sdcflows.interfaces.epi module

Interfaces to deal with the various types of fieldmap sources.

class sdcflows.interfaces.epi.GetReadoutTime(from_file=None, resource_monitor=None, **inputs)[source]

Bases: SimpleInterface

Calculate the readout time from available metadata.

Mandatory Inputs:

metadata (a dictionary with keys which are any value and with values which are any value) – Metadata corresponding to the inputs.

Optional Inputs:

in_file (a pathlike object or string representing an existing file) – EPI image corresponding to the metadata.

Outputs:

  • pe_dir_fsl (‘x’ or ‘x-’ or ‘y’ or ‘y-’ or ‘z’ or ‘z-’)

  • pe_direction (‘i’ or ‘i-’ or ‘j’ or ‘j-’ or ‘k’ or ‘k-’)

  • readout_time (a float)

class sdcflows.interfaces.epi.SortPEBlips(from_file=None, resource_monitor=None, **inputs)[source]

Bases: SimpleInterface

Sort PE blips so they are consistently fed into TOPUP.

Mandatory Inputs:

  • in_data (a list of items which are a pathlike object or string representing an existing file) – List of input data.

  • pe_dirs_fsl (a list of items which are ‘x’ or ‘x-’ or ‘y’ or ‘y-’ or ‘z’ or ‘z-’) – List of PE directions, in FSL’s conventions.

  • readout_times (a list of items which are a float) – List of total readout times.

Outputs:

  • out_data (a list of items which are a pathlike object or string representing a file) – List of input data.

  • pe_dirs (a list of items which are ‘i’ or ‘i-’ or ‘j’ or ‘j-’ or ‘k’ or ‘k-’) – List of PE directions, in BIDS’s conventions.

  • pe_dirs_fsl (a list of items which are ‘x’ or ‘x-’ or ‘y’ or ‘y-’ or ‘z’ or ‘z-’) – List of PE directions, in FSL’s conventions.

  • readout_times (a list of items which are a float) – List of total readout times.