nireports.interfaces.reporting.registration module¶

ReportCapableInterfaces for registration tools.

class nireports.interfaces.reporting.registration.ApplyTOPUPRPT(generate_report=False, **kwargs)[source]¶

Bases: RegistrationRC, ApplyTOPUP

Wrapped executable: applytopup.

Mandatory Inputs:

encoding_file (a pathlike object or string representing an existing file) – Name of text file with PE directions/times. Maps to a command-line argument: --datain=%s.
in_files (a list of items which are a pathlike object or string representing an existing file) – Name of file with images. Maps to a command-line argument: --imain=%s.

Optional Inputs:

args (a string) – Additional parameters to the command. Maps to a command-line argument: %s.
compress_report (‘auto’ or True or False) – Compress the reportlet using SVGO orWEBP. ‘auto’ - compress if relevant software is installed, True = force,False - don’t attempt to compress. (Nipype default value: auto)
datatype (‘char’ or ‘short’ or ‘int’ or ‘float’ or ‘double’) – Force output data type. Maps to a command-line argument: -d=%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: {})
in_index (a list of items which are an integer) – Comma separated list of indices corresponding to –datain. Maps to a command-line argument: --inindex=%s.
in_topup_fieldcoef (a pathlike object or string representing an existing file) – Topup file containing the field coefficients. Maps to a command-line argument: --topup=%s. Requires inputs: in_topup_movpar.
in_topup_movpar (a pathlike object or string representing an existing file) – Topup movpar.txt file. Requires inputs: in_topup_fieldcoef.
interp (‘trilinear’ or ‘spline’) – Interpolation method. Maps to a command-line argument: --interp=%s.
method (‘jac’ or ‘lsr’) – Use jacobian modulation (jac) or least-squares resampling (lsr). Maps to a command-line argument: --method=%s.
out_corrected (a pathlike object or string representing a file) – Output (warped) image. Maps to a command-line argument: --out=%s.
out_report (a pathlike object or string representing a file) – Filename for the visual report. (Nipype default value: report.svg)
output_type (‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’ or ‘GIFTI’) – FSL output type.
wm_seg (a pathlike object or string representing a file) – Reference white matter segmentation mask. Maps to a command-line argument: -wmseg %s.

Outputs:

out_corrected (a pathlike object or string representing an existing file) – Name of 4D image file with unwarped images.
out_report (a pathlike object or string representing a file) – Filename for the visual report.

class nireports.interfaces.reporting.registration.ApplyXFMRPT(generate_report=False, **kwargs)[source]¶

Bases: FLIRTRPT, ApplyXFM

Wrapped executable: flirt.

Mandatory Inputs:

in_file (a pathlike object or string representing an existing file) – Input file. Maps to a command-line argument: -in %s (position: 0).
reference (a pathlike object or string representing an existing file) – Reference file. Maps to a command-line argument: -ref %s (position: 1).

Optional Inputs:

