, bin_val=5)

Creates a hyperbolic field map

Parameters:
  • N (int) – Field map dimensions (NxN)
  • fmax (float) – Frequency range in Hz
  • bin_opt (bool) – Binning option. Default is True
  • bin_val (int) – Binning value, default is 5 Hz
Returns:

field map – Field map matrix with dimensions [NxN] and scaled from -fmax to +fmax Hz
Return type:

numpy.ndarray
OCTOPUS.fieldmap.simulate.parabola_formula(N)

Parabola values to fit an image of N rows/columns

Parameters:N (int) – Matrix size
Returns:yaxis – y axis values of the parabola
Return type:numpy.ndarray
OCTOPUS.fieldmap.simulate.parabolic(N, fmax, bin_opt=True, bin_val=5)

Creates a parabolic field map

Parameters:
  • N (int) – Field map dimensions (NxN)
  • fmax (float) – Frequency range in Hz
  • bin_opt (bool) – Binning option. Default is True
  • bin_val (int) – Binning value. Default is 5 Hz
Returns:

field map – Field map matrix with dimensions [NxN] and scaled from -fmax to +fmax Hz
Return type:

numpy.ndarray
OCTOPUS.fieldmap.simulate.realistic(im, mask, fmax, bin_opt=True, bin_val=5)

Creates a realistic field map based on the input image

Parameters:
  • im (numpy.ndarray) – Input image
  • fmax (float) – Frequency range in Hz
  • bin_opt (bool) – Binning option. Default is True
  • bin_val (int) – Binning value, default is 5 Hz
Returns:

field_map – Field map matrix with dimensions same as im and scaled from -fmax to +fmax Hz
Return type:

numpy.ndarray
OCTOPUS.fieldmap.simulate.spherical_order4(N, fmax, bin_opt=True, bin_val=5)

Creates a field map simulating spherical harmonics of 4th order

Parameters:
  • N (int) – Field map dimensions (NxN)
  • fmax (float) – Frequency range in Hz
  • bin_opt (bool) – Binning option. Default is True
  • bin_val (int) – Binning value, default is 5 Hz
Returns:

field_map – Field map matrix with dimensions NxN and scaled from -fmax to +fmax Hz
Return type:

numpy.ndarray

OCTOPUS.fieldmap.unwrap module

Prepares field map data (from a Siemens scanner) for phase unwrapping with FSL

Author: Marina Manso Jimeno

Last updated: 07/08/2020

OCTOPUS.fieldmap.unwrap.fsl_prep(data_path_raw, data_path_dicom, dst_folder, dTE)

Prepares a Siemens fieldmap for phase unwrapping using FSL. Saves a phase difference image and a magnitude image with the ROI extracted in niftii format to use as inputs for FSL.

Parameters:
  • data_path_raw (str) – Path to the MATLAB/npy file containing the field map raw data with dimensions [lines, columns, echoes, channels]
  • data_path_dicom (str) – Path to the DICOM file containing the phase difference image (.IMA)
  • dst_folder (str) – Path to the destination folder where the niftii files are saved
  • dTE (float) – Difference in TE between the two echoes in seconds