tckvalidate

Synopsis

Validate a tractogram (.tck) file

Usage

tckvalidate [ options ]  tracks_in

  • tracks_in: the input tractogram file

Description

This command checks that a tractogram file is well-formed. The binary data section of a .tck file consists of a sequence of 3-float triplets. Each triplet must be exactly one of: a regular vertex (all three components finite), an inter-streamline delimiter (all three components NaN), or the mandatory end-of-file barrier (all three components infinity). The end-of-file barrier must be the last triplet in the file.

The following hard violations cause the command to fail: (1) a triplet that is partially non-finite (i.e. not all-finite, not all-NaN, and not all-infinity); (2) any data present after the end-of-file barrier; (3) the end of the binary data section is reached without an end-of-file barrier (truncated file); (4) the last streamline body is not terminated by a NaN delimiter before the end-of-file barrier; (5) the “count” field is absent from the file header; (6) the “count” field in the file header does not match the number of streamlines actually present in the file.

The command also reports the presence of streamlines with zero vertices or exactly one vertex, which are degenerate cases that may indicate issues with the tractography algorithm that produced the file.

Options

Standard options

  • -info display information messages.

  • -quiet do not display information messages or progress status; alternatively, this can be achieved by setting the MRTRIX_QUIET environment variable to a non-empty string.

  • -debug display debugging messages & debug input data.

  • -force force overwrite of output files (caution: using the same file as input and output might cause unexpected behaviour).

  • -nthreads number use this number of threads in multi-threaded applications (set to 0 to disable multi-threading).

  • -config key value (multiple uses permitted) temporarily set the value of an MRtrix config file entry.

  • -help display this information page and exit.

  • -version display version information and exit.

References

Tournier, J.-D.; Smith, R. E.; Raffelt, D.; Tabbara, R.; Dhollander, T.; Pietsch, M.; Christiaens, D.; Jeurissen, B.; Yeh, C.-H. & Connelly, A. MRtrix3: A fast, flexible and open software framework for medical image processing and visualisation. NeuroImage, 2019, 202, 116137

Author: Robert E. Smith (robert.smith@florey.edu.au)

Copyright: Copyright (c) 2008-2026 the MRtrix3 contributors.

This Source Code Form is subject to the terms of the Mozilla Public License, v. 2.0. If a copy of the MPL was not distributed with this file, You can obtain one at http://mozilla.org/MPL/2.0/.

Covered Software is provided under this License on an “as is” basis, without warranty of any kind, either expressed, implied, or statutory, including, without limitation, warranties that the Covered Software is free of defects, merchantable, fit for a particular purpose or non-infringing. See the Mozilla Public License v. 2.0 for more details.

For more details, see http://www.mrtrix.org/.