usage: __main__.py [-h] [--out_density_map OUT_DENSITY_MAP]
[--out_density_measures OUT_DENSITY_MEASURES]
[--out_collision_map OUT_COLLISION_MAP]
[--out_collision_measures OUT_COLLISION_MEASURES]
[--samples_per_voxel_axis SAMPLES_PER_VOXEL_AXIS] [-f]
[-v [{DEBUG,INFO,WARNING,ERROR}]] [--indent INDENT]
[--sort_keys]
in_fibertubes
Estimates the per-voxel volumetric density of a set of fibertubes. In other
words, how much space is occupied by fibertubes and how much is emptiness.
1. Segments voxels that contain at least a single fibertube.
2. Valid voxels are finely sampled and we count the number of samples that
landed within a fibertube. For each voxel, this number is then divided by
its total amount of samples.
3. By doing the same steps for samples that landed within 2 or more
fibertubes, we can create a density map of the fibertube collisions.
To form fibertubes from a set of streamlines, you can use the scripts:
- scil_tractogram_filter_collisions to assign a diameter to each streamline
and remove all colliding fibertubes.
- scil_tractogram_dps_math to assign a diameter without filtering.
See also:
- docs/source/documentation/fibertube_tracking.rst
positional arguments:
in_fibertubes Path to the tractogram (must be .trk) file
containing fibertubes. They must have their
respective diameter saved as data_per_streamline.
options:
-h, --help show this help message and exit
--out_density_map OUT_DENSITY_MAP
Path of the density Nifti image.
--out_density_measures OUT_DENSITY_MEASURES
Path of the output file containing central
tendency measures about volumetric density.
(Must be .json)
--out_collision_map OUT_COLLISION_MAP
Path of the collision Nifti image.
--out_collision_measures OUT_COLLISION_MEASURES
Path of the output file containing central
tendency measures about collision density.
(Must be .json)
--samples_per_voxel_axis SAMPLES_PER_VOXEL_AXIS
Number of samples to be created along a single
axis of a voxel. The total number of samples in the
voxel will be this number cubed. [10]
-f Force overwriting of the output files.
-v [{DEBUG,INFO,WARNING,ERROR}]
Produces verbose output depending on the provided level.
Default level is warning, default when using -v is info.
Json options:
--indent INDENT Indent for json pretty print.
--sort_keys Sort keys in output json.