New features
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Support for NIfTI-2 images.
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Support for JSON data. In MRtrix3, JSON files (with the file extension
.json) can be used to store key-value fields associated with a particular image externally from an image header. This is useful for image formats that use a fixed-size header (such as NIfTI), and are consequently limited in the amount of associated data that can be stored within that header. If however you regularly use the MRtrix image formats (.mif,.mih), you will most likely not require this feature since these formats already allow any number of key-value fields to be stored directly within the header. Special thanks to JSON for Modern C++ for providing a great library to enable this functionality. -
System signals (such as manually killing a process, running out of memory etc.) are now handled within the application, so that commands can produce more appropriate error messages, and additionally attempt to clean up any temporary files currently in use. This will hopefully reduce confusion around the dreaded invisible-error-messages and non-interpretable-error-messages that have been reported by a number of users. It should also minimise issues with running out of temporary storage. Note however that this functionality will be incomplete on Windows systems.
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Some new header key-value entries:
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command_historywill keep a running list of the MRtrix3 commands used in producing an image. -
prior_dw_schemewill store the diffusion gradient table used in generating an image, in cases where the image volumes no longer reflect the entries in the diffusion gradient table (e.g. after converting from DWIs to an FOD in spherical harmonic representation).
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New executables
amp2response
Estimates a response function for spherical deconvolution, as is also performed by sh2response; but uses data from all single-fibre voxels concurrently, and enforces non-negativity and monotonicity of the response function. All dwi2response script algorithms will now use this command. Note also that by default all response functions will now be estimated at lmax=10.
connectomestats
Provides the Network-Based Statistic (NBS) method, and the novel threshold-free Enhanced NBS (NBSE) method (publication pending).
dwigradcheck
A script that attempts to determine whether or not there are erroneous permutations or flips in the diffusion gradient table, based on this method.
fixelconvert
A command to convert between the old .msf / .msh sparse image format and the new fixel directory format. Note that if performing bulk conversion of multiple subjects to conform to a particular fixel template, the -template option should be used in order to ensure that fixel correspondence is maintained.
mrhistmatch
Performs non-linear histogram matching between two images, in the hope of being somehow useful.
mtbin
Multi-Tissue Bias field correction and Intensity Normalisation. Simultaneously estimates a B1 bias field, and modulates the amplitude of tissue response functions to converge the sum of tissue volumes toward unity in every voxel.
transformcompose
Combine multiple linear transformations and/or non-linear warps into a single transformation, such that only a single image interpolation step is needed when undergoing multiple transformations.
vectorstats
Simply performs FWE-controlled permutation testing where the input data consist of a vector of values per subject.