usage: __main__.py [-h] [--min_x MIN_X] [--max_x MAX_X] [--min_y MIN_Y]
[--max_y MAX_Y] [--min_z MIN_Z] [--max_z MAX_Z] [--use_abs]
[--no_empty] [--display_counts] [--save_rejected filename]
[--indent INDENT] [--sort_keys] [--reference REFERENCE]
[-v [{DEBUG,INFO,WARNING}]] [-f]
in_tractogram out_tractogram
Script to filter streamlines based on their distance traveled in a specific
dimension (x, y, or z).
Useful to help differentiate bundles.
Examples: In a brain aligned with x coordinates in left - right axis and y
coordinates in anterior-posterior axis, a streamline from the ...
- corpus callosum will likely travel a very short distance in the y axis.
- cingulum will likely travel a very short distance in the x axis.
Note: we consider that x, y, z are the coordinates of the streamlines; we
do not verify if they are aligned with the brain's orientation.
Formerly: scil_filter_streamlines_by_orientation.py
positional arguments:
in_tractogram Streamlines input file name.
out_tractogram Streamlines output file name.
options:
-h, --help show this help message and exit
--min_x MIN_X Minimum distance in the first dimension, in mm.[0.0]
--max_x MAX_X Maximum distance in the first dimension, in mm.[inf]
--min_y MIN_Y Minimum distance in the second dimension, in mm.[0.0]
--max_y MAX_Y Maximum distance in the second dimension, in mm.[inf]
--min_z MIN_Z Minimum distance in the third dimension, in mm.[0.0]
--max_z MAX_Z Maximum distance in the third dimension, in mm.[inf]
--use_abs If set, will use the total of distances in absolute value (ex, coming back on yourself will contribute to the total distance instead of cancelling it).
--no_empty Do not write file if there is no streamline.
--display_counts Print streamline count before and after filtering.
--save_rejected filename
Save the SFT of rejected streamlines.
--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.