usage: __main__.py [-h] [--out_json OUT_JSON] [--swap] [--binary]
[--distance DISTANCE] [--unit {points,mm}]
[--indent INDENT] [--sort_keys] [--reference REFERENCE]
[-v [{DEBUG,INFO,WARNING,ERROR}]] [-f]
in_bundle endpoints_map_head endpoints_map_tail
Computes the endpoints maps of a bundle (head and tail). The endpoints maps are
a count of the number of streamlines that start or end in each voxel.
Note: If the streamlines are not ordered, the head/tail are random and not
really two coherent groups.
- To get a single endpoint map of all endpoints, without grouping the head
and tail, use
>> scil_tractogram_compute_density_map --endpoints_only
- To order streamlines so that they start and end in the same regions, use
>> scil_bundle_uniformize_endpoints
positional arguments:
in_bundle Fiber bundle filename.
endpoints_map_head Output endpoints map head filename.
endpoints_map_tail Output endpoints map tail filename.
options:
-h, --help show this help message and exit
--out_json OUT_JSON Output JSON file with the number of streamlines in each endpoint map. [endpoints_map.json]
--swap Swap head<->tail convention. Can be useful when the reference is not in RAS.
--binary Save outputs as a binary mask instead of a heat map.
--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.
Distance options:
--distance DISTANCE Distance to consider at the extremities of the streamlines.
Ex: if --unit is points, a value of 1 means that the first and last
points of the streamlines only are considered.[1]
--unit {points,mm} Unit of the distance. [points]
Json options:
--indent INDENT Indent for json pretty print.
--sort_keys Sort keys in output json.
2.2.2