nipype.interfaces.niftyreg.regutils module

The regutils module provides classes for interfacing with the niftyreg utility command line tools.

The interfaces were written to work with niftyreg version 1.5.10

RegAverage

Link to code

Bases: NiftyRegCommand

Wrapped executable: reg_average.

Interface for executable reg_average from NiftyReg platform.

Compute average matrix or image from a list of matrices or image. The tool can be use to resample images given input transformation parametrisation as well as to demean transformations in Euclidean or log-Euclidean space.

This interface is different than the others in the way that the options will be written in a command file that is given as a parameter.

Source code

Examples

>>> from nipype.interfaces import niftyreg
>>> node = niftyreg.RegAverage()
>>> one_file = 'im1.nii'
>>> two_file = 'im2.nii'
>>> three_file = 'im3.nii'
>>> node.inputs.avg_files = [one_file, two_file, three_file]
>>> node.cmdline  
'reg_average --cmd_file .../reg_average_cmd'
Optional Inputs:

  • args (a string) – Additional parameters to the command. Maps to a command-line argument: %s.

  • avg_files (a list of items which are a pathlike object or string representing a file) – Averaging of images/affine transformations. Maps to a command-line argument: -avg %s (position: 1). Mutually exclusive with inputs: avg_lts_files, avg_ref_file, demean1_ref_file, demean2_ref_file, demean3_ref_file, warp_files.

  • avg_lts_files (a list of items which are a pathlike object or string representing a file) – Robust average of affine transformations. Maps to a command-line argument: -avg_lts %s (position: 1). Mutually exclusive with inputs: avg_files, avg_ref_file, demean1_ref_file, demean2_ref_file, demean3_ref_file, warp_files.

  • avg_ref_file (a pathlike object or string representing a file) – All input images are resampled into the space of <reference image> and averaged. A cubic spline interpolation scheme is used for resampling. Maps to a command-line argument: -avg_tran %s (position: 1). Mutually exclusive with inputs: avg_files, avg_lts_files, demean1_ref_file, demean2_ref_file, demean3_ref_file. Requires inputs: warp_files.

  • demean1_ref_file (a pathlike object or string representing a file) – Average images and demean average image that have affine transformations to a common space. Maps to a command-line argument: -demean1 %s (position: 1). Mutually exclusive with inputs: avg_files, avg_lts_files, avg_ref_file, demean2_ref_file, demean3_ref_file. Requires inputs: warp_files.

  • demean2_ref_file (a pathlike object or string representing a file) – Average images and demean average image that have non-rigid transformations to a common space. Maps to a command-line argument: -demean2 %s (position: 1). Mutually exclusive with inputs: avg_files, avg_lts_files, avg_ref_file, demean1_ref_file, demean3_ref_file. Requires inputs: warp_files.

  • demean3_ref_file (a pathlike object or string representing a file) – Average images and demean average image that have linear and non-rigid transformations to a common space. Maps to a command-line argument: -demean3 %s (position: 1). Mutually exclusive with inputs: avg_files, avg_lts_files, avg_ref_file, demean1_ref_file, demean2_ref_file. Requires inputs: warp_files.

  • 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: {})

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

  • out_file (a pathlike object or string representing a file) – Output file name. Maps to a command-line argument: %s (position: 0).

  • warp_files (a list of items which are a pathlike object or string representing a file) – Transformation files and floating image pairs/triplets to the reference space. Maps to a command-line argument: %s (position: -1). Mutually exclusive with inputs: avg_files, avg_lts_files.

Outputs:

out_file (a pathlike object or string representing a file) – Output file name.

property RegAverage.cmdline

Rewrite the cmdline to write options in text_file.

RegJacobian

Link to code

Bases: NiftyRegCommand

Wrapped executable: reg_jacobian.

Interface for executable reg_resample from NiftyReg platform.

Tool to generate Jacobian determinant maps from transformation parametrisation generated by reg_f3d

Source code

Examples

>>> from nipype.interfaces import niftyreg
>>> node = niftyreg.RegJacobian()
>>> node.inputs.ref_file = 'im1.nii'
>>> node.inputs.trans_file = 'warpfield.nii'
>>> node.inputs.omp_core_val = 4
>>> node.cmdline
'reg_jacobian -omp 4 -ref im1.nii -trans warpfield.nii -jac warpfield_jac.nii.gz'
Mandatory Inputs:

trans_file (a pathlike object or string representing an existing file) – The input non-rigid transformation. Maps to a command-line argument: -trans %s.

