convert-dof

Synopsis

convert-dof <input> <output> [options]
convert-dof <input> <output> -input-format  image [options] (3D+3 input  image)
convert-dof <input> <output> -output-format image [options] (3D+3 output image)
convert-dof <dx> <dy> <dz> <output> -input-format  image [options] (3x3D input  image)
convert-dof <input> <dx> <dy> <dz>  -output-format image [options] (3x3D output image)

Description

Converts between different transformation file formats:

unknown	Unknown, try to guess it from file header/type.
disp_world|disp|image	Dense displacement field image with world space displacement vectors [mm].
disp_voxel	Dense displacement field image with target space displacement vectors [voxel].
disp_itk|itk_disp	Dense displacement field image in ITK format [mm].
svf_world|svf	Dense velocity field image with world space vectors [mm]. Requires input SVFFD.
svf_voxel	Dense velocity field image with target space vectors [voxel]. Requires input SVFFD.
svf_itk|itk_svf	Dense velocity field image in ITK format (e.g., LogDemons) [mm]
mirtk	MIRTK transformation file format.
mirtk_rigid|rigid	Rigid MIRTK transformation file format (6 DoFs).
mirtk_similarity	Similarity MIRTK transformation file format (7 DoFs).
mirtk_affine|affine	Affine MIRTK transformation file format (12 DoFs).
mirtk_linear_ffd	Linear free-form deformation.
mirtk_linear_svffd	Linear free-form deformation parameterized by stationary velocity field.
mirtk_linear_tdffd	Linear free-form deformation parameterized by non-stationary velocity field.
mirtk_bspline_ffd	Cubic B-spline free-form deformation.
mirtk_bspline_svffd	Cubic B-spline free-form deformation parameterized by stationary velocity field.
mirtk_bspline_tdffd	Cubic B-spline free-form deformation parameterized by non-stationary velocity field.
irtk	IRTK transformation file format.
irtk_rigid	Rigid IRTK transformation file format (6 DoFs).
irtk_affine	Affine IRTK transformation file format (12 DoFs).
irtk_linear_ffd	Linear IRTK free-form deformation.
irtk_bspline_ffd	Cubic B-spline IRTK free-form deformation.
mni_xfm|xfm	Linear FreeSurfer transformation (.xfm file).
fsl	Guess/choose FSL output file format.
flirt	FSL FLIRT output file format.
fnirt	FSL FNIRT output file format.
nreg	Guess/choose Nifty Reg transformation output file format.
aladin	Nifty Reg Aladin output file format.
f3d	Nifty Reg reg_f3d output file format with nifti1.intent_p1 code.
f3d_def_field	Nifty Reg reg_f3d output image deformation field.
f3d_disp_field	Nifty Reg reg_f3d output image displacement field.
f3d_spline_grid	Nifty Reg reg_f3d output control point displacement field.
f3d_def_vel_field	Nifty Reg reg_f3d output image deformation field as stationary velocity field.
f3d_disp_vel_field	Nifty Reg reg_f3d output image displacement field as stationary velocity field.
f3d_spline_vel_grid	Nifty Reg reg_f3d output control point velocity field.
elastix|elastix_ffd	Elastix BSplineTransform parameters text file.
dramms	DRAMMS deformation field.
star_ccm	Output file suitable for import in STAR CCM+.
star_ccm_table	Point displacements as STAR CCM+ XYZ Table.
star_ccm_table_xyz	Transformed points as STAR CCM+ XYZ Table.
table|csv|tsv	ASCII table of target point coordinates and displacement vectors.
table_xyz|csv_xyz|tsv_xyz	ASCII table of transformed point coordinates.

Arguments

input

Input transformation file.

output

Output transformation file.

Command options

-input-format <format>

Format of input file. (default: unknown)

-output-format <format>

Format of output file. (default: .nii[.gz] -> disp_world, .dof[.gz] -> mirtk)

-format <format>

Short for -output-format.

-dofin <fname>

Affine transformation component in MIRTK format which shall be removed from Nifty Reg’s FFD such that the resulting transformation is a MIRTK MFFD consisting of this affine component plus the remaining non-linear component of the input FFD. (default: none)

-target <fname>

Target image. Required for from/to FSL format conversion. Also required when converting linear transformations to displacment fields or (M)FFD transformation types. (default: none)

-source <fname>

Source image. Required for from/to FSL format conversion. (default: none)

-points <fname>

Input point set. Used for CSV/TSV and STAR-CCM+ output of transformed points. By default, all target or FFD lattice points are transformed.

-Tt <time>

Time point of target image. Used by 3D+t, TD, and SV FFDs.

-Ts <time>

Time point of source image. Used by 3D+t, TD, and SV FFDs.

-ds <value>

Output control point spacing. (default: input spacing)

-dx <value>

Output control point spacing in x dimension. (default: input spacing)

-dy <value>

Output control point spacing in y dimension. (default: input spacing)

-dz <value>

Output control point spacing in z dimension. (default: input spacing)

-dt <value>

Temporal sampling used for CSV/TSV and STAR-CCM+ output. (default: input spacing)

-t1, -tmin <value>

Lower time interval limit for output of CSV/TSV and STAR-CCM+ table. (default: -inf)

-t2, -tmax <value>

Upper time interval limit for output of CSV/TSV and STAR-CCM+ table. (default: +inf)

-scaling-steps <int>

Number of scaling and squaring steps. In case of f3d_*_vel_*, use nifti1.intent_p2 by default.

-xyz_units (m|mm|mu)

Spatial units of original target NIfTI header if ignored by Nifty Reg’s reg_f3d. (default: mm)

-delimiter <string>

Delimiting character sequence to use for CSV/TSV or STAR-CCM+ Table output.

-precision <int>

Number of decimal digits for ASCII output of floating point values. (default: 5)

Standard options

-v, -verbose [n]

Increase/Set verbosity of output messages. (default: 0)

-debug [level]

Increase/Set debug level for output of intermediate results. (default: 0)

-version [major.minor]

Print version and exit or set version to emulate.

-revision

Print revision (or version) number only and exit.

-h, -help

Print help and exit.