usage: __main__.py [-h] [--include_dps]
[--edge_keys LABEL1_LABEL2 [LABEL1_LABEL2 ...] |
--node_keys NODE [NODE ...]] [--save_empty [labels_list]]
[-v [{DEBUG,INFO,WARNING}]] [-f]
in_hdf5 out_dir
Save connections of a hdf5 created with
>> scil_tractogram_segment_connections_from_labels.py.
Useful for quality control and visual inspections.
It can either save all connections (default), individual connections specified
with --edge_keys or connections from specific nodes specified with --node_keys.
If a labels_list is provided, it will save all possible connections between the
labels in the list. If no labels_list is provided, it will save all connections
in the hdf5 file. If no argument is provided, it will save only the
connections that are present in the hdf5 file.
The output is a directory containing the thousands of connections:
out_dir/
|-- LABEL1_LABEL1.trk
|-- LABEL1_LABEL2.trk
|-- [...]
|-- LABEL90_LABEL90.trk
Formerly: scil_save_connections_from_hdf5.py
positional arguments:
in_hdf5 HDF5 filename (.h5) containing decomposed connections.
out_dir Path of the output directory.
options:
-h, --help show this help message and exit
--include_dps Include the data_per_streamline the metadata.
--edge_keys LABEL1_LABEL2 [LABEL1_LABEL2 ...]
Keys to identify the edges (connections) of interest.
--node_keys NODE [NODE ...]
Node keys to identify the sub-networks of interest.
Equivalent to adding any --edge_keys node_LABEL2 or LABEL2_node.
--save_empty [labels_list]
Save empty connections.
See script description for more information on labels_list usage.
-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.
CAREFUL. The whole output directory will be deleted if it exists.
Scilpy version: 2.0.2