xcp_d.interfaces.workbench.CiftiSeparateVolumeAll

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

Wrapped executable: wb_command -cifti-separate.

Extract volumetric data from CIFTI file (.dtseries).

Other structures can also be extracted. The input cifti file must have a brain models mapping on the chosen dimension, columns for .dtseries,

Examples

>>> ciftiseparate = CiftiSeparateVolumeAll()
>>> ciftiseparate.inputs.in_file = 'sub-01_task-rest.dtseries.nii'
>>> ciftiseparate.inputs.out_file = 'sub_01_task-rest_volumetric_data.nii.gz'
>>> ciftiseparate.inputs.label_file = 'sub_01_task-rest_labels.nii.gz'
>>> ciftiseparate.inputs.direction = 'COLUMN'
>>> ciftiseparate.cmdline
wb_command  -cifti-separate 'sub-01XX_task-rest.dtseries.nii' COLUMN         -volume-all 'sub_01_task-rest_volumetric_data.nii.gz'         -label 'sub_01_task-rest_labels.nii.gz'

Mandatory Inputs:

direction (‘ROW’ or ‘COLUMN’) – Which dimension to smooth along, ROW or COLUMN. Maps to a command-line argument: %s (position: 1).
in_file (a pathlike object or string representing an existing file) – The input dense series. Maps to a command-line argument: %s (position: 0).

Optional Inputs:

args (a string) – Additional parameters to the command. Maps to a command-line argument: %s.
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: {})
label_file (a pathlike object or string representing a file) – A discrete segmentation NIFTI output. Maps to a command-line argument: -label %s (position: 3).
out_file (a pathlike object or string representing a file) – The NIFTI output. Maps to a command-line argument: -volume-all %s -crop (position: 2).

Outputs:

label_file (a pathlike object or string representing an existing file) – NIFTI file with labels.
out_file (a pathlike object or string representing an existing file) – NIFTI file with volumetric data.

__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`