angle_rep (‘quaternion’ or ‘euler’) – Representation of rotation angles. Maps to a command-line argument: -anglerep %s.
apply_isoxfm (a float) – As applyxfm but forces isotropic resampling. Maps to a command-line argument: -applyisoxfm %f. Mutually exclusive with inputs: apply_xfm.
apply_xfm (a boolean) – Apply transformation supplied by in_matrix_file or uses_qform to use the affine matrix stored in the reference header. Maps to a command-line argument: -applyxfm. (Nipype default value: True)
args (a string) – Additional parameters to the command. Maps to a command-line argument: %s.
bbrslope (a float) – Value of bbr slope. Maps to a command-line argument: -bbrslope %f.
bbrtype (‘signed’ or ‘global_abs’ or ‘local_abs’) – Type of bbr cost function: signed [default], global_abs, local_abs. Maps to a command-line argument: -bbrtype %s.
bgvalue (a float) – Use specified background value for points outside FOV. Maps to a command-line argument: -setbackground %f.
bins (an integer) – Number of histogram bins. Maps to a command-line argument: -bins %d.
coarse_search (an integer) – Coarse search delta angle. Maps to a command-line argument: -coarsesearch %d.
compress_report (‘auto’ or True or False) – Compress the reportlet using SVGO orWEBP. ‘auto’ - compress if relevant software is installed, True = force,False - don’t attempt to compress. (Nipype default value: auto)
cost (‘mutualinfo’ or ‘corratio’ or ‘normcorr’ or ‘normmi’ or ‘leastsq’ or ‘labeldiff’ or ‘bbr’) – Cost function. Maps to a command-line argument: -cost %s.
cost_func (‘mutualinfo’ or ‘corratio’ or ‘normcorr’ or ‘normmi’ or ‘leastsq’ or ‘labeldiff’ or ‘bbr’) – Cost function. Maps to a command-line argument: -searchcost %s.
datatype (‘char’ or ‘short’ or ‘int’ or ‘float’ or ‘double’) – Force output data type. Maps to a command-line argument: -datatype %s.
display_init (a boolean) – Display initial matrix. Maps to a command-line argument: -displayinit.
dof (an integer) – Number of transform degrees of freedom. Maps to a command-line argument: -dof %d.
echospacing (a float) – Value of EPI echo spacing - units of seconds. Maps to a command-line argument: -echospacing %f.
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: {})
fieldmap (a pathlike object or string representing a file) – Fieldmap image in rads/s - must be already registered to the reference image. Maps to a command-line argument: -fieldmap %s.
fieldmapmask (a pathlike object or string representing a file) – Mask for fieldmap image. Maps to a command-line argument: -fieldmapmask %s.
fine_search (an integer) – Fine search delta angle. Maps to a command-line argument: -finesearch %d.
force_scaling (a boolean) – Force rescaling even for low-res images. Maps to a command-line argument: -forcescaling.
in_matrix_file (a pathlike object or string representing a file) – Input 4x4 affine matrix. Maps to a command-line argument: -init %s.
in_weight (a pathlike object or string representing an existing file) – File for input weighting volume. Maps to a command-line argument: -inweight %s.
interp (‘trilinear’ or ‘nearestneighbour’ or ‘sinc’ or ‘spline’) – Final interpolation method used in reslicing. Maps to a command-line argument: -interp %s.
min_sampling (a float) – Set minimum voxel dimension for sampling. Maps to a command-line argument: -minsampling %f.
no_clamp (a boolean) – Do not use intensity clamping. Maps to a command-line argument: -noclamp.
no_resample (a boolean) – Do not change input sampling. Maps to a command-line argument: -noresample.
no_resample_blur (a boolean) – Do not use blurring on downsampling. Maps to a command-line argument: -noresampblur.
no_search (a boolean) – Set all angular searches to ranges 0 to 0. Maps to a command-line argument: -nosearch.
out_file (a pathlike object or string representing a file) – Registered output file. Maps to a command-line argument: -out %s (position: 2).
out_log (a pathlike object or string representing a file) – Output log. Requires inputs: save_log.
out_matrix_file (a pathlike object or string representing a file) – Output affine matrix in 4x4 asciii format. Maps to a command-line argument: -omat %s (position: 3).
out_report (a pathlike object or string representing a file) – Filename for the visual report. (Nipype default value: report.svg)
output_type (‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’ or ‘GIFTI’) – FSL output type.
padding_size (an integer) – For applyxfm: interpolates outside image by size. Maps to a command-line argument: -paddingsize %d.
pedir (an integer) – Phase encode direction of EPI - 1/2/3=x/y/z & -1/-2/-3=-x/-y/-z. Maps to a command-line argument: -pedir %d.
ref_weight (a pathlike object or string representing an existing file) – File for reference weighting volume. Maps to a command-line argument: -refweight %s.
rigid2D (a boolean) – Use 2D rigid body mode - ignores dof. Maps to a command-line argument: -2D.
save_log (a boolean) – Save to log file.
schedule (a pathlike object or string representing an existing file) – Replaces default schedule. Maps to a command-line argument: -schedule %s.
searchr_x (a list of from 2 to 2 items which are an integer) – Search angles along x-axis, in degrees. Maps to a command-line argument: -searchrx %s.
searchr_y (a list of from 2 to 2 items which are an integer) – Search angles along y-axis, in degrees. Maps to a command-line argument: -searchry %s.
searchr_z (a list of from 2 to 2 items which are an integer) – Search angles along z-axis, in degrees. Maps to a command-line argument: -searchrz %s.
sinc_width (an integer) – Full-width in voxels. Maps to a command-line argument: -sincwidth %d.
sinc_window (‘rectangular’ or ‘hanning’ or ‘blackman’) – Sinc window. Maps to a command-line argument: -sincwindow %s.
uses_qform (a boolean) – Initialize using sform or qform. Maps to a command-line argument: -usesqform.
verbose (an integer) – Verbose mode, 0 is least. Maps to a command-line argument: -verbose %d.
wm_seg (a pathlike object or string representing a file) – White matter segmentation volume needed by BBR cost function. Maps to a command-line argument: -wmseg %s.
wmcoords (a pathlike object or string representing a file) – White matter boundary coordinates for BBR cost function. Maps to a command-line argument: -wmcoords %s.
wmnorms (a pathlike object or string representing a file) – White matter boundary normals for BBR cost function. Maps to a command-line argument: -wmnorms %s.

