xcp_d.interfaces.workbench.CiftiCreateDenseScalar
- class xcp_d.interfaces.workbench.CiftiCreateDenseScalar(command=None, terminal_output=None, write_cmdline=False, **inputs)[source]
Wrapped executable:
wb_command -cifti-create-dense-scalar
.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
>>> cifticreatedensescalar = CiftiCreateDenseScalar() >>> cifticreatedensescalar.inputs.out_file = 'sub_01_task-rest.dscalar.nii' >>> cifticreatedensescalar.inputs.left_metric = 'sub_01_task-rest_hemi-L.func.gii' >>> cifticreatedensescalar.inputs.left_metric = 'sub_01_task-rest_hemi-R.func.gii' >>> cifticreatedensescalar.inputs.volume_data = 'sub_01_task-rest_subcortical.nii.gz' >>> cifticreatedensescalar.inputs.structure_label_volume = 'sub_01_task-rest_labels.nii.gz' >>> cifticreatedensescalar.cmdline wb_command -cifti-create-dense-scalar 'sub_01_task-rest.dscalar.nii' -left-metric 'sub_01_task-rest_hemi-L.func.gii' -right-metric 'sub_01_task-rest_hemi-R.func.gii' -volume-data 'sub_01_task-rest_subcortical.nii.gz' 'sub_01_task-rest_labels.nii.gz'
- Mandatory Inputs:
left_metric (a pathlike object or string representing an existing file) – The input surface data from the left hemisphere. Maps to a command-line argument:
-left-metric %s
(position: 1).right_metric (a pathlike object or string representing an existing file) – The input surface data from the right hemisphere. Maps to a command-line argument:
-right-metric %s
(position: 2).structure_label_volume (a pathlike object or string representing an existing file) – A label file indicating the structure of each voxel in volume_data. Maps to a command-line argument:
%s
(position: 4).volume_data (a pathlike object or string representing an existing file) – The input volumetric data. Maps to a command-line argument:
-volume %s
(position: 3).
- 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:
{}
)out_file (a pathlike object or string representing a file) – The CIFTI output. Maps to a command-line argument:
%s
(position: 0).
- Outputs:
out_file (a pathlike object or string representing an existing file) – Output CIFTI 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