qsirecon.interfaces.bids module

Interfaces for handling BIDS-like neuroimaging structures

Fetch some example data:

>>> import os
>>> from niworkflows import data
>>> data_root = data.get_bids_examples(variant='BIDS-examples-1-enh-ds054')
>>> os.chdir(data_root)

Disable warnings:

>>> from nipype import logging
>>> logging.getLogger('nipype.interface').setLevel('ERROR')
class qsirecon.interfaces.bids.DerivativesDataSink(allowed_entities=None, out_path_base=None, **inputs)[source]

Bases: DerivativesDataSink

Store derivative files.

A child class of the niworkflows DerivativesDataSink, using xcp_d’s configuration files.

Mandatory Inputs:

  • in_file (a list of items which are a pathlike object or string representing an existing file) – The object to be saved.

  • source_file (a list of items which are a pathlike object or string representing a file) – The source file(s) to extract entities from.

Optional Inputs:

  • base_directory (a string or os.PathLike object) – Path to the base directory for storing data.

  • check_hdr (a boolean) – Fix headers of NIfTI outputs. (Nipype default value: True)

  • compress (a list of items which are a boolean or None) – Whether in_file should be compressed (True), uncompressed (False) or left unmodified (None, default). (Nipype default value: [])

  • data_dtype (a string) – NumPy datatype to coerce NIfTI data to, or source tomatch the input file dtype.

  • dismiss_entities (a list of items which are a string or None) – A list entities that will not be propagated from the source file. (Nipype default value: [])

  • meta_dict (a dictionary with keys which are a value of class ‘str’ and with values which are any value) – An input dictionary containing metadata.

Outputs:

  • compression (a list of items which are a boolean or None) – Whether in_file should be compressed (True), uncompressed (False) or left unmodified (None).

  • fixed_hdr (a list of items which are a boolean) – Whether derivative header was fixed.

  • out_file (a list of items which are a pathlike object or string representing an existing file)

  • out_meta (a list of items which are a pathlike object or string representing an existing file)

out_path_base = ''
class qsirecon.interfaces.bids.ReconDerivativesDataSink(allowed_entities=None, out_path_base=None, **inputs)[source]

Bases: DerivativesDataSink

Mandatory Inputs:

  • in_file (a string or os.PathLike object referring to an existing directory or a list of items which are a pathlike object or string representing an existing file) – The object to be saved.

  • source_file (a list of items which are a pathlike object or string representing a file) – The source file(s) to extract entities from.

Optional Inputs:

  • atlas (a string) – Label for label field. (Nipype default value: "")

  • base_directory (a string or os.PathLike object) – Path to the base directory for storing data.

  • bundle (a string) – Label for bundle field. (Nipype default value: "")

  • bundles (a string) – Label for bundles field. (Nipype default value: "")

  • check_hdr (a boolean) – Fix headers of NIfTI outputs. (Nipype default value: True)

  • compress (a list of items which are a boolean or None) – Whether in_file should be compressed (True), uncompressed (False) or left unmodified (None, default). (Nipype default value: [])

  • data_dtype (a string) – NumPy datatype to coerce NIfTI data to, or source tomatch the input file dtype.

  • dismiss_entities (a list of items which are a string or None) – A list entities that will not be propagated from the source file. (Nipype default value: [])

  • extension (a string) – Extension (will be ignored). (Nipype default value: "")

  • label (a string) – Label for label field. (Nipype default value: "")

  • meta_dict (a dictionary with keys which are a value of class ‘str’ and with values which are any value) – An input dictionary containing metadata.

  • model (a string) – Label for model field. (Nipype default value: "")

  • param (a string) – Label for parameter field. (Nipype default value: "")

  • qsirecon_suffix (a string) – Name appended to qsirecon- in the derivatives. (Nipype default value: "")

Outputs:

  • compression (a list of items which are a boolean or None) – Whether in_file should be compressed (True), uncompressed (False) or left unmodified (None).

  • fixed_hdr (a list of items which are a boolean) – Whether derivative header was fixed.

  • out_file (a string) – The output file/folder.

  • out_meta (a list of items which are a pathlike object or string representing an existing file)

out_path_base = 'qsirecon'
qsirecon.interfaces.bids.get_bids_params(fullpath)[source]
qsirecon.interfaces.bids.get_recon_output_name(base_dir, source_file, derivative_file, output_bids_entities, use_ext=True, qsirecon_suffix=None, dismiss_entities=None)[source]