nipype.interfaces.ants.legacy module

ANTS Legacy Interfaces

These interfaces are for programs that have been deprecated by ANTs, but are preserved for backwards compatibility.

GenWarpFields

Link to code

Bases: antsIntroduction

Wrapped executable: antsIntroduction.sh.

input_imagea pathlike object or string representing an existing file

Input image to warp to template. Maps to a command-line argument: -i %s.

reference_imagea pathlike object or string representing an existing file

Template file to warp to. Maps to a command-line argument: -r %s.

argsa string

Additional parameters to the command. Maps to a command-line argument: %s.

bias_field_correctiona boolean

Applies bias field correction to moving image. Maps to a command-line argument: -n 1.

dimension3 or 2

Image dimension (2 or 3). Maps to a command-line argument: -d %d (position: 1). (Nipype default value: 3)

environa 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: {})

force_proceeda boolean

Force script to proceed even if headers may be incompatible. Maps to a command-line argument: -f 1.

inverse_warp_template_labelsa boolean

Applies inverse warp to the template labels to estimate label positions in target space (use for template-based segmentation). Maps to a command-line argument: -l.

max_iterationsa list of items which are an integer

Maximum number of iterations (must be list of integers in the form [J,K,L…]: J = coarsest resolution iterations, K = middle resolution interations, L = fine resolution iterations. Maps to a command-line argument: -m %s.

num_threadsan integer

Number of ITK threads to use. (Nipype default value: 1)

out_prefixa string

Prefix that is prepended to all output files (default = ants_). Maps to a command-line argument: -o %s. (Nipype default value: ants_)

quality_checka boolean

Perform a quality check of the result. Maps to a command-line argument: -q 1.

similarity_metric‘PR’ or ‘CC’ or ‘MI’ or ‘MSQ’

Type of similartiy metric used for registration (CC = cross correlation, MI = mutual information, PR = probability mapping, MSQ = mean square difference). Maps to a command-line argument: -s %s.

transformation_model‘GR’ or ‘EL’ or ‘SY’ or ‘S2’ or ‘EX’ or ‘DD’ or ‘RI’ or ‘RA’

Type of transofmration model used for registration (EL = elastic transformation model, SY = SyN with time, arbitrary number of time points, S2 = SyN with time optimized for 2 time points, GR = greedy SyN, EX = exponential, DD = diffeomorphic demons style exponential mapping, RI = purely rigid, RA = affine rigid. Maps to a command-line argument: -t %s. (Nipype default value: GR)

affine_transformationa pathlike object or string representing an existing file

Affine (prefix_Affine.txt).

input_filea pathlike object or string representing an existing file

Input image (prefix_repaired.nii).

inverse_warp_fielda pathlike object or string representing an existing file

Inverse warp field (prefix_InverseWarp.nii).

output_filea pathlike object or string representing an existing file

Output image (prefix_deformed.nii).

warp_fielda pathlike object or string representing an existing file

Warp field (prefix_Warp.nii).

antsIntroduction

Link to code

Bases: ANTSCommand

Wrapped executable: antsIntroduction.sh.

Uses ANTS to generate matrices to warp data from one space to another.

Examples

>>> from nipype.interfaces.ants.legacy import antsIntroduction
>>> warp = antsIntroduction()
>>> warp.inputs.reference_image = 'Template_6.nii'
>>> warp.inputs.input_image = 'structural.nii'
>>> warp.inputs.max_iterations = [30,90,20]
>>> warp.cmdline
'antsIntroduction.sh -d 3 -i structural.nii -m 30x90x20 -o ants_ -r Template_6.nii -t GR'
input_imagea pathlike object or string representing an existing file

Input image to warp to template. Maps to a command-line argument: -i %s.

reference_imagea pathlike object or string representing an existing file

Template file to warp to. Maps to a command-line argument: -r %s.

argsa string

Additional parameters to the command. Maps to a command-line argument: %s.

bias_field_correctiona boolean

Applies bias field correction to moving image. Maps to a command-line argument: -n 1.

dimension3 or 2

Image dimension (2 or 3). Maps to a command-line argument: -d %d (position: 1). (Nipype default value: 3)

environa 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: {})

force_proceeda boolean

Force script to proceed even if headers may be incompatible. Maps to a command-line argument: -f 1.

inverse_warp_template_labelsa boolean

Applies inverse warp to the template labels to estimate label positions in target space (use for template-based segmentation). Maps to a command-line argument: -l.

max_iterationsa list of items which are an integer

Maximum number of iterations (must be list of integers in the form [J,K,L…]: J = coarsest resolution iterations, K = middle resolution interations, L = fine resolution iterations. Maps to a command-line argument: -m %s.

num_threadsan integer

Number of ITK threads to use. (Nipype default value: 1)

out_prefixa string

Prefix that is prepended to all output files (default = ants_). Maps to a command-line argument: -o %s. (Nipype default value: ants_)

quality_checka boolean

Perform a quality check of the result. Maps to a command-line argument: -q 1.

