qsiprep.interfaces.ants module

class qsiprep.interfaces.ants.ConvertTransformFile(command=None, terminal_output=None, write_cmdline=False, **inputs)[source]

Bases: CommandLine

Wrapped executable: ConvertTransformFile.

Mandatory Inputs:

in_transform (a string or os.PathLike object referring to an existing file) – 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.

  • dimension (3 or 2) – Maps to a command-line argument: %d (position: 0). (Nipype default value: 3)

  • 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_transform (a string or os.PathLike object) – Maps to a command-line argument: %s (position: 2).

Outputs:

out_transform (a string or os.PathLike object referring to an existing file)

class qsiprep.interfaces.ants.GetImageType(from_file=None, resource_monitor=None, **inputs)[source]

Bases: SimpleInterface

Use to determine what to send to –input-image-type.

Mandatory Inputs:

image (a pathlike object or string representing an existing file)

Outputs:

image_type (0 or 1 or 2 or 3)

class qsiprep.interfaces.ants.ImageMath(command=None, terminal_output=None, write_cmdline=False, **inputs)[source]

Bases: CommandLine

Wrapped executable: ImageMath.

Mandatory Inputs:

in_file (a pathlike object or string representing an existing file) – Maps to a command-line argument: %s (position: 3).

Optional Inputs:

  • dimension (3 or 2 or 4) – Maps to a command-line argument: %d (position: 0). (Nipype default value: 3)

  • operation (a string) – Maps to a command-line argument: %s (position: 2).

  • out_file (a pathlike object or string representing a file) – Maps to a command-line argument: %s (position: 1).

  • secondary_arg (a string) – Maps to a command-line argument: %s.

  • secondary_file (a pathlike object or string representing a file) – Maps to a command-line argument: %s.

Outputs:

out_file (a pathlike object or string representing an existing file)

class qsiprep.interfaces.ants.MultivariateTemplateConstruction2(**inputs)[source]

Bases: ANTSCommand

Wrapped executable: antsMultivariateTemplateConstruction2.sh.

Mandatory Inputs:

  • gradient_step (a float) – Maps to a command-line argument: -g %.3f. (Nipype default value: 0.25)

  • metric (a string) – Maps to a command-line argument: -m %s. (Nipype default value: CC)

  • transform (‘BSplineSyN’ or ‘SyN’ or ‘Affine’) – Maps to a command-line argument: -t %s. (Nipype default value: BSplineSyN)

Optional Inputs:

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

  • backup_images (a boolean) – Maps to a command-line argument: -b %d.

  • dimension (2 or 3 or 4) – Maps to a command-line argument: -d %d. (Nipype default value: 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: {})

  • image_statistic (0 or 1 or 2) – Statistic used to summarize images. 0=mean, 1= mean of normalized intensities, 2=median. (Nipype default value: 0)

  • input_file (a pathlike object or string representing an existing file) – Txt or csv file with images.

  • input_images (a list of items which are a pathlike object or string representing an existing file or a list of items which are a pathlike object or string representing an existing file) – List of images or lists of images. Maps to a command-line argument: %s (position: -1). Mutually exclusive with inputs: input_file.

  • iteration_limit (an integer) – Maximum number of iterations. Maps to a command-line argument: -i %d. (Nipype default value: 4)

  • modality_weights (a list of items which are any value) – (Nipype default value: [1])

  • n4_bias_correct (a boolean) – Maps to a command-line argument: -n %d. (Nipype default value: True)

  • num_cores (an integer) – Maps to a command-line argument: -j %d. (Nipype default value: 0)

  • num_modalities (an integer) – Number of modalities used to construct the template (default 1): For example, if one wanted to create a multimodal template consisting of T1,T2,and FA components (“-k 3”). Maps to a command-line argument: -k %d. (Nipype default value: 1)

  • num_threads (an integer) – Number of ITK threads to use. (Nipype default value: 1)

  • output_prefix (a string)

  • parallel_control (0 or 1 or 2 or 3 or 4 or 5) – Control for parallel computation 0 = run serially, 1 = SGE qsub, 2 = use PEXEC (localhost), 3 = Apple XGrid, 4 = PBS qsub, 5 = SLURM. Maps to a command-line argument: -c %d. (Nipype default value: 0)

  • use_full_affine (a boolean) – Maps to a command-line argument: -y %d. (Nipype default value: False)

  • usefloat (a boolean) – Maps to a command-line argument: -e %d. (Nipype default value: True)

Outputs:

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

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

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

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