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# nipype.interfaces.niftyreg.reg module

The reg module provides classes for interfacing with the niftyreg registration command line tools.

The interfaces were written to work with niftyreg version 1.5.10

## RegAladin

Link to code

> Bases: NiftyRegCommand

> Wrapped executable: `reg_aladin`.

> Interface for executable reg_aladin from NiftyReg platform.

> Block Matching algorithm for symmetric global registration. Based on Modat et al., “Global image registration using asymmetric block-matching approach” J. Med. Img. 1(2) 024003, 2014, doi: 10.1117/1.JMI.1.2.024003

> Source code

> Examples

>     >>> from nipype.interfaces import niftyreg
>     >>> node = niftyreg.RegAladin()
>     >>> node.inputs.ref_file = 'im1.nii'
>     >>> node.inputs.flo_file = 'im2.nii'
>     >>> node.inputs.rmask_file = 'mask.nii'
>     >>> node.inputs.omp_core_val = 4
>     >>> node.cmdline
>     'reg_aladin -aff im2_aff.txt -flo im2.nii -omp 4 -ref im1.nii -res im2_res.nii.gz -rmask mask.nii'

> flo_filea pathlike object or string representing an existing file

>   The input floating/source image. Maps to a command-line argument: `-flo %s`.

> ref_filea pathlike object or string representing an existing file

>   The input reference/target image. Maps to a command-line argument: `-ref %s`.

> aff_direct_flaga boolean

>   Directly optimise the affine parameters. Maps to a command-line argument: `-affDirect`.

> aff_filea pathlike object or string representing a file

>   The output affine matrix file. Maps to a command-line argument: `-aff %s`.

> argsa string

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

> cog_flaga boolean

>   Use the masks centre of mass to initialise the transformation. Maps to a command-line argument: `-cog`.

> 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: `{}`)

> flo_low_vala float

>   Lower threshold value on floating image. Maps to a command-line argument: `-floLowThr %f`.

> flo_up_vala float

>   Upper threshold value on floating image. Maps to a command-line argument: `-floUpThr %f`.

> fmask_filea pathlike object or string representing an existing file

>   The input floating mask. Maps to a command-line argument: `-fmask %s`.

> gpuid_valan integer

>   Device to use id. Maps to a command-line argument: `-gpuid %i`.

> i_valan integer >= 0

>   Percent of inlier blocks. Maps to a command-line argument: `-pi %d`.

> in_aff_filea pathlike object or string representing an existing file

>   The input affine transformation. Maps to a command-line argument: `-inaff %s`.

> ln_valan integer >= 0

>   Number of resolution levels to create. Maps to a command-line argument: `-ln %d`.

> lp_valan integer >= 0

>   Number of resolution levels to perform. Maps to a command-line argument: `-lp %d`.

> maxit_valan integer >= 0

>   Maximum number of iterations. Maps to a command-line argument: `-maxit %d`.

> nac_flaga boolean

>   Use nifti header to initialise transformation. Maps to a command-line argument: `-nac`.

> nosym_flaga boolean

>   Turn off symmetric registration. Maps to a command-line argument: `-noSym`.

> omp_core_valan integer

>   Number of openmp thread to use. Maps to a command-line argument: `-omp %i`. (Nipype default value: `1`)

> platform_valan integer

>   Platform index. Maps to a command-line argument: `-platf %i`.

> ref_low_vala float

>   Lower threshold value on reference image. Maps to a command-line argument: `-refLowThr %f`.

> ref_up_vala float

>   Upper threshold value on reference image. Maps to a command-line argument: `-refUpThr %f`.

> res_filea pathlike object or string representing a file

>   The affine transformed floating image. Maps to a command-line argument: `-res %s`.

> rig_only_flaga boolean

>   Do only a rigid registration. Maps to a command-line argument: `-rigOnly`.

> rmask_filea pathlike object or string representing an existing file

>   The input reference mask. Maps to a command-line argument: `-rmask %s`.

> smoo_f_vala float

>   Amount of smoothing to apply to floating image. Maps to a command-line argument: `-smooF %f`.

> smoo_r_vala float

>   Amount of smoothing to apply to reference image. Maps to a command-line argument: `-smooR %f`.

