usage: __main__.py [-h]
(--in_labels IN_LABELS | --in_mask IN_MASK | --in_volume IN_VOLUME)
[--list_indices LIST_INDICES [LIST_INDICES ...] |
--each_index] [--value VALUE] [--smooth SMOOTH]
[--erosion EROSION] [--dilation DILATION]
[--opening OPENING] [--closing CLOSING] [--fill]
[--vtk2vox] [-v [{DEBUG,INFO,WARNING,ERROR}]] [-f]
out_surface
Script to create a surface with marching cube from a mask or a label image.
The surface will be readable with software like MI-Brain.
Example : use wmparc.a2009s.nii.gz with some aseg.stats indices
scil_surface_create out_surface.vtk \
--in_labels s1a1/mask/S1-A1_wmparc.a2009s.nii.gz\
--list_indices 16:32 --opening 2 --smooth 2 -v
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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:
out_surface Output surface (.vtk)
options:
-h, --help show this help message and exit
--fill Fill holes in the image. [False]
--vtk2vox Keep output surface in voxel space. [False]
-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.
Input (Labels or Mask):
--in_labels IN_LABELS
Path of the atlas (nii or nii.gz).
You can provide a list of indices with --list_indices or create a surface per index with --each_index.
If no indices are provided, it will merge all indices and converted to a binary mask.
--in_mask IN_MASK Path of the mask (nii or nii.gz).
--in_volume IN_VOLUME
Path of the volume (nii or nii.gz).
Options for labels input:
--list_indices LIST_INDICES [LIST_INDICES ...]
List of labels indices to use for the surface.
--each_index Create a surface per index. It will use the out_surface basename to create the output files.
Options for volume input:
--value VALUE Isosurface threshold value used. This value is called isovalue in mbcube.
Example: For a binary mask (with 0 and 1), 0.5 will generate a surface in the middle of the transition. [0.5]
Morphology options:
--smooth SMOOTH Smoothing size with 1 implicit step. [None]
--erosion EROSION Erosion: number of iterations. [None]
--dilation DILATION Dilation: number of iterations. [None]
--opening OPENING Opening (dilation of the erosion): number of iterations. [None]
--closing CLOSING Closing (erosion of the dilation): number of iterations. [None]
2.2.2