usage: __main__.py [-h] [--binary] [--processes NBR]
[-v [{DEBUG,INFO,WARNING,ERROR}]] [-f]
in_hdf5 [in_hdf5 ...] out_dir
Compute a density map for each connection from a hdf5 file.
Typically use after scil_tractogram_segment_connections_from_labels in
order to obtain the average density map of each connection to allow the use
of --similarity in scil_connectivity_compute_matrices.
This script is parallelized, but will run much slower on non-SSD if too many
processes are used. The output is a directory containing the thousands of
connections:
out_dir/
|-- LABEL1_LABEL1.nii.gz
|-- LABEL1_LABEL2.nii.gz
|-- [...]
|-- LABEL90_LABEL90.nii.gz
positional arguments:
in_hdf5 List of HDF5 filenames (.h5) from scil_tractogram_segment_connections_from_labels.
out_dir Path of the output directory.
options:
-h, --help show this help message and exit
--binary Binarize density maps before the population average.
--processes NBR Number of sub-processes to start.
Default: [1]
-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.
2.2.2