dwinormalise

Synopsis

Perform various forms of intensity normalisation of DWIs

Usage

dwinormalise algorithm [ options ] ...

  • algorithm: Select the algorithm to be used to complete the script operation; additional details and options become available once an algorithm is nominated. Options are: group, individual

Description

This script provides access to different techniques for globally scaling the intensity of diffusion-weighted images. The different algorithms have different purposes, and different requirements with respect to the data with which they must be provided & will produce as output. Further information on the individual algorithms available can be accessed via their individual help pages; eg. “dwinormalise group -help”.

Options

Additional standard options for Python scripts

  • -nocleanup do not delete intermediate files during script execution, and do not delete scratch directory at script completion.

  • -scratch /path/to/scratch/ manually specify the path in which to generate the scratch directory.

  • -continue <ScratchDir> <LastFile> continue the script from a previous execution; must provide the scratch directory path, and the name of the last successfully-generated file.

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.

  • -force force overwrite of output files.

  • -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) 2008-2025 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/.

dwinormalise group

Synopsis

Performs a global DWI intensity normalisation on a group of subjects using the median b=0 white matter value as the reference

Usage

dwinormalise group input_dir mask_dir output_dir fa_template wm_mask [ options ]

  • input_dir: The input directory containing all DWI images

  • mask_dir: Input directory containing brain masks, corresponding to one per input image (with the same file name prefix)

  • output_dir: The output directory containing all of the intensity normalised DWI images

  • fa_template: The output population specific FA template, which is threshold to estimate a white matter mask

  • wm_mask: The output white matter mask (in template space), used to estimate the median b=0 white matter value for normalisation

Description

The white matter mask is estimated from a population average FA template then warped back to each subject to perform the intensity normalisation. Note that bias field correction should be performed prior to this step.

All input DWI files must contain an embedded diffusion gradient table; for this reason, these images must all be in either .mif or .mif.gz format.

Options

  • -fa_threshold The threshold applied to the Fractional Anisotropy group template used to derive an approximate white matter mask (default: 0.4)

Additional standard options for Python scripts

  • -nocleanup do not delete intermediate files during script execution, and do not delete scratch directory at script completion.

  • -scratch /path/to/scratch/ manually specify the path in which to generate the scratch directory.

  • -continue <ScratchDir> <LastFile> continue the script from a previous execution; must provide the scratch directory path, and the name of the last successfully-generated file.

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.

  • -force force overwrite of output files.

  • -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: David Raffelt (david.raffelt@florey.edu.au)

Copyright: Copyright (c) 2008-2025 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/.

dwinormalise individual

Synopsis

Intensity normalise a DWI series based on the b=0 signal within a supplied mask

Usage

dwinormalise individual input_dwi input_mask output_dwi [ options ]

  • input_dwi: The input DWI series

  • input_mask: The mask within which a reference b=0 intensity will be sampled

  • output_dwi: The output intensity-normalised DWI series

Options

  • -intensity Normalise the b=0 signal to a specified value (Default: 1000)

  • -percentile Define the percentile of the b=0 image intensties within the mask used for normalisation; if this option is not supplied then the median value (50th percentile) will be normalised to the desired intensity value

Options for importing the diffusion gradient table

  • -grad Provide the diffusion gradient table in MRtrix format

  • -fslgrad bvecs bvals Provide the diffusion gradient table in FSL bvecs/bvals format

Additional standard options for Python scripts

  • -nocleanup do not delete intermediate files during script execution, and do not delete scratch directory at script completion.

  • -scratch /path/to/scratch/ manually specify the path in which to generate the scratch directory.

  • -continue <ScratchDir> <LastFile> continue the script from a previous execution; must provide the scratch directory path, and the name of the last successfully-generated file.

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.

  • -force force overwrite of output files.

  • -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) and David Raffelt (david.raffelt@florey.edu.au)

Copyright: Copyright (c) 2008-2025 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/.