usage: __main__.py [-h] --in_maps IN_MAPS [IN_MAPS ...] --out_dpp_name
OUT_DPP_NAME [OUT_DPP_NAME ...] [--trilinear]
[--endpoints_only] [--keep_all_dpp] [--overwrite_dpp]
[--reference REFERENCE] [-f] [-v [{DEBUG,INFO,WARNING}]]
in_tractogram out_tractogram
Projects maps extracted from a map onto the points of streamlines.
The default options will take data from a nifti image (3D or 4D) and
project it onto the points of streamlines. If the image is 4D, the data
is stored as a list of 1D arrays per streamline. If the image is 3D,
the data is stored as a list of values per streamline.
See also scil_tractogram_project_streamlines_to_map.py for the reverse action.
* Note that the data from your maps will be projected only on the coordinates
of the points of your streamlines. Data underlying the whole segments between
two consecutive points is not used. If your streamlines are strongly
compressed, or if they have a very big step size, the result will possibly
reflect poorly your map. You may use scil_tractogram_resample.py to upsample
your streamlines first.
* Hint: The streamlines themselves are not modified here, only their dpp. To
avoid multiplying data on disk, you could use the following arguments to save
the new dpp in your current tractogram:
>> scil_tractogram_project_map_to_streamlines.py $in_bundle $in_bundle
--keep_all_dpp -f
positional arguments:
in_tractogram Fiber bundle file.
out_tractogram Output file.
options:
-h, --help show this help message and exit
--in_maps IN_MAPS [IN_MAPS ...]
Nifti map to project onto streamlines.
--out_dpp_name OUT_DPP_NAME [OUT_DPP_NAME ...]
Name of the data_per_point to be saved in the
output tractogram.
--trilinear If set, will use trilinear interpolation
else will use nearest neighbor interpolation
by default.
--endpoints_only If set, will only project the map onto the
endpoints of the streamlines (all other values along
streamlines will be NaN). If not set, will project
the map onto all points of the streamlines.
--keep_all_dpp If set, previous data_per_point will be preserved
in the output tractogram. Else, only --out_dpp_name
keys will be saved.
--overwrite_dpp If set, if --keep_all_dpp is set and some
--out_dpp_name keys already existed in your
data_per_point, allow overwriting old data_per_point.
--reference REFERENCE
Reference anatomy for tck/vtk/fib/dpy file
support (.nii or .nii.gz).
-f Force overwriting of the output files.
-v [{DEBUG,INFO,WARNING}]
Produces verbose output depending on the provided level.
Default level is warning, default when using -v is info.