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_file : a pathlike object or string representing an existing file
- The input floating/source image. Maps to a command-line argument:
-flo %s.- ref_file : a pathlike object or string representing an existing file
- The input reference/target image. Maps to a command-line argument:
-ref %s.
- aff_direct_flag : a boolean
- Directly optimise the affine parameters. Maps to a command-line argument:
-affDirect.- aff_file : a pathlike object or string representing a file
- The output affine matrix file. Maps to a command-line argument:
-aff %s.- args : a unicode string
- Additional parameters to the command. Maps to a command-line argument:
%s.- cog_flag : a boolean
- Use the masks centre of mass to initialise the transformation. Maps to a command-line argument:
-cog.- 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:
{})- flo_low_val : a float
- Lower threshold value on floating image. Maps to a command-line argument:
-floLowThr %f.- flo_up_val : a float
- Upper threshold value on floating image. Maps to a command-line argument:
-floUpThr %f.- fmask_file : a pathlike object or string representing an existing file
- The input floating mask. Maps to a command-line argument:
-fmask %s.- gpuid_val : an integer (int or long)
- Device to use id. Maps to a command-line argument:
-gpuid %i.- i_val : a long integer >= 0
- Percent of inlier blocks. Maps to a command-line argument:
-pi %d.- in_aff_file : a pathlike object or string representing an existing file
- The input affine transformation. Maps to a command-line argument:
-inaff %s.- ln_val : a long integer >= 0
- Number of resolution levels to create. Maps to a command-line argument:
-ln %d.- lp_val : a long integer >= 0
- Number of resolution levels to perform. Maps to a command-line argument:
-lp %d.- maxit_val : a long integer >= 0
- Maximum number of iterations. Maps to a command-line argument:
-maxit %d.- nac_flag : a boolean
- Use nifti header to initialise transformation. Maps to a command-line argument:
-nac.- nosym_flag : a boolean
- Turn off symmetric registration. Maps to a command-line argument:
-noSym.- omp_core_val : an integer (int or long)
- Number of openmp thread to use. Maps to a command-line argument:
-omp %i. (Nipype default value:1)- platform_val : an integer (int or long)
- Platform index. Maps to a command-line argument:
-platf %i.- ref_low_val : a float
- Lower threshold value on reference image. Maps to a command-line argument:
-refLowThr %f.- ref_up_val : a float
- Upper threshold value on reference image. Maps to a command-line argument:
-refUpThr %f.- res_file : a pathlike object or string representing a file
- The affine transformed floating image. Maps to a command-line argument:
-res %s.- rig_only_flag : a boolean
- Do only a rigid registration. Maps to a command-line argument:
-rigOnly.- rmask_file : a pathlike object or string representing an existing file
- The input reference mask. Maps to a command-line argument:
-rmask %s.- smoo_f_val : a float
- Amount of smoothing to apply to floating image. Maps to a command-line argument:
-smooF %f.- smoo_r_val : a float
- Amount of smoothing to apply to reference image. Maps to a command-line argument:
-smooR %f.- v_val : a long integer >= 0
- Percent of blocks that are active. Maps to a command-line argument:
-pv %d.- verbosity_off_flag : a boolean
- Turn off verbose output. Maps to a command-line argument:
-voff.
- aff_file : a pathlike object or string representing a file
- The output affine file.
- avg_output : a string
- Output string in the format for reg_average.
- res_file : a 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_file : a pathlike object or string representing an existing file
- The input floating/source image. Maps to a command-line argument:
-flo %s.- ref_file : a pathlike object or string representing an existing file
- The input reference/target image. Maps to a command-line argument:
-ref %s.