Outputs:

out_file (a pathlike object or string representing an existing file) – Path/name of registered file (if generated).
out_log (a pathlike object or string representing a file) – Path/name of output log (if generated).
out_matrix_file (a pathlike object or string representing an existing file) – Path/name of calculated affine transform (if generated).
out_report (a pathlike object or string representing a file) – Filename for the visual report.

class nireports.interfaces.reporting.registration.BBRegisterRPT(generate_report=False, **kwargs)[source]¶

Bases: RegistrationRC, BBRegister

Wrapped executable: bbregister.

Mandatory Inputs:

contrast_type (‘t1’ or ‘t2’ or ‘bold’ or ‘dti’) – Contrast type of image. Maps to a command-line argument: --%s.
source_file (a pathlike object or string representing a file) – Source file to be registered. Maps to a command-line argument: --mov %s.
subject_id (a string) – Freesurfer subject id. Maps to a command-line argument: --s %s.

Optional Inputs:

args (a string) – Additional parameters to the command. Maps to a command-line argument: %s.
compress_report (‘auto’ or True or False) – Compress the reportlet using SVGO orWEBP. ‘auto’ - compress if relevant software is installed, True = force,False - don’t attempt to compress. (Nipype default value: auto)
dof (6 or 9 or 12) – Number of transform degrees of freedom. Maps to a command-line argument: --%d.
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: {})
epi_mask (a boolean) – Mask out B0 regions in stages 1 and 2. Maps to a command-line argument: --epi-mask.
fsldof (an integer) – Degrees of freedom for initial registration (FSL). Maps to a command-line argument: --fsl-dof %d.
init (‘coreg’ or ‘rr’ or ‘spm’ or ‘fsl’ or ‘header’ or ‘best’) – Initialize registration with mri_coreg, spm, fsl, or header. Maps to a command-line argument: --init-%s. Mutually exclusive with inputs: init_reg_file.
init_cost_file (a boolean or a pathlike object or string representing a file) – Output initial registration cost file. Maps to a command-line argument: --initcost %s.
init_reg_file (a pathlike object or string representing an existing file) – Existing registration file. Maps to a command-line argument: --init-reg %s. Mutually exclusive with inputs: init.
intermediate_file (a pathlike object or string representing an existing file) – Intermediate image, e.g. in case of partial FOV. Maps to a command-line argument: --int %s.
out_fsl_file (a boolean or a pathlike object or string representing a file) – Write the transformation matrix in FSL FLIRT format. Maps to a command-line argument: --fslmat %s.
out_lta_file (a boolean or a pathlike object or string representing a file) – Write the transformation matrix in LTA format. Maps to a command-line argument: --lta %s. (Nipype default value: True)
out_reg_file (a pathlike object or string representing a file) – Output registration file. Maps to a command-line argument: --reg %s.
out_report (a pathlike object or string representing a file) – Filename for the visual report. (Nipype default value: report.svg)
reg_frame (an integer) – 0-based frame index for 4D source file. Maps to a command-line argument: --frame %d. Mutually exclusive with inputs: reg_middle_frame.
reg_middle_frame (a boolean) – Register middle frame of 4D source file. Maps to a command-line argument: --mid-frame. Mutually exclusive with inputs: reg_frame.
registered_file (a boolean or a pathlike object or string representing a file) – Output warped sourcefile either True or filename. Maps to a command-line argument: --o %s.
spm_nifti (a boolean) – Force use of nifti rather than analyze with SPM. Maps to a command-line argument: --spm-nii.
subjects_dir (a pathlike object or string representing an existing directory) – Subjects directory.

