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_bundles_for_connectivity.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.
With the option --save_empty, a label_lists, as a txt file, must be provided.
This option saves existing connections and empty connections.
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. Then, the list of possible connections is
not found from the hdf5 but inferred from labels_list, a txt file
containing a list of nodes saved by the decomposition script.
*If used together with edge_keys or node_keys, the provided nodes must
exist in labels_list.
-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.