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cli statismo fit image
statismo-fit-image - fits a model iteratively to an image.
statismo-fit-image [options] -i input-file output-file
statismo-fit-image iteratively fits a target image with the help of a model and a reference image. It's possible to fit with and without landmarks. The optimizer can get stuck in a local minima that doesn't represent a satisfactory result if no landmarks are provided.
-i, --input-model MODEL_FILE : MODEL_FILE is the path to the model.
-m, --input-movingimage IMAGE_FILE : IMAGE_FILE is the path to the moving image.
-f, --input-fixedimage IMAGE_FILE : IMAGE_FILE is the path to the fixed image.
-w, --regularization-weight WEIGHT : WEIGHT is the regularization weight that is used to ensure that the model parameters don't deviate too much from the mean. The higher this weight is, the closer the model parameters should stay to the mean. Note: The regularization is the sum over the square of all model parameters.
-d, --dimensionality : Specifies the dimensionality of the images and the model (either 2 or 3).
-o, --output-fit FITTED_IMAGE_FILE : FITTED_IMAGE_FILE is the path where the fitted image will be saved.
-a, --output-model-deformationfield DEFORMATION_FIELD_FILE : DEFORMATION_FIELD_FILE is the path where the deformation field caused by the model will be saved. This is equivalent to the entrie deformation field if landmarks were provided and in the case that no landmarks were provided, it doesn't include the translation and rotation.
-e, --output-deformationfield DEFORMATION_FIELD_FILE : DEFORMATION_FIELD_FILE is the path where the entire deformation field will be saved. If no landmarks were provided, this includes the rotation and a translation.
--fixed-landmarks FIXED_LANDMARKS_FILE : FIXED_LANDMARKS_FILE is the path to the the file containing the fixed landmarks.
--moving-landmarks MOVING_LANDMARKS_FILE : MOVING_LANDMARKS_FILE is the path to the the file containing the moving landmarks. (That's the landmarks on the target image)
-v, --landmarks-variance VARIANCE : VARIANCE is the landmarks variance (an estimate for how accurate your landmarks are).
-p, --print-fitting-information : If this option is set, then fitting information such as the iteration number, the score as assigned by the metric and the current parameters will be printed.
The Landmarks format is as follows : Landmark name,1.coordinate,2.coordinate,3.coordinate
Example : pointA,2,-2,3
pointB,3.1,3,-5
pointC,7,8,9.08
Remark : In the case of 2D Images, either set the 3.coordinate to 0 or don't set it at all.
Fit a 3D image without landmarks:
statismo-fit-image -i model.h5 -w 0 -m moving-image.vtk -f fixed-image.vtk -o projection.vtk
Fit a 3D image with landmarks and print fitting information:
statismo-fit-image -i model.h5 -m moving-image.vtk -w 0.1 -f fixed-image.vtk -o projection.vtk --fixed-landmarks fixed-landmarks.csv --moving-landmarks moving-landmarks-from-target-image.csv -v 0.1 -p
Fit a 2D image with landmarks and print fitting information:
statismo-fit-image -d 2 -i model.h5 -m moving-image.vtk -w 0.25 -f fixed-image.vtk -o projection.vtk --fixed-landmarks fixed-landmarks.csv --moving-landmarks moving-landmarks-from-target-image.csv -v 0.1 -p
Fit a 2D image without landmarks, print fitting information and save both the deformation field caused by the model and the entire deformation field:
statismo-fit-image -d 2 -i model.h5 -m moving-image.vtk -w 0.25 -f fixed-image.vtk -o projection.vtk -e model-deform-field.vtk -a entire-deform-field.vtk -p
Hint : Use statismo-warp-image to apply the deformation fields to images.
##Building Models: statismo-build-shape-model (8). Builds shape models from a list of meshes.
statismo-build-deformation-model (8). Builds deformation models from a list of deformation fields
statismo-build-gp-model (8). Builds shape or deformation models from a given gaussian process definition.
##Working with models:
statismo-sample (8). Draws samples from a model.
statismo-reduce-model (8). Reduces the number of components in a model.
statismo-posterior (8). Creates a posterior model from an existing model.
statismo-fit-surface (8). Fits a model iteratively in to a target mesh.
statismo-fit-image (8). Fits a model iteratively to an image.
statismo-warp-image (8). Applies a deformation field to an image.