Outputs:

init_cost_file (a pathlike object or string representing an existing file) – Output initial registration cost file.
min_cost_file (a pathlike object or string representing an existing file) – Output registration minimum cost file.
out_fsl_file (a pathlike object or string representing an existing file) – Output FLIRT-style registration file.
out_lta_file (a pathlike object or string representing an existing file) – Output LTA-style registration file.
out_reg_file (a pathlike object or string representing an existing file) – Output registration file.
out_report (a pathlike object or string representing a file) – Filename for the visual report.
registered_file (a pathlike object or string representing an existing file) – Registered and resampled source file.

class nireports.interfaces.reporting.registration.FLIRTRPT(generate_report=False, **kwargs)[source]¶

Bases: RegistrationRC, FLIRT

Wrapped executable: flirt.

Mandatory Inputs:

in_file (a pathlike object or string representing an existing file) – Input file. Maps to a command-line argument: -in %s (position: 0).
reference (a pathlike object or string representing an existing file) – Reference file. Maps to a command-line argument: -ref %s (position: 1).

Optional Inputs:

angle_rep (‘quaternion’ or ‘euler’) – Representation of rotation angles. Maps to a command-line argument: -anglerep %s.
apply_isoxfm (a float) – As applyxfm but forces isotropic resampling. Maps to a command-line argument: -applyisoxfm %f. Mutually exclusive with inputs: apply_xfm.
apply_xfm (a boolean) – Apply transformation supplied by in_matrix_file or uses_qform to use the affine matrix stored in the reference header. Maps to a command-line argument: -applyxfm.
args (a string) – Additional parameters to the command. Maps to a command-line argument: %s.
bbrslope (a float) – Value of bbr slope. Maps to a command-line argument: -bbrslope %f.
bbrtype (‘signed’ or ‘global_abs’ or ‘local_abs’) – Type of bbr cost function: signed [default], global_abs, local_abs. Maps to a command-line argument: -bbrtype %s.
bgvalue (a float) – Use specified background value for points outside FOV. Maps to a command-line argument: -setbackground %f.
bins (an integer) – Number of histogram bins. Maps to a command-line argument: -bins %d.
coarse_search (an integer) – Coarse search delta angle. Maps to a command-line argument: -coarsesearch %d.
compress_report (‘auto’ or True or False) – Compress the reportlet using SVGO orWEBP. ‘auto’ - compress if relevant software is installed, True = force,False - don’t attempt to compress. (Nipype default value: auto)
cost (‘mutualinfo’ or ‘corratio’ or ‘normcorr’ or ‘normmi’ or ‘leastsq’ or ‘labeldiff’ or ‘bbr’) – Cost function. Maps to a command-line argument: -cost %s.
cost_func (‘mutualinfo’ or ‘corratio’ or ‘normcorr’ or ‘normmi’ or ‘leastsq’ or ‘labeldiff’ or ‘bbr’) – Cost function. Maps to a command-line argument: -searchcost %s.
datatype (‘char’ or ‘short’ or ‘int’ or ‘float’ or ‘double’) – Force output data type. Maps to a command-line argument: -datatype %s.
display_init (a boolean) – Display initial matrix. Maps to a command-line argument: -displayinit.
dof (an integer) – Number of transform degrees of freedom. Maps to a command-line argument: -dof %d.
echospacing (a float) – Value of EPI echo spacing - units of seconds. Maps to a command-line argument: -echospacing %f.
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: {})
fieldmap (a pathlike object or string representing a file) – Fieldmap image in rads/s - must be already registered to the reference image. Maps to a command-line argument: -fieldmap %s.
fieldmapmask (a pathlike object or string representing a file) – Mask for fieldmap image. Maps to a command-line argument: -fieldmapmask %s.
fine_search (an integer) – Fine search delta angle. Maps to a command-line argument: -finesearch %d.
force_scaling (a boolean) – Force rescaling even for low-res images. Maps to a command-line argument: -forcescaling.
in_matrix_file (a pathlike object or string representing a file) – Input 4x4 affine matrix. Maps to a command-line argument: -init %s.
