purifibre¶
removes spurious streamlines from tractograms
Purifibre computes a smoothed Track Orientation Density Image (TODI) to measure how well each streamline aligns with the collective organization of its neighbors, assigning a Fiber Coupling (FICO) score based on the streamline’s least aligned segment (minimum SECO). It then filters the tractogram by removing a user-defined percentage of streamlines with the lowest FICO scores, thereby eliminating spatially incoherent “spurious” fibers.
References
[Aydogan2022] Aydogan D.B., “Fiber coupling (FICO) measure using anisotropic smoothing of track orientation density images for tractogram filtering”, ISMRM 2022
Usage
./trekker purifibre [OPTIONS] <input tractogram> <output tractogram>
Positionals
<input tractogram> TEXT:FILE REQUIRED Input tractogram (.vtk, .tck, .trk)
<output tractogram> TEXT REQUIRED Output tractogram (.vtk, .tck)
Options
| Option | Description |
|---|---|
| -t, --trim FLOAT | Trim excludes ends of streamlines from being analyzed. E.g., when trim is 10, 90% of the streamline is analyzed. 5% of the streamline length from each end is excluded from the computation. Default: 10. |
| -p, --purify FLOAT | Percentage of streamlines to remove from the tractogram. Default: 5. |
| --voxDim FLOAT | Isotropic voxel dimension for sTODI computation. Default: 4. |
| --anisotropicSmoothing FLOAT INT | Standard deviation of the Gaussian kernel (in mm), and computation density for anisotropic smoothing (number of streamlines). E.g. when set to 2 100, smoothing is done using 100 streamlines randomly distributed around each streamline using a Gaussion distribution with standard deviation of 2 mm. Default=0 0. |
| --sphericalSmoothing FLOAT | Amount of sTODI spherical smoothing. Default: 15. |
| --save_fico TEXT | Saves a .vtk formatted copy of input tractogram with FICO values written as a field. |
General options
| Option | Description |
|---|---|
| -h, --help | Print this help message and exit. |
| -n, --numberOfThreads INT | Number of threads. |
| -v, --verbose TEXT | Verbose level. Options are "quiet", "fatal", "error", "warn", "info", and "debug". Default=info. |
| -f, --force | Force overwriting of existing file. |
