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¶
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.
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¶
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
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¶
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
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¶
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
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¶
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.
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¶
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.
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).