filterΒΆ
filters tractograms
Usage
./trekker filter [OPTIONS] <input tractogram> <output tractogram>
Positionals
<input tractogram> FILE REQUIRED Input tractogram (.vtk, .tck)
<output tractogram> FILE REQUIRED Output tractogram (.vtk, .tck)
Tip
Please check the documentation for pathways for a detailed explanation.
Options
| Option | Description |
|---|---|
| -p, --pathway TEXT ... | Pathway rule. |
| -s, --seed TEXT ... | Seed definition. |
| --discard_seed TEXT ... | Discard seed definition. |
| --minlength FLOAT | Minimum length of the tracks. Default=0. |
| --maxlength FLOAT | Maximum length of the tracks. Default=infinite. |
| --stopAtMax | If set to "stop", when `maxLength` is reached, the propagation stops, and the streamline is written in the output. If set to "discard", the streamline is not written in the output. Default=discard. |
| --oneSided | If enabled, tracking is done only towards one direction. |
| --skipSeed | Does not output the points that are within the seed region. |
| --seedTrials INT | Number of random trials for assigning seed. Default: 0. |
| --inOrder | If enabled, all pathway requirements are going to be satisfied in the order that they are given. All pathway options should be defined for `pathway_A/pathway_B` in order to use this option. |
| --maxOut INT | Maximum number of output streamlines. |
| -a, --ascii | Write ASCII output (.vtk only). |
| --saveDiscarded TEXT | Path for saving discarded streamlines. |
| --saveUncropped TEXT | Path for saving uncropped versions of streamlines if they were cropped during filtering. |
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. |
