usage: __main__.py [-h] [--inverse] [--in_deformation file]
[--reverse_operation]
[--cut_invalid | --remove_invalid | --keep_invalid]
[--reference REFERENCE] [-v [{DEBUG,INFO,WARNING}]] [-f]
in_hdf5 in_target_file in_transfo out_hdf5
Transform tractogram(s) contained in the hdf5 output from a connectivity
script, using an affine/rigid transformation and nonlinear deformation
(optional).
See scil_tractogram_apply_transform.py to apply directly to a tractogram.
For more information on how to use the registration script, follow this link:
https://scilpy.readthedocs.io/en/latest/documentation/tractogram_registration.html
Or use >> scil_tractogram_apply_transform.py --help
Formerly: scil_apply_transform_to_hdf5.py
positional arguments:
in_hdf5 Path of the hdf5 containing the moving tractogram, to be transformed. (.h5 extension).
in_target_file Path of the reference target file (.trk or .nii).
in_transfo Path of the file containing the 4x4
transformation, matrix (.txt, .npy or .mat).
out_hdf5 Output tractogram filename (transformed data).
options:
-h, --help show this help message and exit
--reference REFERENCE
Reference anatomy for tck/vtk/fib/dpy file
support (.nii or .nii.gz).
-v [{DEBUG,INFO,WARNING}]
Produces verbose output depending on the provided level.
Default level is warning, default when using -v is info.
-f Force overwriting of the output files.
Transformation options:
--inverse Apply the inverse linear transformation.
--in_deformation file
Path to the file containing a deformation field.
--reverse_operation Apply the transformation in reverse (see doc), warp
first, then linear.
Management of invalid streamlines:
--cut_invalid Cut invalid streamlines rather than removing them.
Keep the longest segment only.
--remove_invalid Remove the streamlines landing out of the bounding box.
--keep_invalid Keep the streamlines landing out of the bounding box.