usage: __main__.py [-h] [--keep_background] [--hide_labels label [label ...]]
[--hide_fig] [--out_fig file.png] [--binary | --percentage]
[-v [{DEBUG,INFO,WARNING,ERROR}]] [--reference REFERENCE]
[-f]
in_tractogram in_labels out_matrix out_labels
Computes a very simple connectivity matrix, using the streamline count and the
position of the streamlines' endpoints.
This script is intented for exploration of your data. For a more thorough
computation (using the longest streamline segment), and for more options about
the weights of the matrix, see:
>> scil_connectivity_compute_matrices
Contrary to scil_connectivity_compute_matrices, works with an incomplete
parcellation (i.e. with streamlines ending in the background).
In the output figure, 4 matrices are shown, all using the streamline count:
- Raw count
- Raw count (log view)
- Binary matrix (if at least 1 streamline connects the two regions)
- Percentage of the total streamline count.
You may select which matrix to save to disk (as .npy) using options --binary or
--percentage. Default ouput matrix is the raw count.
positional arguments:
in_tractogram Tractogram (trk or tck).
in_labels Input nifti volume.
out_matrix Out .npy file.
out_labels Out .txt file. Will show the ordered labels (i.e. the columns and lines' tags).
options:
-h, --help show this help message and exit
-v [{DEBUG,INFO,WARNING,ERROR}]
Produces verbose output depending on the provided level.
Default level is warning, default when using -v is info.
--reference REFERENCE
Reference anatomy for tck/vtk/fib/dpy file
support (.nii or .nii.gz).
-f Force overwriting of the output files.
Label management options:
--keep_background By default, the background (label 0) is not included in the matrix.
Use this option to keep it.
--hide_labels label [label ...]
Set given labels' weights to 0 in the matrix.
Their row and columns wil be kept but set to 0.
Figure options:
--hide_fig If set, does not show the matrices with matplotlib (you can still use --out_fig)
--out_fig file.png If set, saves the figure to file.
Extension can be any format understood by matplotlib (ex, .png).
Output matrix (.npy) options:
--binary If set, saves the result as binary. Else, the streamline count is saved.
--percentage
2.2.2