usage: __main__.py [-h] [--inverse] [--in_deformation file]
[--reverse_operation]
[--cut_invalid | --remove_invalid | --keep_invalid]
[--no_empty] [--reference REFERENCE]
[-v [{DEBUG,INFO,WARNING}]] [-f]
in_moving_tractogram in_target_file in_transfo
out_tractogram
Transform a tractogram using an affine/rigid transformation and nonlinear
deformation (optional).
For more information on how to use the registration script, follow this link:
https://scilpy.readthedocs.io/en/latest/documentation/tractogram_registration.html
Applying transformation to a tractogram can lead to invalid streamlines (out of
the bounding box), and thus three strategies are available:
1) Do nothing, may crash at saving if invalid streamlines are present.
[This is the default]
2) --keep_invalid, save invalid streamlines. Leave it to the user to run
scil_tractogram_remove_invalid.py if needed.
3) --remove_invalid, automatically remove invalid streamlines before saving.
Should not remove more than a few streamlines. Typically, the streamlines
that are rejected are the ones reaching the limits of the brain, ex, near
the pons.
4) --cut_invalid, automatically cut invalid streamlines before saving, i.e. the
streamlines are kept but the points out of the bounding box are cut.
Example:
To apply a transformation from ANTs to a tractogram, if the ANTs command was
MOVING->REFERENCE...
1) To apply the original transformation:
scil_tractogram_apply_transform.py ${MOVING_FILE} ${REFERENCE_FILE}
0GenericAffine.mat ${OUTPUT_NAME}
--inverse
--in_deformation 1InverseWarp.nii.gz
2) To apply the inverse transformation, i.e. REFERENCE->MOVING:
scil_tractogram_apply_transform.py ${MOVING_FILE} ${REFERENCE_FILE}
0GenericAffine.mat ${OUTPUT_NAME}
--in_deformation 1Warp.nii.gz
--reverse_operation
Formerly: scil_apply_transform_to_tractogram.py
positional arguments:
in_moving_tractogram Path of the tractogram to be transformed.
Bounding box validity will not be checked (could
contain invalid streamlines).
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_tractogram Output tractogram filename (transformed data).
options:
-h, --help show this help message and exit
--no_empty Do not write file if there is no streamline.
You may save an empty file if you use remove_invalid.
--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.