> v_valan integer >= 0

>   Percent of blocks that are active. Maps to a command-line argument: `-pv %d`.

> verbosity_off_flaga boolean

>   Turn off verbose output. Maps to a command-line argument: `-voff`.

> aff_filea pathlike object or string representing a file

>   The output affine file.

> avg_outputa string

>   Output string in the format for reg_average.

> res_filea pathlike object or string representing a file

>   The output transformed image.

## RegF3D

Link to code

> Bases: NiftyRegCommand

> Wrapped executable: `reg_f3d`.

> Interface for executable reg_f3d from NiftyReg platform.

> Fast Free-Form Deformation (F3D) algorithm for non-rigid registration. Initially based on Modat et al., “Fast Free-Form Deformation using graphics processing units”, CMPB, 2010

> Source code

> Examples

>     >>> from nipype.interfaces import niftyreg
>     >>> node = niftyreg.RegF3D()
>     >>> node.inputs.ref_file = 'im1.nii'
>     >>> node.inputs.flo_file = 'im2.nii'
>     >>> node.inputs.rmask_file = 'mask.nii'
>     >>> node.inputs.omp_core_val = 4
>     >>> node.cmdline
>     'reg_f3d -cpp im2_cpp.nii.gz -flo im2.nii -omp 4 -ref im1.nii -res im2_res.nii.gz -rmask mask.nii'

> flo_filea pathlike object or string representing an existing file

>   The input floating/source image. Maps to a command-line argument: `-flo %s`.

> ref_filea pathlike object or string representing an existing file

>   The input reference/target image. Maps to a command-line argument: `-ref %s`.

> aff_filea pathlike object or string representing an existing file

>   The input affine transformation file. Maps to a command-line argument: `-aff %s`.

> amc_flaga boolean

>   Use additive NMI. Maps to a command-line argument: `-amc`.

> argsa string

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

> be_vala float

>   Bending energy value. Maps to a command-line argument: `-be %f`.

> cpp_filea pathlike object or string representing a file

>   The output CPP file. Maps to a command-line argument: `-cpp %s`.

> 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: `{}`)

> fbn2_vala tuple of the form: (an integer >= 0, an integer >= 0)

>   Number of bins in the histogram for reference image for given time point. Maps to a command-line argument: `-fbn %d %d`.

> fbn_valan integer >= 0

>   Number of bins in the histogram for reference image. Maps to a command-line argument: `--fbn %d`.

> flo_smooth_vala float

>   Smoothing kernel width for floating image. Maps to a command-line argument: `-smooF %f`.

> flwth2_thr_vala tuple of the form: (an integer >= 0, a float)

>   Lower threshold for floating image at the specified time point. Maps to a command-line argument: `-fLwTh %d %f`.

> flwth_thr_vala float

>   Lower threshold for floating image. Maps to a command-line argument: `--fLwTh %f`.

> fmask_filea pathlike object or string representing an existing file

>   Floating image mask. Maps to a command-line argument: `-fmask %s`.

> fupth2_thr_vala tuple of the form: (an integer >= 0, a float)

>   Upper threshold for floating image at the specified time point. Maps to a command-line argument: `-fUpTh %d %f`.

> fupth_thr_vala float

>   Upper threshold for floating image. Maps to a command-line argument: `--fUpTh %f`.

> incpp_filea pathlike object or string representing an existing file

>   The input cpp transformation file. Maps to a command-line argument: `-incpp %s`.

> jl_vala float

>   Log of jacobian of deformation penalty value. Maps to a command-line argument: `-jl %f`.

> kld2_flagan integer >= 0

>   Use KL divergence as the similarity measure for a given time point. Maps to a command-line argument: `-kld %d`.

> kld_flaga boolean

>   Use KL divergence as the similarity measure. Maps to a command-line argument: `--kld`.

> le_vala float

>   Linear elasticity penalty term. Maps to a command-line argument: `-le %f`.

> ln_valan integer >= 0

>   Number of resolution levels to create. Maps to a command-line argument: `-ln %d`.

> lncc2_vala tuple of the form: (an integer >= 0, a float)

>   SD of the Gaussian for computing LNCC for a given time point. Maps to a command-line argument: `-lncc %d %f`.