in_weight (a pathlike object or string representing an existing file) – File for input weighting volume. Maps to a command-line argument: -inweight %s.
interp (‘trilinear’ or ‘nearestneighbour’ or ‘sinc’ or ‘spline’) – Final interpolation method used in reslicing. Maps to a command-line argument: -interp %s.
min_sampling (a float) – Set minimum voxel dimension for sampling. Maps to a command-line argument: -minsampling %f.
no_clamp (a boolean) – Do not use intensity clamping. Maps to a command-line argument: -noclamp.
no_resample (a boolean) – Do not change input sampling. Maps to a command-line argument: -noresample.
no_resample_blur (a boolean) – Do not use blurring on downsampling. Maps to a command-line argument: -noresampblur.
no_search (a boolean) – Set all angular searches to ranges 0 to 0. Maps to a command-line argument: -nosearch.
out_file (a pathlike object or string representing a file) – Registered output file. Maps to a command-line argument: -out %s (position: 2).
out_log (a pathlike object or string representing a file) – Output log. Requires inputs: save_log.
out_matrix_file (a pathlike object or string representing a file) – Output affine matrix in 4x4 asciii format. Maps to a command-line argument: -omat %s (position: 3).
out_report (a pathlike object or string representing a file) – Filename for the visual report. (Nipype default value: report.svg)
output_type (‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’ or ‘GIFTI’) – FSL output type.
padding_size (an integer) – For applyxfm: interpolates outside image by size. Maps to a command-line argument: -paddingsize %d.
pedir (an integer) – Phase encode direction of EPI - 1/2/3=x/y/z & -1/-2/-3=-x/-y/-z. Maps to a command-line argument: -pedir %d.
ref_weight (a pathlike object or string representing an existing file) – File for reference weighting volume. Maps to a command-line argument: -refweight %s.
rigid2D (a boolean) – Use 2D rigid body mode - ignores dof. Maps to a command-line argument: -2D.
save_log (a boolean) – Save to log file.
schedule (a pathlike object or string representing an existing file) – Replaces default schedule. Maps to a command-line argument: -schedule %s.
searchr_x (a list of from 2 to 2 items which are an integer) – Search angles along x-axis, in degrees. Maps to a command-line argument: -searchrx %s.
searchr_y (a list of from 2 to 2 items which are an integer) – Search angles along y-axis, in degrees. Maps to a command-line argument: -searchry %s.
searchr_z (a list of from 2 to 2 items which are an integer) – Search angles along z-axis, in degrees. Maps to a command-line argument: -searchrz %s.
sinc_width (an integer) – Full-width in voxels. Maps to a command-line argument: -sincwidth %d.
sinc_window (‘rectangular’ or ‘hanning’ or ‘blackman’) – Sinc window. Maps to a command-line argument: -sincwindow %s.
uses_qform (a boolean) – Initialize using sform or qform. Maps to a command-line argument: -usesqform.
verbose (an integer) – Verbose mode, 0 is least. Maps to a command-line argument: -verbose %d.
wm_seg (a pathlike object or string representing a file) – White matter segmentation volume needed by BBR cost function. Maps to a command-line argument: -wmseg %s.
wmcoords (a pathlike object or string representing a file) – White matter boundary coordinates for BBR cost function. Maps to a command-line argument: -wmcoords %s.
wmnorms (a pathlike object or string representing a file) – White matter boundary normals for BBR cost function. Maps to a command-line argument: -wmnorms %s.

Outputs:

out_file (a pathlike object or string representing an existing file) – Path/name of registered file (if generated).
out_log (a pathlike object or string representing a file) – Path/name of output log (if generated).
out_matrix_file (a pathlike object or string representing an existing file) – Path/name of calculated affine transform (if generated).
out_report (a pathlike object or string representing a file) – Filename for the visual report.

class nireports.interfaces.reporting.registration.FUGUERPT(generate_report=False, **kwargs)[source]¶

Bases: RegistrationRC, FUGUE

Wrapped executable: fugue.

