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¶
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
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¶
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
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.