DWI masking

Many DWI processing operations either necessitate the use of a binary mask image in order to spatially constrain the operation in some way, or can be executed in less time by not performing the relevant calculations in those voxels that are not of interest. However, while this would seem like a relatively trivial operation, it is in fact deceptively difficult to devise an appropriate heuristic for deriving an appropriate mask that works for a wide range of DWI data. It is not uncommon for the derivation of this mask to go awry in a range of scenarios, which can have serious implications for downstream processing steps. For this reason, as of MRtrix version 3.1.0, a range of DWI mask derivation algorithms are provided, allowing users to assess which heuristics work best for their particular data. The purpose of this documentation page is to describe those algorithms that are available, the circumstances in which they may or may not work, the features that are available for users to manipulate this behaviour, and the applications in which these details are most relevant for user attention.

dwi2mask algorithms

dwi2mask 3dautomask

Provides the mean b=0 image directly to AFNI command 3dAutomask .

dwi2mask ants

Provides the mean b=0 image directly to ANTs command antsBrainExtraction.sh, configured for T2-weighted image input.

This algorithm necessitates the specification of a template image and corresponding binary mask image defined on that template. These two images must be provided by the user either using the -template command-line option, or the Dwi2maskTemplateImage and Dwi2maskTemplateMask configuration file options (see Configuration file options).

dwi2mask b02template

Registers the subject’s mean b=0 image to a template image, and back-propagates a binary mask back into the individual’s DWI voxel grid. Achieved as follows:

1. Non-linearly register subject’s mean b=0 image to a specified template image;
2. (If not calculated implicitly as part of step 1) Invert the non-linear deformation field;
3. Transform binary mask associated with template image onto voxel grid of mean b=0 image (with interpolation);
4. Apply a threshold of 0.5 to transformed image to produce a mask.

There are multiple external software tools that can be utilised for performing the core image registration and transformation processes:

• antsquick: Utilises the ANTs command antsRegistrationSyNQuick.sh for registration; transforms mask image to subject space using ANTs command antsApplyTransforms.

• antsfull: Utilises the ANTs commands antsRegistration for registration, using the registration parameters specified in the article:

  Tustison, Nicholas J., and Brian B. Avants. Explicit B-Spline Regularization in Diffeomorphic Image Registration. Frontiers in Neuroinformatics 7 (December 23, 2013): 39. https://doi.org/10.3389/fninf.2013.00039.

  Template mask image is then transformed to subject space using ANTs command antsApplyTransforms.

• fsl: Utilises FSL commands as follows:

  • flirt: Initial affine registration;
  • fnirt: Non-linear registration;
  • invwarp: Inversion of warp from subject to template;
  • applywarp: Transform template mask to subject space.

By default, if no manual selection is made here using either the -software command-line option or the Dwi2maskTemplateSoftware configuration file entry, the antsquick approach will be used.

This algorithm necessitates the specification of a template image and corresponding binary mask image defined on that template. These two images must be provided by the user either using the -template command-line option, or the Dwi2maskTemplateImage and Dwi2maskTemplateMask configuration file options (see Configuration file options).

The registration operation can be expected to perform best if the specified template image is of comparable shape and image contrast to that of the b=0 volumes of the DWI data being processed. As such, if using an existing template image, a T2-weighted image would be recommended. Alternatively, one could produce a population template b=0 image based on one’s own data, and manually define a mask on that template that could then subsequently be used for DWI masking.

For all registration algorithms, there are dwi2mask command-line options available for fine-tuning the behaviour of the registration by passing command-line options down to the relevant command(s); further, it is possible to set such parameters within the MRtrix configuration file, which may be of particular use if configuration file option Dwi2maskAlgorithm is set to b02template (see Configuration file options).

dwi2mask consensus

This algorithm is unique compared to all other dwi2mask algorithms, in that it does not provide one specific heuristic for DWI mask estimation; instead, it executes all other dwi2mask algorithms, and produces a single mask based on the consensus of those algorithms. Currently this consensus is simply those voxels that were included in the estimated masks of more than 50% of the algorithms utilised. Note that if the external software requirements of any specific dwi2mask algorithm are not installed, the consensus algorithm will report that not all algorithms could be executed, and will utilise only the outputs of those algorithms that could be executed successfully.

dwi2mask fslbet

Provides the mean b=0 image directly to FSL command bet.

dwi2mask hdbet

Provides the mean b=0 image directly to HD-BET command hd-bet.

dwi2mask legacy

Reproduces the behaviour of the dwi2mask binary executable that was included in MRtrix3 prior to version 3.1.0.

It involves the following steps:

1. Compute the mean diffusion-weighted signal intensity for each b-value;
2. For each b-value independently, automatically determine a threshold to apply to produce a binary mask;
3. Sum the masks from step 2 across b-values;
4. Apply a median filter;
5. Select the largest connected component and fill holes;
6. Apply mask cleaning filter to remove small areas only connected to the largest component via thin “bridges”.

dwi2mask mean

A heuristic algorithm that is based on simply taking the mean DWI intensity across all volumes, and then applying a threshold. It was reported to provide good results for some forms of data, but is not necessarily guaranteed to do so for other DWI acquisition protocols; algorithm dwi2mask trace is intended to operate on a similar concept, but be more robust against variations in acquisition.

Operations are as follows:

1. Compute the mean DWI intensity across all volumes, regardless of b-value;
2. Automatically determine an intensity threshold for this image to produce a binary mask;
3. Select the largest connected component and fill any holes;
4. Apply mask cleaning filter to remove small areas only connected to the largest component via thin “bridges”.

dwi2mask trace

Heuristic algorithms for generating masks from DWI data based on trace-weighted images (i.e. mean image intensity within each shell) in a manner different to that of the dwi2mask legacy algorithm.