Optional Inputs:

args (a string) – Additional parameters to the command. Maps to a command-line argument: %s.
asym_se_time (a float) – Set the fieldmap asymmetric spin echo time (sec). Maps to a command-line argument: --asym=%.10f.
compress_report (‘auto’ or True or False) – Compress the reportlet using SVGO orWEBP. ‘auto’ - compress if relevant software is installed, True = force,False - don’t attempt to compress. (Nipype default value: auto)
despike_2dfilter (a boolean) – Apply a 2D de-spiking filter. Maps to a command-line argument: --despike.
despike_threshold (a float) – Specify the threshold for de-spiking (default=3.0). Maps to a command-line argument: --despikethreshold=%s.
dwell_time (a float) – Set the EPI dwell time per phase-encode line - same as echo spacing - (sec). Maps to a command-line argument: --dwell=%.10f.
dwell_to_asym_ratio (a float) – Set the dwell to asym time ratio. Maps to a command-line argument: --dwelltoasym=%.10f.
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: {})
fmap_in_file (a pathlike object or string representing an existing file) – Filename for loading fieldmap (rad/s). Maps to a command-line argument: --loadfmap=%s.
fmap_out_file (a pathlike object or string representing a file) – Filename for saving fieldmap (rad/s). Maps to a command-line argument: --savefmap=%s.
forward_warping (a boolean) – Apply forward warping instead of unwarping. (Nipype default value: False)
fourier_order (an integer) – Apply Fourier (sinusoidal) fitting of order N. Maps to a command-line argument: --fourier=%d.
icorr (a boolean) – Apply intensity correction to unwarping (pixel shift method only). Maps to a command-line argument: --icorr. Requires inputs: shift_in_file.
icorr_only (a boolean) – Apply intensity correction only. Maps to a command-line argument: --icorronly. Requires inputs: unwarped_file.
in_file (a pathlike object or string representing an existing file) – Filename of input volume. Maps to a command-line argument: --in=%s.
mask_file (a pathlike object or string representing an existing file) – Filename for loading valid mask. Maps to a command-line argument: --mask=%s.
median_2dfilter (a boolean) – Apply 2D median filtering. Maps to a command-line argument: --median.
no_extend (a boolean) – Do not apply rigid-body extrapolation to the fieldmap. Maps to a command-line argument: --noextend.
no_gap_fill (a boolean) – Do not apply gap-filling measure to the fieldmap. Maps to a command-line argument: --nofill.
nokspace (a boolean) – Do not use k-space forward warping. Maps to a command-line argument: --nokspace.
out_report (a pathlike object or string representing a file) – Filename for the visual report. (Nipype default value: report.svg)
output_type (‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’ or ‘GIFTI’) – FSL output type.
pava (a boolean) – Apply monotonic enforcement via PAVA. Maps to a command-line argument: --pava.
phase_conjugate (a boolean) – Apply phase conjugate method of unwarping. Maps to a command-line argument: --phaseconj.
phasemap_in_file (a pathlike object or string representing an existing file) – Filename for input phase image. Maps to a command-line argument: --phasemap=%s.
poly_order (an integer) – Apply polynomial fitting of order N. Maps to a command-line argument: --poly=%d.
save_fmap (a boolean) – Write field map volume. Mutually exclusive with inputs: save_unmasked_fmap.
save_shift (a boolean) – Write pixel shift volume. Mutually exclusive with inputs: save_unmasked_shift.
save_unmasked_fmap (a boolean) – Saves the unmasked fieldmap when using –savefmap. Maps to a command-line argument: --unmaskfmap. Mutually exclusive with inputs: save_fmap.
save_unmasked_shift (a boolean) – Saves the unmasked shiftmap when using –saveshift. Maps to a command-line argument: --unmaskshift. Mutually exclusive with inputs: save_shift.
shift_in_file (a pathlike object or string representing an existing file) – Filename for reading pixel shift volume. Maps to a command-line argument: --loadshift=%s.
shift_out_file (a pathlike object or string representing a file) – Filename for saving pixel shift volume. Maps to a command-line argument: --saveshift=%s.
smooth2d (a float) – Apply 2D Gaussian smoothing of sigma N (in mm). Maps to a command-line argument: --smooth2=%.2f.
smooth3d (a float) – Apply 3D Gaussian smoothing of sigma N (in mm). Maps to a command-line argument: --smooth3=%.2f.
unwarp_direction (‘x’ or ‘y’ or ‘z’ or ‘x-’ or ‘y-’ or ‘z-’) – Specifies direction of warping (default y). Maps to a command-line argument: --unwarpdir=%s.
unwarped_file (a pathlike object or string representing a file) – Apply unwarping and save as filename. Maps to a command-line argument: --unwarp=%s. Mutually exclusive with inputs: warped_file. Requires inputs: in_file.
warped_file (a pathlike object or string representing a file) – Apply forward warping and save as filename. Maps to a command-line argument: --warp=%s. Mutually exclusive with inputs: unwarped_file. Requires inputs: in_file.
wm_seg (a pathlike object or string representing a file) – Reference white matter segmentation mask. Maps to a command-line argument: -wmseg %s.