- aff_file : a pathlike object or string representing an existing file
- The input affine transformation file. Maps to a command-line argument:
-aff %s.- amc_flag : a boolean
- Use additive NMI. Maps to a command-line argument:
-amc.- args : a unicode string
- Additional parameters to the command. Maps to a command-line argument:
%s.- be_val : a float
- Bending energy value. Maps to a command-line argument:
-be %f.- cpp_file : a pathlike object or string representing a file
- The output CPP file. Maps to a command-line argument:
-cpp %s.- 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:
{})- fbn2_val : a 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_val : a long integer >= 0
- Number of bins in the histogram for reference image. Maps to a command-line argument:
--fbn %d.- flo_smooth_val : a float
- Smoothing kernel width for floating image. Maps to a command-line argument:
-smooF %f.- flwth2_thr_val : a 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_val : a float
- Lower threshold for floating image. Maps to a command-line argument:
--fLwTh %f.- fmask_file : a pathlike object or string representing an existing file
- Floating image mask. Maps to a command-line argument:
-fmask %s.- fupth2_thr_val : a 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_val : a float
- Upper threshold for floating image. Maps to a command-line argument:
--fUpTh %f.- incpp_file : a pathlike object or string representing an existing file
- The input cpp transformation file. Maps to a command-line argument:
-incpp %s.- jl_val : a float
- Log of jacobian of deformation penalty value. Maps to a command-line argument:
-jl %f.- kld2_flag : a long integer >= 0
- Use KL divergence as the similarity measure for a given time point. Maps to a command-line argument:
-kld %d.- kld_flag : a boolean
- Use KL divergence as the similarity measure. Maps to a command-line argument:
--kld.- le_val : a float
- Linear elasticity penalty term. Maps to a command-line argument:
-le %f.- ln_val : a long integer >= 0
- Number of resolution levels to create. Maps to a command-line argument:
-ln %d.- lncc2_val : a 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_val : a float
- SD of the Gaussian for computing LNCC. Maps to a command-line argument:
--lncc %f.- lp_val : a long integer >= 0
- Number of resolution levels to perform. Maps to a command-line argument:
-lp %d.- maxit_val : a long integer >= 0
- Maximum number of iterations per level. Maps to a command-line argument:
-maxit %d.- nmi_flag : a boolean
- Use NMI even when other options are specified. Maps to a command-line argument:
--nmi.- no_app_jl_flag : a boolean
- Do not approximate the log of jacobian penalty at control points only. Maps to a command-line argument:
-noAppJL.- noconj_flag : a boolean
- Use simple GD optimization. Maps to a command-line argument:
-noConj.- nopy_flag : a boolean
- Do not use the multiresolution approach. Maps to a command-line argument:
-nopy.- nox_flag : a boolean
- Don’t optimise in x direction. Maps to a command-line argument:
-nox.- noy_flag : a boolean
- Don’t optimise in y direction. Maps to a command-line argument:
-noy.- noz_flag : a boolean
- Don’t optimise in z direction. Maps to a command-line argument:
-noz.- omp_core_val : an integer (int or long)
- Number of openmp thread to use. Maps to a command-line argument:
-omp %i. (Nipype default value:1)- pad_val : a float
- Padding value. Maps to a command-line argument:
-pad %f.- pert_val : a long integer >= 0
- Add perturbation steps after each optimization step. Maps to a command-line argument:
-pert %d.- rbn2_val : a 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_val : a long integer >= 0
- Number of bins in the histogram for reference image. Maps to a command-line argument:
--rbn %d.- ref_smooth_val : a float
- Smoothing kernel width for reference image. Maps to a command-line argument:
-smooR %f.- res_file : a pathlike object or string representing a file
- The output resampled image. Maps to a command-line argument:
-res %s.- rlwth2_thr_val : a 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_val : a float
- Lower threshold for reference image. Maps to a command-line argument:
--rLwTh %f.- rmask_file : a pathlike object or string representing an existing file
- Reference image mask. Maps to a command-line argument:
-rmask %s.- rupth2_thr_val : a 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_val : a float
- Upper threshold for reference image. Maps to a command-line argument:
--rUpTh %f.- smooth_grad_val : a float
- Kernel width for smoothing the metric gradient. Maps to a command-line argument:
-smoothGrad %f.- ssd2_flag : a long integer >= 0
- Use SSD as the similarity measure for a given time point. Maps to a command-line argument:
-ssd %d.- ssd_flag : a boolean
- Use SSD as the similarity measure. Maps to a command-line argument:
--ssd.- sx_val : a float
- Final grid spacing along the x axes. Maps to a command-line argument:
-sx %f.- sy_val : a float
- Final grid spacing along the y axes. Maps to a command-line argument:
-sy %f.- sz_val : a float
- Final grid spacing along the z axes. Maps to a command-line argument:
-sz %f.- vel_flag : a boolean
- Use velocity field integration. Maps to a command-line argument:
-vel.- verbosity_off_flag : a boolean
- Turn off verbose output. Maps to a command-line argument:
-voff.
- avg_output : a string
- Output string in the format for reg_average.
- cpp_file : a pathlike object or string representing a file
- The output CPP file.
- invcpp_file : a pathlike object or string representing a file
- The output inverse CPP file.
- invres_file : a pathlike object or string representing a file
- The output inverse res file.
- res_file : a pathlike object or string representing a file
- The output resampled image.