Its behaviour is as follows:

1. Calculate the trace-weighted image for each shell;
2. For each shell, find a multiplicative factor that gives the trace-weighted image approximately the same intensity of that of the first shell (this is so that each shell contributes approximately equally toward determination of the mask);
3. Calculate the mean trace-weighted image across shells;
4. Automatically determine an intensity threshold for this image to produce a binary mask;
5. Select the largest connected component and fill any holes;
6. Apply mask cleaning filter to remove small areas only connected to the largest component via thin “bridges”;
7. If the command-line option -iterative is not used, the algorithm ceases at this point (i.e. the default behaviour);
8. For each b-value shell, compute the mean and standard deviation of the trace-weighted image intensities inside and outside of the current mask, and use this to derive Cohen’s d statistic;
9. Perform a recombination of the trace-weighted images; but the multiplicative weights applied to each b-value shell trace image are, instead of being based on intensity matching as in step 2, the Cohen’s d statistics calculated in step 8;
10. Apply a threshold and mask filtering operations as in steps 4-6;
11. If the resulting mask differs from the previous estimate, go back to step 8; if not, or if a maximum number of iterations is reached, the algorithm is completed.

Note that the iterative version of this algorithm can currently be considered a hypothetical heuristic, and it is not yet known whether or not its behaviour is reasonable across a range of DWI data; it should therefore be considered entirely experimental.

Algorithm comparison

Algorithm	External dependencies	Uses more that b=0	Assumptions	Robust to bias field	Can use GPU
3dAutomask	Yes (AFNI)	No	Unknown	Unknown	No
ants	Yes (ANTs)	No	Brain; WM darker than GM	Unknown	No
b02template	Yes (ANTs / FSL)	No	Matches template	Yes	No
consensus	Only if installed	Yes	Various	Various	No
fslbet	Yes (FSL)	No	Approx. spherical	Yes	No
hdbet	Yes (HD-BET)	No	Brain	Yes	Yes
legacy	No	Yes	Single connected component	No	No
trace	No	Yes	Single connected component	No	No

Python scripts utilising dwi2mask

There are a number of Python scripts provided within MRtrix3 that operate on DWI data and necessitate use of a mask, and therefore (if not provided with one explicitly at the command-line) will internally execute the dwi2mask command.

Because it is not possible for the user to manually specify how dwi2mask should be utilised in this scenario, there are configuration file options provided to assist in controlling the behaviour of dwi2mask in these scenarios (see below).

MRtrix3 Python command	Purpose of DWI mask
dwibiascorrect	Only voxels within the mask are utilised in optimisation of bias field parameters. For ants algorithm, field is estimated within the mask but applied to all voxels within the field of view (field basis is extrapolated beyond the extremities of the mask); for fsl algorithm, field is both estimated within, and applied to, only those voxels within the mask, producing a discontinuity in image intensity at the outer edge of the mask that can be deleterious for subsequent quantitative analyses.
dwifslpreproc	Constrains optimisation of distortion parameter estimates in FSL eddy. If performing susceptibility distortion correction, this is applied to the DWI data subsequently to the appplication of FSL command applytopup.
dwigradcheck	Utilised as both seed and mask image for streamlines tractography in the tckgen command.
dwi2response	Voxels outside of the initial mask are never considered as candidates for response function(s), nor do they contribute to any optimisation of the selection of such.

Configuration file options

There are many options that can be set within the MRtrix3 Configuration file that directly influence the operation of the dwi2mask command. These are included in the List of MRtrix3 configuration file options page, but are mentioned here also for discoverability:

• Dwi2maskAlgorithm

  For those Python scripts utilising dwi2mask, this is the dwi2mask algorithm that will be invoked. If not explicitly set, the legacy algorithm will be used.

  Note

  Setting this configuration file option does not enable the utilisation of dwi2mask without manually specifying the algorithm to be used. For manual usage, the algorithm must always be specified. This option only controls the algorithm that will be used when dwi2mask is invoked from inside one of the Python scripts provided with MRtrix3.

• Dwi2maskTemplateSoftware

  If dwi2mask b02template is invoked, and the -software command-line option is not used, the value of this option determines the software tool that will be utilised for registration to the template and back-propagation of the mask in template space to the subject’s DWI data. In the absence of this configuration file option, antsquick (i.e. ANTs antsRegistrationSyNQuick.sh) will be used.

• Dwi2maskTemplateImage and Dwi2maskTemplateMask

  This pair of configuration file options allow the user to pre-specify the filesystem locations of the two images (T2-weighted template and corresponding binary mask) to be utilised by the dwi2mask ants and dwi2mask b02template algorithms. Note that there is no “default” template to be utilised by these algorithms; so the user must either include these entries in their configuration file, or manually specify the -template command-line option whenever they use dwi2mask ants or dwi2mask b02template. If the value of configuration file option “Dwi2maskAlgorithm” is “ants” or “b02template”, then these two entries must also be specified.

• Dwi2maskTemplateANTsQuickOptions, Dwi2maskTemplateANTsFullOptions, Dwi2maskTemplateFSLFlirtOptions and Dwi2maskTemplateFSLFnirtConfig

  These options allow full automated control over the parameters with which the external neuroimaging software package registration commands are executed. If one of the relevant dwi2mask b02template command-line options is used explicitly (-ants_options, -flirt_options, -fnirt_config), that information takes precedence; otherwise, if one of these configuration file entries is set, that information will be propagated directly to the relevant command.