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)


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.
--allowEdgeSeeds Allows seeding at the edges of pathway rules. Default: false.
--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.