Outputs:

fmap_out_file (a pathlike object or string representing a file) – Fieldmap file.
out_report (a pathlike object or string representing a file) – Filename for the visual report.
shift_out_file (a pathlike object or string representing a file) – Voxel shift map file.
unwarped_file (a pathlike object or string representing a file) – Unwarped file.
warped_file (a pathlike object or string representing a file) – Forward warped file.

class nireports.interfaces.reporting.registration.MRICoregRPT(generate_report=False, **kwargs)[source]¶

Bases: RegistrationRC, MRICoreg

Wrapped executable: mri_coreg.

Mandatory Inputs:

reference_file (a pathlike object or string representing a file) – Reference (target) file. Maps to a command-line argument: --ref %s. Mutually exclusive with inputs: subject_id.
source_file (a pathlike object or string representing a file) – Source file to be registered. Maps to a command-line argument: --mov %s.
subject_id (a string) – Freesurfer subject ID (implies reference_mask == aparc+aseg.mgz unless otherwise specified). Maps to a command-line argument: --s %s (position: 1). Mutually exclusive with inputs: reference_file. Requires inputs: subjects_dir.

Optional Inputs:

args (a string) – Additional parameters to the command. Maps to a command-line argument: %s.
brute_force_limit (a float) – Constrain brute force search to +/- lim. Maps to a command-line argument: --bf-lim %g. Mutually exclusive with inputs: no_brute_force.
brute_force_samples (an integer) – Number of samples in brute force search. Maps to a command-line argument: --bf-nsamp %d. Mutually exclusive with inputs: no_brute_force.
compress_report (‘auto’ or True or False) – Compress the reportlet using SVGO orWEBP. ‘auto’ - compress if relevant software is installed, True = force,False - don’t attempt to compress. (Nipype default value: auto)
conform_reference (a boolean) – Conform reference without rescaling. Maps to a command-line argument: --conf-ref.
dof (6 or 9 or 12) – Number of transform degrees of freedom. Maps to a command-line argument: --dof %d.
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: {})
ftol (a float) – Floating-point tolerance (default=1e-7). Maps to a command-line argument: --ftol %e.
initial_rotation (a tuple of the form: (a float, a float, a float)) – Initial rotation in degrees. Maps to a command-line argument: --rot %g %g %g.
initial_scale (a tuple of the form: (a float, a float, a float)) – Initial scale. Maps to a command-line argument: --scale %g %g %g.
initial_shear (a tuple of the form: (a float, a float, a float)) – Initial shear (Hxy, Hxz, Hyz). Maps to a command-line argument: --shear %g %g %g.
initial_translation (a tuple of the form: (a float, a float, a float)) – Initial translation in mm (implies no_cras0). Maps to a command-line argument: --trans %g %g %g.
linmintol (a float) – Maps to a command-line argument: --linmintol %e.
max_iters (an integer >= 1) – Maximum iterations (default: 4). Maps to a command-line argument: --nitersmax %d.
no_brute_force (a boolean) – Do not brute force search. Maps to a command-line argument: --no-bf.
no_coord_dithering (a boolean) – Turn off coordinate dithering. Maps to a command-line argument: --no-coord-dither.
no_cras0 (a boolean) – Do not set translation parameters to align centers of source and reference files. Maps to a command-line argument: --no-cras0.
no_intensity_dithering (a boolean) – Turn off intensity dithering. Maps to a command-line argument: --no-intensity-dither.
no_smooth (a boolean) – Do not apply smoothing to either reference or source file. Maps to a command-line argument: --no-smooth.
num_threads (an integer) – Number of OpenMP threads. Maps to a command-line argument: --threads %d.
out_lta_file (a bool or None or a pathlike object or string representing a file) – Output registration file (LTA format). Maps to a command-line argument: --lta %s. (Nipype default value: True)
out_params_file (a bool or None or a pathlike object or string representing a file) – Output parameters file. Maps to a command-line argument: --params %s.
out_reg_file (a bool or None or a pathlike object or string representing a file) – Output registration file (REG format). Maps to a command-line argument: --regdat %s.
out_report (a pathlike object or string representing a file) – Filename for the visual report. (Nipype default value: report.svg)
ref_fwhm (a float) – Apply smoothing to reference file. Maps to a command-line argument: --ref-fwhm.
reference_mask (a bool or None or a string) – Mask reference volume with given mask, or None if False. Maps to a command-line argument: --ref-mask %s (position: 2).
saturation_threshold (0.0 <= a floating point number <= 100.0) – Saturation threshold (default=9.999). Maps to a command-line argument: --sat %g.
sep (a list of from 1 to 2 items which are any value) – Set spatial scales, in voxels (default [2, 4]). Maps to a command-line argument: --sep %s....
source_mask (a string) – Mask source file with given mask. Maps to a command-line argument: --mov-mask.
source_oob (a boolean) – Count source voxels that are out-of-bounds as 0. Maps to a command-line argument: --mov-oob.
subjects_dir (a pathlike object or string representing an existing directory) – FreeSurfer SUBJECTS_DIR. Maps to a command-line argument: --sd %s.

