sdcflows.interfaces.fmap module

Interfaces to deal with the various types of fieldmap sources.

class sdcflows.interfaces.fmap.CheckB0Units(from_file=None, resource_monitor=None, **inputs)[source]

Bases: nipype.interfaces.base.core.SimpleInterface

Ensure the input fieldmap is given in Hz.

Mandatory Inputs

  • in_file (a pathlike object or string representing an existing file) – Input fieldmap.

  • units (‘Hz’ or ‘rad/s’) – Fieldmap units.

Outputs

out_file (a pathlike object or string representing an existing file) – Output fieldmap in Hz.

class sdcflows.interfaces.fmap.DisplacementsField2Fieldmap(from_file=None, resource_monitor=None, **inputs)[source]

Bases: nipype.interfaces.base.core.SimpleInterface

Convert from a transform to a B0 fieldmap in Hz.

Mandatory Inputs

  • pe_dir (‘j-’ or ‘j’ or ‘i’ or ‘i-’ or ‘k’ or ‘k-’) – Phase encoding direction.

  • ro_time (a float) – Total readout time.

  • transform (a pathlike object or string representing an existing file) – Input displacements field.

Optional Inputs

  • demean (a boolean) – Regress field to the mean. (Nipype default value: False)

  • itk_transform (a boolean) – Whether this is an ITK/ANTs transform. (Nipype default value: True)

Outputs

out_file (a pathlike object or string representing an existing file) – Output fieldmap in Hz.

class sdcflows.interfaces.fmap.PhaseMap2rads(from_file=None, resource_monitor=None, **inputs)[source]

Bases: nipype.interfaces.base.core.SimpleInterface

Convert a phase map given in a.u. (e.g., 0-4096) to radians.

Mandatory Inputs

in_file (a pathlike object or string representing an existing file) – Input (wrapped) phase map.

Outputs

out_file (a pathlike object or string representing a file) – The phase map in the range 0 - 6.28.

class sdcflows.interfaces.fmap.Phasediff2Fieldmap(from_file=None, resource_monitor=None, **inputs)[source]

Bases: nipype.interfaces.base.core.SimpleInterface

Convert a phase difference map into a fieldmap in Hz.

Mandatory Inputs

  • in_file (a pathlike object or string representing an existing file) – Input fieldmap.

  • metadata (a dictionary with keys which are any value and with values which are any value) – BIDS metadata dictionary.

Outputs

out_file (a pathlike object or string representing a file) – The output fieldmap.

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

Bases: nipype.interfaces.base.core.SimpleInterface

Calculate a phase difference map.

Optional Inputs

  • in_meta (a list of items which are a dictionary with keys which are any value and with values which are any value) – Metadata corresponding to the inputs.

  • in_phases (a list of items which are a pathlike object or string representing an existing file) – Input phase maps.

Outputs

  • metadata (a dictionary with keys which are any value and with values which are any value) – Output metadata.

  • phase_diff (a pathlike object or string representing an existing file) – Phase difference map.