Neural connections geometrical and functional analysis
Compute multiple statistics about fiber bundles. Descriptive statistics and quantitative information about image information and geometrical characteristics.
- Bundle properties
- Number of fibers: number of streamlines composing the tractogram.
- Number of points: number of points composing a streamline
- Geometrical properties
- Lengths: length of the fiber (in mm). Computed by adding up the lengths of all segments. Feature: EDT
- Shortest path: length of the straight segment connecting fibers endpoints
- Turning angle: turning angle projected (Winding). Cumulative signed angle between each line segment and the previous one, expressed in degrees.
- Connectivity properties
- Seeds position: position of the starting point (seed) of a streamline
- Termination position: position of the endpoint (termination condition respected) of a streamline
- Mid-point position: position of the central point of a streamline
- Diffusion properties
- b-zero intensity: mapping of every point of the streamline on the baseline image. The exact mapped value is computed with a weighted interpolation of the b-zeros of the 12-connected voxel space around the point.
- FA value: Mapping of every point of the streamline on the FA map.
- MD value: Mapping of every point of the streamline on the MD map.
Installation:
$ git clone https://github.com/aledelmo/TractographyMetrics
$ cd TractographyMetrics
$ pip install -r requirements.txt
$ python -m tractography_metrics.py <tractogram_filepath> <output_txt_file>To enrich analysis with diffusion information use the following optional keywords:
| short flag | long flag | Action |
|---|---|---|
-bzero <filepath> |
--b_zero <filepath> |
Compute stats on the bzero volume |
-fa <metric_filepath> |
--Fractional_Anisotropy <metric_filepath> |
Compute stats on the FA metric volume |
-md <metric_filepath> |
--metric_filepath |
Compute stats on the MD metric volume |
Save the output in a different format with the optional flags:
| short flag | long flag |
|---|---|
-csv |
--save_csv |
-xlsx |
--save_xlsx |
Add a header:
| short flag | long flag | Action |
|---|---|---|
-hd <text> |
--header <text> |
Add any string of text to the stats |
When working on huge amounts of fibers you might experience computational issues. Try to downsample the tractogram with:
| short flag | long flag | Action |
|---|---|---|
-r <resampling_percentage> |
--resample <resampling_percentage> |
Specify the downsample percentage of the tractogram fibers (value between 0 and 100) |
For any inquiries please contact: Alessandro Delmonte @ alessandro.delmonte@institutimagine.org
This project is licensed under the Apache License 2.0 - see the LICENSE file for details