register
Use gradient-based optimization to register XRAY to a CT/MR.
XRAY can be a space-separated list of DICOM files or a directory.
Usage:
register [OPTIONS] COMMAND [ARGS]...
Options:
-h, --help Show this message and exit.
dicom
Initialize from pose parameters in the DICOM header.
Usage:
register dicom [OPTIONS] XRAY...
Options:
--orientation [AP|PA] Orientation of the C-arm [required]
-v, --volume PATH Input CT volume (3D image) [required]
-m, --mask PATH Labelmap for the CT volume
-o, --outpath PATH Directory for saving registration results
[required]
--crop INTEGER Center crop the X-ray image [default: 0]
--subtract_background Subtract mode X-ray image intensity
--linearize Convert X-ray from exponential to linear form
--equalize Apply histogram equalization to X-rays/DRRs
during optimization
--reducefn TEXT If DICOM is multiframe, method to extract a
single 2D image [default: max]
--labels TEXT Labels in mask to exclusively render (comma-
separated)
--scales TEXT Scales of downsampling for multiscale
registration (comma-separated) [default: 8]
--n_itrs TEXT Number of iterations to run at each scale
(comma-separated) [default: 500]
--reverse_x_axis Enable to obey radiologic convention (e.g.,
heart on right)
--renderer [siddon|trilinear] Renderer equation [default: trilinear]
--parameterization TEXT Parameterization of SO(3) for regression
[default: euler_angles]
--convention TEXT If parameterization is Euler angles, specify
order [default: ZXY]
--voxel_shift FLOAT Position of voxel (top left corner or center)
[default: 0.0]
--lr_rot FLOAT Initial step size for rotational parameters
[default: 0.01]
--lr_xyz FLOAT Initial step size for translational
parameters [default: 1.0]
--patience INTEGER Number of itrs without improvement before
decreasing the learning rate [default: 10]
--threshold FLOAT Threshold for measuring the new optimum
[default: 0.0001]
--max_n_plateaus INTEGER Number of times loss can plateau before
moving to next scale [default: 3]
--init_only Directly return the initial pose estimate (no
iterative pose refinement)
--saveimg Save ground truth X-ray and predicted DRRs
--pattern TEXT Pattern rule for glob is XRAY is directory
[default: *.dcm]
--verbose INTEGER RANGE Verbosity level for logging [default: 1;
0<=x<=3]
-h, --help Show this message and exit.
fixed
Initialize from a fixed pose.
Usage:
register fixed [OPTIONS] XRAY...
Options:
--orientation [AP|PA] Orientation of the C-arm [required]
--rot TEXT Rotation (comma-separated); see
`parameterization` and `convention`
[required]
--xyz TEXT Translation (comma-separated); see
`parameterization` and `convention`
[required]
-v, --volume PATH Input CT volume (3D image) [required]
-m, --mask PATH Labelmap for the CT volume
-o, --outpath PATH Directory for saving registration results
[required]
--crop INTEGER Center crop the X-ray image [default: 0]
--subtract_background Subtract mode X-ray image intensity
--linearize Convert X-ray from exponential to linear form
--equalize Apply histogram equalization to X-rays/DRRs
during optimization
--reducefn TEXT If DICOM is multiframe, method to extract a
single 2D image [default: max]
--labels TEXT Labels in mask to exclusively render (comma-
separated)
--scales TEXT Scales of downsampling for multiscale
registration (comma-separated) [default: 8]
--n_itrs TEXT Number of iterations to run at each scale
(comma-separated) [default: 500]
--reverse_x_axis Enable to obey radiologic convention (e.g.,
heart on right)
--renderer [siddon|trilinear] Renderer equation [default: trilinear]
--parameterization TEXT Parameterization of SO(3) for regression
[default: euler_angles]
--convention TEXT If parameterization is Euler angles, specify
order [default: ZXY]
--voxel_shift FLOAT Position of voxel (top left corner or center)
[default: 0.0]
--lr_rot FLOAT Initial step size for rotational parameters
[default: 0.01]
--lr_xyz FLOAT Initial step size for translational
parameters [default: 1.0]
--patience INTEGER Number of itrs without improvement before
decreasing the learning rate [default: 10]
--threshold FLOAT Threshold for measuring the new optimum
[default: 0.0001]
--max_n_plateaus INTEGER Number of times loss can plateau before
moving to next scale [default: 3]
--init_only Directly return the initial pose estimate (no
iterative pose refinement)
--saveimg Save ground truth X-ray and predicted DRRs
--pattern TEXT Pattern rule for glob is XRAY is directory
[default: *.dcm]
--verbose INTEGER RANGE Verbosity level for logging [default: 1;
0<=x<=3]
-h, --help Show this message and exit.
model
Initialize from a pose regression model.
