5ttvalidate

Synopsis

Validate that one or more images conform to the expected ACT five-tissue-type (5TT) format

Usage

5ttvalidate [ options ]  input [ input ... ]

  • input: the 5TT image(s) to be validated

Description

A 5TT image encodes the partial volume fractions of five tissue types in every voxel: cortical grey matter, sub-cortical grey matter, white matter, CSF, and pathological tissue. Each tissue partial volume fraction (PVF) must be a value in [0.0, 1.0], and for any brain voxel the five PVFs must sum to 1.0.

The following checks are performed on each input image:

  1. The image must be of floating-point type, 4-dimensional, and contain exactly 5 volumes. Failure causes the image to be immediately rejected as structurally invalid.

  2. For every brain voxel (identified by a non-zero partial-volume sum), each of the five tissue PVFs must lie within [0.0, 1.0]. Voxels that violate this constraint contain non-physical values and the image is rejected as a hard error.

  3. For every brain voxel, the sum of all five tissue PVFs must equal 1.0 to within a tolerance of

0.001

. Voxels that violate this constraint are reported as a soft warning: the image may still be usable for ACT but does not perfectly conform to the format.

The path to be provided to the -voxels option depends on the image(s) provided as input to the command. if ony a single input image is provided, then the path provided to the -voxels option should be the path to an output image file that will be created if necessary. If however there are multiple input files provided to the command, then the path provided to the -voxels option should instead be a path to a directory that will be created and populated with an individual image per problematic input image.

Options

  • -voxels image_or_dir output path for mask image(s) highlighting voxels where the input(s) violate 5TT requirements (see Description)

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/.