usage: __main__.py [-h] --mode {dpp,dps} --in_dpp_name key [key ...]
--out_keys key [key ...] [--endpoints_only]
[--keep_all_dpp_dps] [--overwrite_dpp_dps]
[--reference REFERENCE] [-v [{DEBUG,INFO,WARNING}]] [-f]
[--no_bbox_check]
OPERATION INPUT_FILE OUTPUT_FILE
Performs an operation on data per point (dpp) from input streamlines.
Although the input data always comes from the dpp, the output can be either
a dpp or a data_per_streamline (dps), depending on the chosen options.
Two modes of operation are supported: dpp and dps.
- In dps mode, the operation is performed on dpp across the dimension of
the streamlines resulting in a single value (or array in the 4D case)
per streamline, stored as dps.
- In dpp mode, the operation is performed on each point separately,
resulting in a new dpp.
If endpoints_only and dpp mode is set the operation will only be calculated at
the streamline endpoints the rest of the values along the streamline will be
NaN.
If endpoints_only and dps mode is set operation will be calculated across the
data at the endpoints and stored as a single value (or array in the 4D case)
per streamline.
Endpoint only operation:
correlation: correlation calculated between arrays extracted from streamline
endpoints (data must be multivalued per point) and dps mode must be set.
positional arguments:
OPERATION The type of operation to be performed on the
streamlines. Must be one of the following:
[mean, sum, min, max, correlation.]
INPUT_FILE Input tractogram containing streamlines and metadata.
OUTPUT_FILE The file where the remaining streamlines
are saved.
options:
-h, --help show this help message and exit
--mode {dpp,dps} Set to dps if the operation is to be performed
across all dimensions resulting in a single value per
streamline. Set to dpp if the operation is to be
performed on each point separately resulting in a
single value per point.
--in_dpp_name key [key ...]
Name or list of names of the data_per_point for
operation to be performed on. If more than one dpp
is selected, the same operation will be applied
separately to each one.
--out_keys key [key ...]
Name of the resulting data_per_point or
data_per_streamline to be saved in the output
tractogram. If more than one --in_dpp_name was used,
enter the same number of --out_keys values.
--endpoints_only If set, will only perform operation on endpoints
If not set, will perform operation on all streamline
points.
--keep_all_dpp_dps If set, previous data_per_point will be preserved
in the output tractogram. Else, only --out_dpp_name
keys will be saved.
--overwrite_dpp_dps If set, if --keep_all_dpp_dps is set and some
--out_keys keys already existed in your
data_per_point or data_per_streamline, allow
overwriting old data_per_point.
--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.
--no_bbox_check Activate to ignore validity of the bounding box during loading / saving of
tractograms (ignores the presence of invalid streamlines).