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

class nipype.interfaces.niftyreg.regutils.RegAverage(required_version=None, **inputs)

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

argsa string

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

avg_filesa 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_filesa 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_filea 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_filea 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_filea 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_filea 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.

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: {})

omp_core_valan integer

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

out_filea pathlike object or string representing a file

Output file name. Maps to a command-line argument: %s (position: 0).

warp_filesa 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_filea pathlike object or string representing a file

Output file name.

property cmdline

Rewrite the cmdline to write options in text_file.

class nipype.interfaces.niftyreg.regutils.RegJacobian(required_version=None, **inputs)

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_filea pathlike object or string representing an existing file

The input non-rigid transformation. Maps to a command-line argument: -trans %s.

Optional Inputs

argsa string

Additional parameters to the command. Maps to a command-line argument: %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: {})

omp_core_valan integer

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

out_filea pathlike object or string representing a file

The output jacobian determinant file name. Maps to a command-line argument: %s (position: -1).

ref_filea 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_filea pathlike object or string representing a file

The output file.

class nipype.interfaces.niftyreg.regutils.RegMeasure(required_version=None, **inputs)

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_filea 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_filea pathlike object or string representing an existing file

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

Optional Inputs

argsa string

Additional parameters to the command. Maps to a command-line argument: %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: {})

omp_core_valan integer

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

out_filea pathlike object or string representing a file

The output text file containing the measure. Maps to a command-line argument: -out %s.

Outputs

out_filea pathlike object or string representing a file

The output text file containing the measure.

class nipype.interfaces.niftyreg.regutils.RegResample(required_version=None, **inputs)

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_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.

Optional Inputs

argsa string

Additional parameters to the command. Maps to a command-line argument: %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: {})

inter_val‘NN’ or ‘LIN’ or ‘CUB’ or ‘SINC’

Interpolation type. Maps to a command-line argument: -inter %d.

omp_core_valan integer

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

out_filea pathlike object or string representing a file

The output filename of the transformed image. Maps to a command-line argument: %s (position: -1).

pad_vala float

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

psf_alg0 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_flaga boolean

Perform the resampling in two steps to resample an image to a lower resolution. Maps to a command-line argument: -psf.

tensor_flaga boolean

Resample Tensor Map. Maps to a command-line argument: -tensor.

trans_filea 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_flaga boolean

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

Outputs

out_filea pathlike object or string representing a file

The output filename of the transformed image.

class nipype.interfaces.niftyreg.regutils.RegTools(required_version=None, **inputs)

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_filea pathlike object or string representing an existing file

The input image file path. Maps to a command-line argument: -in %s.

Optional Inputs

add_vala 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.

argsa string

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

bin_flaga boolean

Binarise the input image. Maps to a command-line argument: -bin.

chg_res_vala 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_vala 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_flaga boolean

Downsample the image by a factor of 2. Maps to a command-line argument: -down.

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: {})

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_flaga boolean

Make output image isotropic. Maps to a command-line argument: -iso.

mask_filea 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_vala 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_flaga boolean

Set scale, slope to 0 and 1. Maps to a command-line argument: -noscl.

omp_core_valan integer

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

out_filea pathlike object or string representing a file

The output file name. Maps to a command-line argument: -out %s.

rms_vala 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_vala 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_vala 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_vala 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_vala float

Binarise the input image with the given threshold. Maps to a command-line argument: -thr %f.

Outputs

out_filea pathlike object or string representing an existing file

The output file.

class nipype.interfaces.niftyreg.regutils.RegTransform(required_version=None, **inputs)

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_inputa 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.

argsa string

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

comp_inputa 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_input2a pathlike object or string representing an existing file

Compose two transformations. Maps to a command-line argument: %s (position: -2).

def_inputa 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_inputa 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.

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: {})

flirt_2_nr_inputa 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_inputa 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_inputa 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_inputa 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_inputa 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_inputa 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_valan integer

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

out_filea pathlike object or string representing a file

Transformation file to write. Maps to a command-line argument: %s (position: -1).

ref1_filea pathlike object or string representing an existing file

The input reference/target image. Maps to a command-line argument: -ref %s (position: 0).

ref2_filea 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_inputa 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_input2a 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_filea pathlike object or string representing a file

Output File (transformation in any format).