usage: __main__.py [-h] (--load_dpp DPP_FILE | --from_anatomy FILE)
[--colormap COLORMAP] [--log]
[--source_space {vox,voxmm,rasmm,lpsmm}]
[--destination_space {vox,voxmm,rasmm,lpsmm}]
[--source_origin {corner,center}]
[--destination_origin {corner,center}]
[--legacy_vtk_format] [--reference REFERENCE]
[-v [{DEBUG,INFO,WARNING,ERROR}]] [-f]
in_surface out_surface
Assign a custom color to a surface based on a data per point (dpp) file
or an anatomical image.
If a dpp file is provided, it must contain a scalar value for each vertex.
If an anatomical image is provided, the color is sampled from the image
at each vertex location.
The values are then mapped to a colormap (default: jet).
Example:
scil_surface_assign_custom_color surf.vtk colored.vtk --load_dpp data.txt
scil_surface_assign_custom_color surf.vtk colored.vtk --from_anatomy t1.nii.gz
positional arguments:
in_surface Input surface(s) (VTK + PIAL + GII supported).
out_surface Output surface(s) (VTK supported).
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.
Coloring method:
--load_dpp DPP_FILE Load data per point (scalar) for coloring. Can be a .txt or .npy file.
--from_anatomy FILE Use the voxel data for coloring, linear scaling from min/max of the image.
Coloring options:
--colormap COLORMAP Select the colormap for colored surface [jet].
Use two Matplotlib named color separated by a - to create your own colormap.
--log Apply a base 10 logarithm for values.
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].