scil_connectivity_hdf5_average_density_map.py

usage: __main__.py [-h] [--binary] [--processes NBR]
                   [-v [{DEBUG,INFO,WARNING}]] [-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.py in
order to obtain the average density map of each connection to allow the use
of --similarity in scil_connectivity_compute_matrices.py.

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

Formerly: scil_compute_hdf5_average_density_map.py

positional arguments:
  in_hdf5               List of HDF5 filenames (.h5) from scil_tractogram_segment_connections_from_labels.py.
  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}]
                        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