similarity_metric‘PR’ or ‘CC’ or ‘MI’ or ‘MSQ’

Type of similartiy metric used for registration (CC = cross correlation, MI = mutual information, PR = probability mapping, MSQ = mean square difference). Maps to a command-line argument: -s %s.

transformation_model‘GR’ or ‘EL’ or ‘SY’ or ‘S2’ or ‘EX’ or ‘DD’ or ‘RI’ or ‘RA’

Type of transofmration model used for registration (EL = elastic transformation model, SY = SyN with time, arbitrary number of time points, S2 = SyN with time optimized for 2 time points, GR = greedy SyN, EX = exponential, DD = diffeomorphic demons style exponential mapping, RI = purely rigid, RA = affine rigid. Maps to a command-line argument: -t %s. (Nipype default value: GR)

affine_transformationa pathlike object or string representing an existing file

Affine (prefix_Affine.txt).

input_filea pathlike object or string representing an existing file

Input image (prefix_repaired.nii).

inverse_warp_fielda pathlike object or string representing an existing file

Inverse warp field (prefix_InverseWarp.nii).

output_filea pathlike object or string representing an existing file

Output image (prefix_deformed.nii).

warp_fielda pathlike object or string representing an existing file

Warp field (prefix_Warp.nii).

buildtemplateparallel

Link to code

Bases: ANTSCommand

Wrapped executable: buildtemplateparallel.sh.

Generate a optimal average template

Warning

This can take a VERY long time to complete

Examples

>>> from nipype.interfaces.ants.legacy import buildtemplateparallel
>>> tmpl = buildtemplateparallel()
>>> tmpl.inputs.in_files = ['T1.nii', 'structural.nii']
>>> tmpl.inputs.max_iterations = [30, 90, 20]
>>> tmpl.cmdline
'buildtemplateparallel.sh -d 3 -i 4 -m 30x90x20 -o antsTMPL_ -c 0 -t GR T1.nii structural.nii'
in_filesa list of items which are a pathlike object or string representing an existing file

List of images to generate template from. Maps to a command-line argument: %s (position: -1).

argsa string

Additional parameters to the command. Maps to a command-line argument: %s.

bias_field_correctiona boolean

Applies bias field correction to moving image. Maps to a command-line argument: -n 1.

dimension3 or 2 or 4

Image dimension (2, 3 or 4). Maps to a command-line argument: -d %d (position: 1). (Nipype default value: 3)

environa 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: {})

gradient_step_sizea float

Smaller magnitude results in more cautious steps (default = .25). Maps to a command-line argument: -g %f.

iteration_limitan integer

Iterations of template construction. Maps to a command-line argument: -i %d. (Nipype default value: 4)

max_iterationsa list of items which are an integer

Maximum number of iterations (must be list of integers in the form [J,K,L…]: J = coarsest resolution iterations, K = middle resolution interations, L = fine resolution iterations. Maps to a command-line argument: -m %s.

num_coresan integer

Requires parallelization = 2 (PEXEC). Sets number of cpu cores to use. Maps to a command-line argument: -j %d. Requires inputs: parallelization.

num_threadsan integer

Number of ITK threads to use. (Nipype default value: 1)

out_prefixa string

Prefix that is prepended to all output files (default = antsTMPL_). Maps to a command-line argument: -o %s. (Nipype default value: antsTMPL_)

parallelization0 or 1 or 2

Control for parallel processing (0 = serial, 1 = use PBS, 2 = use PEXEC, 3 = use Apple XGrid. Maps to a command-line argument: -c %d. (Nipype default value: 0)

rigid_body_registrationa boolean

Registers inputs before creating template (useful if no initial template available). Maps to a command-line argument: -r 1.

similarity_metric‘PR’ or ‘CC’ or ‘MI’ or ‘MSQ’

Type of similartiy metric used for registration (CC = cross correlation, MI = mutual information, PR = probability mapping, MSQ = mean square difference). Maps to a command-line argument: -s %s.

transformation_model‘GR’ or ‘EL’ or ‘SY’ or ‘S2’ or ‘EX’ or ‘DD’

Type of transofmration model used for registration (EL = elastic transformation model, SY = SyN with time, arbitrary number of time points, S2 = SyN with time optimized for 2 time points, GR = greedy SyN, EX = exponential, DD = diffeomorphic demons style exponential mapping. Maps to a command-line argument: -t %s. (Nipype default value: GR)

use_first_as_targeta boolean

Uses first volume as target of all inputs. When not used, an unbiased average image is used to start.

final_template_filea pathlike object or string representing an existing file

Final ANTS template.

subject_outfilesa list of items which are a pathlike object or string representing an existing file

Outputs for each input image. Includes warp field, inverse warp, Affine, original image (repaired) and warped image (deformed).

template_filesa list of items which are a pathlike object or string representing an existing file

Templates from different stages of iteration.