usage: __main__.py [-h] [--per_point in_labels | --include_dps]
[--density_weighting] [--distance_weighting DISTANCE_NII]
[--correlation_weighting CORRELATION_NII]
[--out_json OUT_JSON] [--reference REFERENCE]
[--indent INDENT] [--sort_keys] [-v [{DEBUG,INFO,WARNING}]]
in_bundle in_metrics [in_metrics ...]
Compute mean and std for each metric.
- Default: For the whole bundle. This is achieved by averaging the metric
values of all voxels occupied by the bundle.
- Option --per_point: For all streamlines points in the bundle for each metric
combination, along the bundle, i.e. for each point.
**To create label_map and distance_map, see
scil_bundle_label_map.py
Density weighting modifies the contribution of voxel with lower/higher
streamline count to reduce influence of spurious streamlines.
Formerly: scil_compute_bundle_mean_std_per_point.py or
scil_compute_bundle_mean_std.py
positional arguments:
in_bundle Fiber bundle file to compute statistics on.
in_metrics Nifti file to compute statistics on. Probably some tractometry measure(s) such as FA, MD, RD, ...
options:
-h, --help show this help message and exit
--per_point in_labels
If set, computes the metrics per point instead of on the whole bundle.
You must then give the label map (.nii.gz) of the corresponding fiber bundle.
--include_dps Save values from data_per_streamline.
Currently not offered with option --per_point.
--density_weighting If set, weights statistics by the number of fibers passing through each voxel.
--distance_weighting DISTANCE_NII
If set, weights statistics by the inverse of the distance between a streamline and the centroid.
--correlation_weighting CORRELATION_NII
If set, weight statistics by the correlation strength between longitudinal data.
--out_json OUT_JSON Path of the output file. If not given, the output is simply printed on screen.
--reference REFERENCE
Reference anatomy for tck/vtk/fib/dpy file
support (.nii or .nii.gz).
-v [{DEBUG,INFO,WARNING}]
Produces verbose output depending on the provided level.
Default level is warning, default when using -v is info.
Json options:
--indent INDENT Indent for json pretty print.
--sort_keys Sort keys in output json.