xcp_d.interfaces.plotting.SlicesDir

class xcp_d.interfaces.plotting.SlicesDir(**inputs)[source]

Wrapped executable: slicesdir.

Run slicesdir.

Notes

Usage: slicesdir [-o] [-p <image>] [-e <thr>] [-S] <filelist> -o : filelist is pairs ( <underlying> <red-outline> ) of images -p <image> : use <image> as red-outline image on top of all images in <filelist> -e <thr> : use the specified threshold for edges (if >0 use this proportion of max-min,

if <0, use the absolute value)

-S

: output every second axial slice rather than just 9 ortho slices

Mandatory Inputs:

in_files (a list of items which are a pathlike object or string representing an existing file) – List of files to process. Maps to a command-line argument: %s (position: -1).

Optional Inputs:

  • args (a string) – Additional parameters to the command. Maps to a command-line argument: %s.

  • edge_threshold (a float) – Use the specified threshold for edges (if >0 use this proportion of max-min, if <0, use the absolute value). Maps to a command-line argument: -e %.03f (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: {})

  • is_pairs (a boolean) – Filelist is pairs ( <underlying> <red-outline> ) of images. Maps to a command-line argument: -o (position: 0).

  • out_extension (‘.gif’ or ‘.png’ or ‘.svg’) – Convenience parameter to let xcp_d select the extension. (Nipype default value: .gif)

  • outline_image (a pathlike object or string representing an existing file) – Use <image> as red-outline image on top of all images in <filelist>. Maps to a command-line argument: -p %s (position: 1).

  • output_odd_axials (a boolean) – Output every second axial slice rather than just 9 ortho slices. Maps to a command-line argument: -S (position: 3).

  • output_type (‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’) – FSL output type.

Outputs:

  • out_dir (a pathlike object or string representing an existing directory) – Output directory.

  • out_files (a list of items which are a pathlike object or string representing an existing file) – List of generated PNG files.

__init__(**inputs)[source]

Subclasses must implement __init__

Methods

__init__(**inputs)

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_output_type(output_type)

Set the default output type for FSL classes.

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