> lncc_vala float

>   SD of the Gaussian for computing LNCC. Maps to a command-line argument: `--lncc %f`.

> lp_valan integer >= 0

>   Number of resolution levels to perform. Maps to a command-line argument: `-lp %d`.

> maxit_valan integer >= 0

>   Maximum number of iterations per level. Maps to a command-line argument: `-maxit %d`.

> nmi_flaga boolean

>   Use NMI even when other options are specified. Maps to a command-line argument: `--nmi`.

> no_app_jl_flaga boolean

>   Do not approximate the log of jacobian penalty at control points only. Maps to a command-line argument: `-noAppJL`.

> noconj_flaga boolean

>   Use simple GD optimization. Maps to a command-line argument: `-noConj`.

> nopy_flaga boolean

>   Do not use the multiresolution approach. Maps to a command-line argument: `-nopy`.

> nox_flaga boolean

>   Don’t optimise in x direction. Maps to a command-line argument: `-nox`.

> noy_flaga boolean

>   Don’t optimise in y direction. Maps to a command-line argument: `-noy`.

> noz_flaga boolean

>   Don’t optimise in z direction. Maps to a command-line argument: `-noz`.

> omp_core_valan integer

>   Number of openmp thread to use. Maps to a command-line argument: `-omp %i`. (Nipype default value: `1`)

> pad_vala float

>   Padding value. Maps to a command-line argument: `-pad %f`.

> pert_valan integer >= 0

>   Add perturbation steps after each optimization step. Maps to a command-line argument: `-pert %d`.

> rbn2_vala tuple of the form: (an integer >= 0, an integer >= 0)

>   Number of bins in the histogram for reference image for given time point. Maps to a command-line argument: `-rbn %d %d`.

> rbn_valan integer >= 0

>   Number of bins in the histogram for reference image. Maps to a command-line argument: `--rbn %d`.

> ref_smooth_vala float

>   Smoothing kernel width for reference image. Maps to a command-line argument: `-smooR %f`.

> res_filea pathlike object or string representing a file

>   The output resampled image. Maps to a command-line argument: `-res %s`.

> rlwth2_thr_vala tuple of the form: (an integer >= 0, a float)

>   Lower threshold for reference image at the specified time point. Maps to a command-line argument: `-rLwTh %d %f`.

> rlwth_thr_vala float

>   Lower threshold for reference image. Maps to a command-line argument: `--rLwTh %f`.

> rmask_filea pathlike object or string representing an existing file

>   Reference image mask. Maps to a command-line argument: `-rmask %s`.

> rupth2_thr_vala tuple of the form: (an integer >= 0, a float)

>   Upper threshold for reference image at the specified time point. Maps to a command-line argument: `-rUpTh %d %f`.

> rupth_thr_vala float

>   Upper threshold for reference image. Maps to a command-line argument: `--rUpTh %f`.

> smooth_grad_vala float

>   Kernel width for smoothing the metric gradient. Maps to a command-line argument: `-smoothGrad %f`.

> ssd2_flagan integer >= 0

>   Use SSD as the similarity measure for a given time point. Maps to a command-line argument: `-ssd %d`.

> ssd_flaga boolean

>   Use SSD as the similarity measure. Maps to a command-line argument: `--ssd`.

> sx_vala float

>   Final grid spacing along the x axes. Maps to a command-line argument: `-sx %f`.

> sy_vala float

>   Final grid spacing along the y axes. Maps to a command-line argument: `-sy %f`.

> sz_vala float

>   Final grid spacing along the z axes. Maps to a command-line argument: `-sz %f`.

> vel_flaga boolean

>   Use velocity field integration. Maps to a command-line argument: `-vel`.

> verbosity_off_flaga boolean

>   Turn off verbose output. Maps to a command-line argument: `-voff`.

> avg_outputa string

>   Output string in the format for reg_average.

> cpp_filea pathlike object or string representing a file

>   The output CPP file.

> invcpp_filea pathlike object or string representing a file

>   The output inverse CPP file.

> invres_filea pathlike object or string representing a file

>   The output inverse res file.

> res_filea pathlike object or string representing a file

>   The output resampled image.