Optional Inputs:

  • args (a string) – Additional parameters to the command. Maps to a command-line argument: %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: {})

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

  • out_file (a pathlike object or string representing a file) – The output jacobian determinant file name. Maps to a command-line argument: %s (position: -1).

  • ref_file (a pathlike object or string representing an existing file) – Reference/target file (required if specifying CPP transformations. Maps to a command-line argument: -ref %s.

  • type (‘jac’ or ‘jacL’ or ‘jacM’) – Type of jacobian outcome. Maps to a command-line argument: -%s (position: -2). (Nipype default value: jac)

Outputs:

out_file (a pathlike object or string representing a file) – The output file.

RegMeasure

Link to code

Bases: NiftyRegCommand

Wrapped executable: reg_measure.

Interface for executable reg_measure from NiftyReg platform.

Given two input images, compute the specified measure(s) of similarity

Source code

Examples

>>> from nipype.interfaces import niftyreg
>>> node = niftyreg.RegMeasure()
>>> node.inputs.ref_file = 'im1.nii'
>>> node.inputs.flo_file = 'im2.nii'
>>> node.inputs.measure_type = 'lncc'
>>> node.inputs.omp_core_val = 4
>>> node.cmdline
'reg_measure -flo im2.nii -lncc -omp 4 -out im2_lncc.txt -ref im1.nii'
Mandatory Inputs:

  • flo_file (a pathlike object or string representing an existing file) – The input floating/source image. Maps to a command-line argument: -flo %s.

  • measure_type (‘ncc’ or ‘lncc’ or ‘nmi’ or ‘ssd’) – Measure of similarity to compute. Maps to a command-line argument: -%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.

Optional Inputs:

  • args (a string) – Additional parameters to the command. Maps to a command-line argument: %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: {})

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

  • out_file (a pathlike object or string representing a file) – The output text file containing the measure. Maps to a command-line argument: -out %s.

Outputs:

out_file (a pathlike object or string representing a file) – The output text file containing the measure.

RegResample

Link to code

Bases: NiftyRegCommand

Wrapped executable: reg_resample.

Interface for executable reg_resample from NiftyReg platform.

Tool to resample floating image in the space of a defined reference image given a transformation parametrisation generated by reg_aladin, reg_f3d or reg_transform

Source code

Examples

>>> from nipype.interfaces import niftyreg
>>> node = niftyreg.RegResample()
>>> node.inputs.ref_file = 'im1.nii'
>>> node.inputs.flo_file = 'im2.nii'
>>> node.inputs.trans_file = 'warpfield.nii'
>>> node.inputs.inter_val = 'LIN'
>>> node.inputs.omp_core_val = 4
>>> node.cmdline
'reg_resample -flo im2.nii -inter 1 -omp 4 -ref im1.nii -trans warpfield.nii -res im2_res.nii.gz'
Mandatory Inputs:

  • 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.

Optional Inputs:

  • args (a string) – Additional parameters to the command. Maps to a command-line argument: %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: {})

  • inter_val (‘NN’ or ‘LIN’ or ‘CUB’ or ‘SINC’) – Interpolation type. Maps to a command-line argument: -inter %d.

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

  • out_file (a pathlike object or string representing a file) – The output filename of the transformed image. Maps to a command-line argument: %s (position: -1).

  • pad_val (a float) – Padding value. Maps to a command-line argument: -pad %f.

  • psf_alg (0 or 1) – Minimise the matrix metric (0) or the determinant (1) when estimating the PSF [0]. Maps to a command-line argument: -psf_alg %d.

  • psf_flag (a boolean) – Perform the resampling in two steps to resample an image to a lower resolution. Maps to a command-line argument: -psf.

  • tensor_flag (a boolean) – Resample Tensor Map. Maps to a command-line argument: -tensor.

  • trans_file (a pathlike object or string representing an existing file) – The input transformation file. Maps to a command-line argument: -trans %s.

  • type (‘res’ or ‘blank’) – Type of output. Maps to a command-line argument: -%s (position: -2). (Nipype default value: res)

  • verbosity_off_flag (a boolean) – Turn off verbose output. Maps to a command-line argument: -voff.

Outputs:

out_file (a pathlike object or string representing a file) – The output filename of the transformed image.

RegTools

Link to code

Bases: NiftyRegCommand

Wrapped executable: reg_tools.

Interface for executable reg_tools from NiftyReg platform.

