usage: __main__.py [-h] [--dpp_key DPP_KEY] [--save_as_color]
[--save_mean_map filename] [--cmap CMAP]
[--cmap_max [CMAP_MAX]] [--processes NBR]
[-v [{DEBUG,INFO,WARNING,ERROR}]] [-f] [--no_bbox_check]
in_tractogram in_peaks out_tractogram
Compute the angular error (AE) for each segment of the streamlines.
For each segment of each streamline, the direction is compared with the
underlying peak (for single peak files, e.g. the first eigen-vector of tensors
for DTI) or with the closest peak (ex, with fODF peaks). AE is computed as the
cosine difference.
Currently, interpolation is not supported: peaks of the closest voxel are used
(nearest neighbor).
The AE is added as data_per_point (dpp) for each point, using the first point
of the segment. The last point of each streamline has an AE of zero.
Optionnally, you may also save it as a color.
When using --save_mean_map, if you want to be sure that your streamlines have
points in most voxels that they touch, you could resample your tractogram
first, with a small step size. See scil_tractogram_resample_nb_points.
Hints:
- If you want to see which streamlines have the best AE / worst AE, explore
the script scil_tractogram_filter_by_streamlines_properties.
- If you want to average the DPP into a mean DPS over each streamline, see
the script scil_tractogram_dpp_math.
positional arguments:
in_tractogram Path of the input tractogram file (trk or tck).
in_peaks Path of the input peaks file.
out_tractogram Path of the output tractogram file (trk or tck) with AE in dpp.
options:
-h, --help show this help message and exit
--dpp_key DPP_KEY Name of the dpp key containg the AE in the output. Default: AE
--processes NBR Number of sub-processes to start.
Default: [1]
-v [{DEBUG,INFO,WARNING,ERROR}]
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.
--no_bbox_check Activate to ignore validity of the bounding box during loading / saving of
tractograms (ignores the presence of invalid streamlines).
Optional outputs:
--save_as_color Save the AE as a color. Colors will range between black (0) and yellow (--cmap_max)
See also scil_tractogram_assign_custom_color, option --use_dpp.
--save_mean_map filename
If set, save the mean value of each streamline per voxel. Name of the map file (nifti).
See also scil_tractogram_project_streamlines_to_map.
Coloring options:
--cmap CMAP Choice of matplotlib colormap. Default: jet.
--cmap_max [CMAP_MAX]
If set, the maximum color on the colormap (yellow) will be associated
to this value. If not set, the maxium value found in the data will be used instead.
Default if set: 180 degrees.
2.3.0