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 unicode 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 (int or long)

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

i_vala long 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_vala long integer >= 0

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

lp_vala long integer >= 0

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

maxit_vala long 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 (int or long)

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

platform_valan integer (int or long)

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_vala long 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 unicode 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: (a long integer >= 0, a long 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_vala long 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: (a long 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: (a long 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_flaga long 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_vala long integer >= 0

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

lncc2_vala tuple of the form: (a long 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_vala long integer >= 0

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

maxit_vala long 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 (int or long)

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_vala long integer >= 0

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

rbn2_vala tuple of the form: (a long integer >= 0, a long 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_vala long 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: (a long 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: (a long 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_flaga long 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.