Tool delivering various actions related to registration such as resampling the input image to a chosen resolution or remove the nan and inf in the input image by a specified value.

Source code

Examples

>>> from nipype.interfaces import niftyreg
>>> node = niftyreg.RegTools()
>>> node.inputs.in_file = 'im1.nii'
>>> node.inputs.mul_val = 4
>>> node.inputs.omp_core_val = 4
>>> node.cmdline
'reg_tools -in im1.nii -mul 4.0 -omp 4 -out im1_tools.nii.gz'
Mandatory Inputs:

in_file (a pathlike object or string representing an existing file) – The input image file path. Maps to a command-line argument: -in %s.

Optional Inputs:

  • add_val (a float or a pathlike object or string representing an existing file) – Add to the input image or value. Maps to a command-line argument: -add %s.

  • args (a string) – Additional parameters to the command. Maps to a command-line argument: %s.

  • bin_flag (a boolean) – Binarise the input image. Maps to a command-line argument: -bin.

  • chg_res_val (a tuple of the form: (a float, a float, a float)) – Change the resolution of the input image. Maps to a command-line argument: -chgres %f %f %f.

  • div_val (a float or a pathlike object or string representing an existing file) – Divide the input by image or value. Maps to a command-line argument: -div %s.

  • down_flag (a boolean) – Downsample the image by a factor of 2. Maps to a command-line argument: -down.

  • 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: {})

  • inter_val (‘NN’ or ‘LIN’ or ‘CUB’ or ‘SINC’) – Interpolation order to use to warp the floating image. Maps to a command-line argument: -interp %d.

  • iso_flag (a boolean) – Make output image isotropic. Maps to a command-line argument: -iso.

  • mask_file (a pathlike object or string representing an existing file) – Values outside the mask are set to NaN. Maps to a command-line argument: -nan %s.

  • mul_val (a float or a pathlike object or string representing an existing file) – Multiply the input by image or value. Maps to a command-line argument: -mul %s.

  • noscl_flag (a boolean) – Set scale, slope to 0 and 1. Maps to a command-line argument: -noscl.

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

  • out_file (a pathlike object or string representing a file) – The output file name. Maps to a command-line argument: -out %s.

  • rms_val (a pathlike object or string representing an existing file) – Compute the mean RMS between the images. Maps to a command-line argument: -rms %s.

  • smo_g_val (a tuple of the form: (a float, a float, a float)) – Smooth the input image using a Gaussian kernel. Maps to a command-line argument: -smoG %f %f %f.

  • smo_s_val (a tuple of the form: (a float, a float, a float)) – Smooth the input image using a cubic spline kernel. Maps to a command-line argument: -smoS %f %f %f.

  • sub_val (a float or a pathlike object or string representing an existing file) – Add to the input image or value. Maps to a command-line argument: -sub %s.

  • thr_val (a float) – Binarise the input image with the given threshold. Maps to a command-line argument: -thr %f.

Outputs:

out_file (a pathlike object or string representing an existing file) – The output file.

RegTransform

Link to code

Bases: NiftyRegCommand

Wrapped executable: reg_transform.

Interface for executable reg_transform from NiftyReg platform.

Tools to convert transformation parametrisation from one type to another as well as to compose, inverse or half transformations.

Source code

Examples

>>> from nipype.interfaces import niftyreg
>>> node = niftyreg.RegTransform()
>>> node.inputs.def_input = 'warpfield.nii'
>>> node.inputs.omp_core_val = 4
>>> node.cmdline  
'reg_transform -omp 4 -def warpfield.nii .../warpfield_trans.nii.gz'
Optional Inputs:

  • aff_2_rig_input (a pathlike object or string representing an existing file) – Extract the rigid component from affine transformation. Maps to a command-line argument: -aff2rig %s (position: -2). Mutually exclusive with inputs: def_input, disp_input, flow_input, comp_input, upd_s_form_input, inv_aff_input, inv_nrr_input, half_input, make_aff_input, flirt_2_nr_input.

  • args (a string) – Additional parameters to the command. Maps to a command-line argument: %s.

  • comp_input (a pathlike object or string representing an existing file) – Compose two transformations. Maps to a command-line argument: -comp %s (position: -3). Mutually exclusive with inputs: def_input, disp_input, flow_input, upd_s_form_input, inv_aff_input, inv_nrr_input, half_input, make_aff_input, aff_2_rig_input, flirt_2_nr_input. Requires inputs: comp_input2.

