xcp_d.interfaces.workbench.CiftiConvert

class xcp_d.interfaces.workbench.CiftiConvert(command=None, terminal_output=None, write_cmdline=False, **inputs)[source]

Wrapped executable: wb_command -cifti-convert.

Convert between CIFTI and NIFTI file formats.

Examples

>>> cifticonvert = CiftiConvert()
>>> cifticonvert.inputs.in_file = 'sub-01_task-rest_bold.dscalar.nii'
>>> cifticonvert.target = "to"
>>> cifticonvert.cmdline
wb_command -cifti-convert -to-nifti 'sub-01_task-rest_bold.dscalar.nii'         'sub-01_task-rest_bold_converted.nii.gz'

Mandatory Inputs:

in_file (a pathlike object or string representing an existing file) – The input file. Maps to a command-line argument: %s (position: 1).
target (‘from’ or ‘to’) – Convert either to or from nifti. Maps to a command-line argument: -%s-nifti (position: 0).

Optional Inputs:

TR (a float) – Repetition time in seconds. Used to reset timepoints. Maps to a command-line argument: -reset-timepoints %s 0 (position: 4).
args (a string) – Additional parameters to the command. Maps to a command-line argument: %s.
cifti_template (a pathlike object or string representing an existing file) – A cifti file with the dimension(s) and mapping(s) that should be used. Maps to a command-line argument: %s (position: 2).
environ (a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’) – Environment variables. (Nipype default value: {})
out_file (a pathlike object or string representing an existing file) – The output file. Maps to a command-line argument: %s (position: 3).

Outputs:

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

__init__(command=None, terminal_output=None, write_cmdline=False, **inputs)[source]: Subclasses must implement __init__

Methods

`__init__`([command, terminal_output, ...])	Subclasses must implement __init__
`aggregate_outputs`([runtime, needed_outputs])	Collate expected outputs and apply output traits validation.
`help`([returnhelp])	Prints class help
`load_inputs_from_json`(json_file[, overwrite])	A convenient way to load pre-set inputs from a JSON file.
`raise_exception`(runtime)
`run`([cwd, ignore_exception])	Execute this interface.
`save_inputs_to_json`(json_file)	A convenient way to save current inputs to a JSON file.
`set_default_terminal_output`(output_type)	Set the default terminal output for CommandLine Interfaces.
`version_from_command`([flag, cmd])

Attributes

`always_run`	Should the interface be always run even if the inputs were not changed? Only applies to interfaces being run within a workflow context.
`can_resume`	Defines if the interface can reuse partial results after interruption.
`cmd`	sets base command, immutable
`cmdline`	command plus any arguments (args) validates arguments and generates command line
`resource_monitor`
`terminal_output`
`version`	interfaces should implement a version property
`write_cmdline`