Usage:
register model [OPTIONS] XRAY...
Options:
-c, --ckptpath PATH Checkpoint of a pretrained pose regressor
[required]
--warp PATH SimpleITK transform to warp input CT to a
template reference frame
--invert Whether to invert the warp or not
--antipodal Initialize from antipode of predicted pose
-v, --volume PATH Input CT volume (3D image) [required]
-m, --mask PATH Labelmap for the CT volume
-o, --outpath PATH Directory for saving registration results
[required]
--crop INTEGER Center crop the X-ray image [default: 0]
--subtract_background Subtract mode X-ray image intensity
--linearize Convert X-ray from exponential to linear form
--equalize Apply histogram equalization to X-rays/DRRs
during optimization
--reducefn TEXT If DICOM is multiframe, method to extract a
single 2D image [default: max]
--labels TEXT Labels in mask to exclusively render (comma-
separated)
--scales TEXT Scales of downsampling for multiscale
registration (comma-separated) [default: 8]
--n_itrs TEXT Number of iterations to run at each scale
(comma-separated) [default: 500]
--reverse_x_axis Enable to obey radiologic convention (e.g.,
heart on right)
--renderer [siddon|trilinear] Renderer equation [default: trilinear]
--parameterization TEXT Parameterization of SO(3) for regression
[default: euler_angles]
--convention TEXT If parameterization is Euler angles, specify
order [default: ZXY]
--voxel_shift FLOAT Position of voxel (top left corner or center)
[default: 0.0]
--lr_rot FLOAT Initial step size for rotational parameters
[default: 0.01]
--lr_xyz FLOAT Initial step size for translational
parameters [default: 1.0]
--patience INTEGER Number of itrs without improvement before
decreasing the learning rate [default: 10]
--threshold FLOAT Threshold for measuring the new optimum
[default: 0.0001]
--max_n_plateaus INTEGER Number of times loss can plateau before
moving to next scale [default: 3]
--init_only Directly return the initial pose estimate (no
iterative pose refinement)
--saveimg Save ground truth X-ray and predicted DRRs
--pattern TEXT Pattern rule for glob is XRAY is directory
[default: *.dcm]
--verbose INTEGER RANGE Verbosity level for logging [default: 1;
0<=x<=3]
-h, --help Show this message and exit.
restart
Initialize from a previous final pose estimate.
Usage:
register restart [OPTIONS] XRAY...
Options:
--orientation [AP|PA] Orientation of the C-arm [required]
-c, --ckpt PATH Path to `parameters.pt` for previous
iterative optimization run [required]
-v, --volume PATH Input CT volume (3D image) [required]
-m, --mask PATH Labelmap for the CT volume
-o, --outpath PATH Directory for saving registration results
[required]
--crop INTEGER Center crop the X-ray image [default: 0]
--subtract_background Subtract mode X-ray image intensity
--linearize Convert X-ray from exponential to linear form
--equalize Apply histogram equalization to X-rays/DRRs
during optimization
--reducefn TEXT If DICOM is multiframe, method to extract a
single 2D image [default: max]
--labels TEXT Labels in mask to exclusively render (comma-
separated)
--scales TEXT Scales of downsampling for multiscale
registration (comma-separated) [default: 8]
--n_itrs TEXT Number of iterations to run at each scale
(comma-separated) [default: 500]
--reverse_x_axis Enable to obey radiologic convention (e.g.,
heart on right)
--renderer [siddon|trilinear] Renderer equation [default: trilinear]
--parameterization TEXT Parameterization of SO(3) for regression
[default: euler_angles]
--convention TEXT If parameterization is Euler angles, specify
order [default: ZXY]
--voxel_shift FLOAT Position of voxel (top left corner or center)
[default: 0.0]
--lr_rot FLOAT Initial step size for rotational parameters
[default: 0.01]
--lr_xyz FLOAT Initial step size for translational
parameters [default: 1.0]
--patience INTEGER Number of itrs without improvement before
decreasing the learning rate [default: 10]
--threshold FLOAT Threshold for measuring the new optimum
[default: 0.0001]
--max_n_plateaus INTEGER Number of times loss can plateau before
moving to next scale [default: 3]
--init_only Directly return the initial pose estimate (no
iterative pose refinement)
--saveimg Save ground truth X-ray and predicted DRRs
--pattern TEXT Pattern rule for glob is XRAY is directory
[default: *.dcm]
--verbose INTEGER RANGE Verbosity level for logging [default: 1;
0<=x<=3]
-h, --help Show this message and exit.