  • comp_input2 (a pathlike object or string representing an existing file) – Compose two transformations. Maps to a command-line argument: %s (position: -2).

  • def_input (a pathlike object or string representing an existing file) – Compute deformation field from transformation. Maps to a command-line argument: -def %s (position: -2). Mutually exclusive with inputs: disp_input, flow_input, comp_input, upd_s_form_input, inv_aff_input, inv_nrr_input, half_input, make_aff_input, aff_2_rig_input, flirt_2_nr_input.

  • disp_input (a pathlike object or string representing an existing file) – Compute displacement field from transformation. Maps to a command-line argument: -disp %s (position: -2). Mutually exclusive with inputs: def_input, flow_input, comp_input, upd_s_form_input, inv_aff_input, inv_nrr_input, half_input, make_aff_input, aff_2_rig_input, flirt_2_nr_input.

  • 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: {})

  • flirt_2_nr_input (a tuple of the form: (a pathlike object or string representing an existing file, a pathlike object or string representing an existing file, a pathlike object or string representing an existing file)) – Convert a FLIRT affine transformation to niftyreg affine transformation. Maps to a command-line argument: -flirtAff2NR %s %s %s (position: -2). Mutually exclusive with inputs: def_input, disp_input, flow_input, comp_input, upd_s_form_input, inv_aff_input, inv_nrr_input, half_input, make_aff_input, aff_2_rig_input.

  • flow_input (a pathlike object or string representing an existing file) – Compute flow field from spline SVF. Maps to a command-line argument: -flow %s (position: -2). Mutually exclusive with inputs: def_input, disp_input, comp_input, upd_s_form_input, inv_aff_input, inv_nrr_input, half_input, make_aff_input, aff_2_rig_input, flirt_2_nr_input.

  • half_input (a pathlike object or string representing an existing file) – Half way to the input transformation. Maps to a command-line argument: -half %s (position: -2). Mutually exclusive with inputs: def_input, disp_input, flow_input, comp_input, upd_s_form_input, inv_aff_input, inv_nrr_input, make_aff_input, aff_2_rig_input, flirt_2_nr_input.

  • inv_aff_input (a pathlike object or string representing an existing file) – Invert an affine transformation. Maps to a command-line argument: -invAff %s (position: -2). Mutually exclusive with inputs: def_input, disp_input, flow_input, comp_input, upd_s_form_input, inv_nrr_input, half_input, make_aff_input, aff_2_rig_input, flirt_2_nr_input.

  • inv_nrr_input (a tuple of the form: (a pathlike object or string representing an existing file, a pathlike object or string representing an existing file)) – Invert a non-linear transformation. Maps to a command-line argument: -invNrr %s %s (position: -2). Mutually exclusive with inputs: def_input, disp_input, flow_input, comp_input, upd_s_form_input, inv_aff_input, half_input, make_aff_input, aff_2_rig_input, flirt_2_nr_input.

  • make_aff_input (a tuple of the form: (a float, a float, a float, a float, a float, a float, a float, a float, a float, a float, a float, a float)) – Make an affine transformation matrix. Maps to a command-line argument: -makeAff %f %f %f %f %f %f %f %f %f %f %f %f (position: -2). Mutually exclusive with inputs: def_input, disp_input, flow_input, comp_input, upd_s_form_input, inv_aff_input, inv_nrr_input, half_input, aff_2_rig_input, flirt_2_nr_input.

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

  • out_file (a pathlike object or string representing a file) – Transformation file to write. Maps to a command-line argument: %s (position: -1).

  • ref1_file (a pathlike object or string representing an existing file) – The input reference/target image. Maps to a command-line argument: -ref %s (position: 0).

  • ref2_file (a pathlike object or string representing an existing file) – The input second reference/target image. Maps to a command-line argument: -ref2 %s (position: 1). Requires inputs: ref1_file.

  • upd_s_form_input (a pathlike object or string representing an existing file) – Update s-form using the affine transformation. Maps to a command-line argument: -updSform %s (position: -3). Mutually exclusive with inputs: def_input, disp_input, flow_input, comp_input, inv_aff_input, inv_nrr_input, half_input, make_aff_input, aff_2_rig_input, flirt_2_nr_input. Requires inputs: upd_s_form_input2.

  • upd_s_form_input2 (a pathlike object or string representing an existing file) – Update s-form using the affine transformation. Maps to a command-line argument: %s (position: -2). Requires inputs: upd_s_form_input.

Outputs:

out_file (a pathlike object or string representing a file) – Output File (transformation in any format).