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# 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'

> argsa unicode 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 (int or long)

>   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`.

> out_filea 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'

> trans_filea pathlike object or string representing an existing file

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

> argsa unicode 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 (int or long)

>   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`)

> out_filea 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'

> 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`.

> argsa unicode 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 (int or long)

>   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`.

> out_filea 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'

> 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`.

> argsa unicode 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 (int or long)

>   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`.

> out_filea 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'

> in_filea pathlike object or string representing an existing file

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

> 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 unicode 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 (int or long)

>   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`.

> out_filea 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'

> 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 unicode 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 (int or long)

>   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`.

> out_filea pathlike object or string representing a file

>   Output File (transformation in any format).