usage: __main__.py [-h] [--looping_tractogram out_filename] [--qb [threshold]]
[--angle ANGLE] [--display_counts] [--no_empty]
[--indent INDENT] [--sort_keys] [--processes NBR]
[--reference REFERENCE] [-v [{DEBUG,INFO,WARNING}]] [-f]
in_tractogram out_tractogram
This script can be used to remove loops in two types of streamline datasets:
- Whole brain: For this type, the script removes streamlines if they
make a loop with an angle of more than 360 degrees. It's possible to change
this angle with the --angle option. Warning: Don't use --qb option for a
whole brain tractography.
- Bundle dataset: For this type, it is possible to remove loops and
streamlines outside the bundle. For the sharp angle turn, use --qb option.
Formerly: scil_detect_streamlines_loops.py
positional arguments:
in_tractogram Tractogram input file name.
out_tractogram Output tractogram without loops.
options:
-h, --help show this help message and exit
--looping_tractogram out_filename
If set, saves detected looping streamlines.
--qb [threshold] If set, uses QuickBundles to detect outliers (loops, sharp angle
turns). Given threshold is the maximal streamline to bundle
distance for a streamline to be considered as a tracking error.
Default if set: [8.0]
--angle ANGLE Maximum looping (or turning) angle of
a streamline in degrees. [360]
--display_counts Print streamline count before and after filtering
--no_empty If set, will not save outputs if they are empty.
--processes NBR Number of sub-processes to start.
Default: [1]
--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.
-f Force overwriting of the output files.
Json options:
--indent INDENT Indent for json pretty print.
--sort_keys Sort keys in output json.
References:
QuickBundles, based on [Garyfallidis12] Frontiers in Neuroscience, 2012.