usage: __main__.py [-h] [--no_empty] (--from_dps dpp_key | --from_dpp dpp_key)
(--top | --bottom | --center)
(--nb NB | --percent [PERCENT] | --mean_std [N])
[-v [{DEBUG,INFO,WARNING,ERROR}]] [-f] [--no_bbox_check]
[--reference REFERENCE]
in_tractogram out_tractogram
Extract some streamlines from your tractogram, using chosen criterion based on
streamlines' dpp (data_per_point) or dps (data_per_streamline), or filter out
streamlines.
See also:
- To modify your dpp / dps values: see scil_tractogram_dpp_math and
scil_tractogram_dps_math.
- See all our other scil_tractogram_filter_* scripts!
- To extract streamlines based on regions of interest (ROI), see
scil_tractogram_segment_with_ROI.
- To extract U-shaped streamlines, see scil_tractogram_extract_ushape
positional arguments:
in_tractogram Path of the input tractogram file (trk or tck).
out_tractogram Path of the output tractogram file (trk or tck).
options:
-h, --help show this help message and exit
--no_empty Do not save the output tractogram if no streamline fit the criterion.
-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).
--reference REFERENCE
Reference anatomy for tck/vtk/fib/dpy file
support (.nii or .nii.gz).
Criterion's data:
--from_dps dpp_key Use DPS as criteria.
--from_dpp dpp_key Use DPP as criteria. Uses the average value over each streamline.
Direction of the criterion::
--top If set, selects a portion of streamlines that has the highest value in its dps
or mean dpp.
--bottom If set, selects a portion of streamlines that has the lowest value in its dps
or mean dpp.
--center Selects the average streamlines.
Criterion:
--nb NB Selects a chosen number of streamlines.
--percent [PERCENT] Saves the streamlines in the top / lowest percentile.
Default if set: The top / bottom 5%
--mean_std [N] Saves streamlines with value above mean + N*std (option --top), below
mean - N*std (option --below) or in the range [mean - N*std, mean + N*std]
(option --center).Default if set: uses mean +- 3std.
2.3.0