usage: __main__.py [-h] [--stored_space {rasmm,voxmm,vox}]
[--stored_origin {nifti,trackvis}] [--include_dps]
[--save_empty] [-v [{DEBUG,INFO,WARNING}]] [-f]
in_bundles [in_bundles ...] out_hdf5
Save connections as TRK to HDF5.
This script is useful to convert a set of connections or bundles to a single
HDF5 file. The HDF5 file will contain a group for each input file, with the
streamlines stored in the specified space and origin (keep the default if you
are going to use the connectivity scripts in scilpy).
To make a file compatible with scil_tractogram_commit.py or
scil_connectivity_compute_matrices.py you will have to follow this nomenclature
for the input files:
in_dir/
|-- LABEL1_LABEL1.trk
|-- LABEL1_LABEL2.trk
|-- [...]
|-- LABEL90_LABEL90.trk
The value of first labels should be smaller or equal to the second labels.
Connectivity scripts in scilpy only consider the upper triangular part of the
connectivity matrix.
By default, ignores the empty connections. To save them, use --save_empty.
Note that data_per_point is never included.
positional arguments:
in_bundles Path of the input connection(s) or bundle(s).
out_hdf5 Output HDF5 filename (.h5).
options:
-h, --help show this help message and exit
--stored_space {rasmm,voxmm,vox}
Space convention in which the streamlines are stored [vox].
--stored_origin {nifti,trackvis}
Voxel origin convention in which the streamlines are stored [trackvis].
--include_dps Include the data_per_streamline the metadata.
--save_empty Save empty connections.
-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