Outputs:

out_lta_file (a pathlike object or string representing an existing file) – Output LTA-style registration file.
out_params_file (a pathlike object or string representing an existing file) – Output parameters file.
out_reg_file (a pathlike object or string representing an existing file) – Output registration file.
out_report (a pathlike object or string representing a file) – Filename for the visual report.

class nireports.interfaces.reporting.registration.ResampleBeforeAfterRPT(generate_report=True, **kwargs)[source]¶

Bases: SimpleBeforeAfterRPT

Mandatory Inputs:

after (a pathlike object or string representing an existing file) – File after.
base (‘before’ or ‘after’) – (Nipype default value: before)
before (a pathlike object or string representing an existing file) – File before.

Optional Inputs:

after_label (a string) – (Nipype default value: after)
before_label (a string) – (Nipype default value: before)
compress_report (‘auto’ or True or False) – Compress the reportlet using SVGO orWEBP. ‘auto’ - compress if relevant software is installed, True = force,False - don’t attempt to compress. (Nipype default value: auto)
dismiss_affine (a boolean) – Rotate image(s) to cardinal axes. (Nipype default value: False)
out_report (a pathlike object or string representing a file) – Filename for the visual report. (Nipype default value: report.svg)
wm_seg (a pathlike object or string representing a file) – Reference white matter segmentation mask.

Outputs:

out_report (a pathlike object or string representing a file) – Filename for the visual report.

class nireports.interfaces.reporting.registration.SimpleBeforeAfterRPT(generate_report=True, **kwargs)[source]¶

Bases: RegistrationRC, ReportingInterface

Mandatory Inputs:

after (a pathlike object or string representing an existing file) – File after.
before (a pathlike object or string representing an existing file) – File before.

Optional Inputs:

after_label (a string) – (Nipype default value: after)
before_label (a string) – (Nipype default value: before)
compress_report (‘auto’ or True or False) – Compress the reportlet using SVGO orWEBP. ‘auto’ - compress if relevant software is installed, True = force,False - don’t attempt to compress. (Nipype default value: auto)
dismiss_affine (a boolean) – Rotate image(s) to cardinal axes. (Nipype default value: False)
out_report (a pathlike object or string representing a file) – Filename for the visual report. (Nipype default value: report.svg)
wm_seg (a pathlike object or string representing a file) – Reference white matter segmentation mask.

Outputs:

out_report (a pathlike object or string representing a file) – Filename for the visual report.