usage: __main__.py [-h] [--binary [FIXED_VALUE]] [--no_bbox_check]
[-v [{DEBUG,INFO,WARNING}]] [-f]
tractogram_filename seed_density_filename
Compute a density map of seeds saved in .trk file.
* They are saved as a data_per_streamline 'seeds' when using our tractography
scripts with option --save_seeds.
- scil_tracking_local.py
- scil_tracking_local_dev.py
- scil_tracking_pft.py.
If you use your own tractograms, you can create a 'seeds' data_per_streamline.
Don't forget to save the coordinates in voxel space, corner origin.
Formerly: scil_compute_seed_density_map.py
positional arguments:
tractogram_filename Tracts filename. Format must be .trk.
File should contain a "seeds" value in the data_per_streamline.
These seeds must be in space: voxel, origin: corner.
seed_density_filename
Output seed density filename. Format must be Nifti.
options:
-h, --help show this help message and exit
--binary [FIXED_VALUE]
If set, will store the same value for all intersected voxels, creating a binary map.
When set without a value, 1 is used (and dtype uint8).
If a value is given, it will be used as the stored value.
--no_bbox_check Activate to ignore validity of the bounding box during loading / saving of
tractograms (ignores the presence of invalid streamlines).
-v [{DEBUG,INFO,WARNING}]
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.
Scilpy version: 2.0.2