usage: __main__.py [-h] [--inverse] [--in_deformation file]
[--legacy_vtk_format]
[--source_space {vox,voxmm,rasmm,lpsmm}]
[--destination_space {vox,voxmm,rasmm,lpsmm}]
[--source_origin {corner,center}]
[--destination_origin {corner,center}]
[--reference REFERENCE] [-v [{DEBUG,INFO,WARNING,ERROR}]]
[-f]
in_moving_surface in_target_reference in_transfo
out_surface
Script to apply a transform to a surface (FreeSurfer or VTK supported),
using output from ANTs registration tools (i.e. vtk_transfo.txt, output1InverseWarp.nii.gz).
Example usage from T1 to b0 using ANTs transforms:
> ConvertTransformFile 3 output0GenericAffine.mat vtk_transfo.txt --hm
> scil_surface_apply_transform lh_white_lps.vtk vtk_transfo.txt lh_white_b0.vtk\
--in_deformation output1InverseWarp.nii.gz --inverse
Important: The input surface needs to be in *T1 world LPS* coordinates
(aligned over the T1 in MI-Brain).
The script will use the linear affine first and then the warp image.
The resulting surface will be in *b0 world LPS* coordinates
(aligned over the b0 in MI-Brain).
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Reference:
[1] St-Onge, E., Daducci, A., Girard, G. and Descoteaux, M. 2018.
Surface-enhanced tractography (SET). NeuroImage.
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positional arguments:
in_moving_surface Input surface (.vtk).
in_target_reference Input target reference surface (.vtk).
in_transfo Path of the file containing the 4x4
transformation, matrix (.txt, .npy or .mat).
out_surface Output surface (.vtk).
options:
-h, --help show this help message and exit
--legacy_vtk_format Save the VTK file in the legacy format.
--reference REFERENCE
Reference anatomy for tck/vtk/fib/dpy file
support (.nii or .nii.gz).
-v [{DEBUG,INFO,WARNING,ERROR}]
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.
Surface spatial options:
--source_space {vox,voxmm,rasmm,lpsmm}
Source space of the input surface [rasmm].
--destination_space {vox,voxmm,rasmm,lpsmm}
Destination space of the output surface [rasmm].
--source_origin {corner,center}
Source origin of the input surface [center].
--destination_origin {corner,center}
Destination origin of the output surface [center].
2.3.0