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Cited by 2,974Advanced Neuroimaging Techniques and ApplicationsAdvanced MRI Techniques and ApplicationsFunctional Brain Connectivity Studies

MRtrix3: A fast, flexible and open software framework for medical image processing and visualisation

Open access
Tournier, J-Donald, Smith, Robert, Raffelt, David, Tabbara, Rami, Dhollander, Thijs, Pietsch, Maximilian, Christiaens, Daan, Jeurissen, Ben +2 more·2019·NeuroImage
DOI 10.1016/j.neuroimage.2019.116137

Published version of a preprint

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Abstract

MRtrix3 is an open-source, cross-platform software package for medical image processing, analysis and visualisation, with a particular emphasis on the investigation of the brain using diffusion MRI. It is implemented using a fast, modular and flexible general-purpose code framework for image data access and manipulation, enabling efficient development of new applications, whilst retaining high computational performance and a consistent command-line interface between applications. In this article, we provide a high-level overview of the features of the MRtrix3 framework and general-purpose image processing applications provided with the software.

AI snapshot

Written from the paper’s full text.

TL;DR

MRtrix3 is an open-source, cross-platform C++11/OpenGL software framework for medical image processing, analysis and visualisation, with a particular emphasis on diffusion MRI. The paper is a high-level overview of its architecture, guiding principles, viewer (MRView), bundled command-line tools, and a benchmark of a typical multi-shell dMRI pipeline.

Key findings

  • MRtrix3 provides a modular, general-purpose image access and multi-threading framework with a consistent command-line interface; it is released under the Mozilla Public Licence 2.0, version-controlled with Git, and includes continuous integration testing.
  • The framework supports native reading/writing of DICOM (read-only), Analyze, NIfTI1, NIfTI2, MGH and its own formats, with arbitrary data strides (only its own formats support arbitrary stride ordering) and automatic history tracking in output file headers.
  • Bundled tools span basic image operations (mrinfo, mrconvert, mrcat, mrcalc, mrmath, mrstats) and dMRI analyses including MP-PCA denoising, Gibbs ringing removal, DTI, single- and multi-tissue CSD, deterministic/probabilistic/global tractography, ACT, SIFT/SIFT2, and fixel-based analysis.
  • Benchmark: a full pipeline from raw DICOM through pre-processing to 1 million probabilistic streamlines took 52 minutes total on an Intel i7-4930K (6 cores, 3.40 GHz), 32 GB RAM, NVIDIA GTX 780; the largest single step was distortion/eddy correction via FSL (32m59s), followed by tckgen (7m33s) and 5ttgen (7m29s).

Methods

  • Design/description paper: the authors present the guiding principles, software architecture (image access, strides, DICOM handling, Unix pipes, ThreadedLoop and run_queue multi-threading APIs, build system, Python scripting library) and the MRView visualisation tool.
  • Runtime benchmark used the B.A.T.M.A.N. tutorial dataset: Siemens Prisma 3T, 64-channel head coil, structural T1 (1 mm isotropic, 160 slices, 5 min) plus multi-shell dMRI (2.5 mm isotropic, b = 0/1000/2000/3000 s/mm² with 15/17/31/50 volumes, 17 min acquisition), processed on the desktop system described above.
  • No formal validation study, accuracy comparison, or user study is reported; the paper is a software overview with an illustrative timing table.

Limitations

  • The paper states no explicit limitations; it instead lists future directions (continued high-performance method implementations, broader adoption and tutorials, and encouraging C++ library use beyond diffusion MRI).
  • Evident from the text: the runtime benchmark is a single dataset on a single hardware configuration, so timings are illustrative rather than a general performance characterisation; no accuracy or correctness evaluation against alternative packages is presented; and the software's historical focus remains diffusion MRI despite the general-purpose API.

Model-written summary. Check it against the paper before relying on it.

Integrity signals

Registry

Crossref · 10.1016/j.neuroimage.2019.116137

Cites

59 of 59 references verified0 citation errors · 0 not checkable

Statistics

Nothing to recompute.

Claims the paper makes

5 of 9 cited sources checked · 4 supported · 0 flagged · accuracy not yet measured

  • Findingcitation

    MRtrix3 can import and export dMRI gradient encoding and other metadata in JSON and BIDS bvec/bval format.

    “These include importing and exporting dMRI gradient encoding and other metadata in JSON and BIDS bvec/bval format, ultimately enabling integrating MRtrix3 commands in BIDS Apps (Gorgolewski et al., 2017) .”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites Gorgolewski et al., 2017 source

      The Results table (Available BIDS Apps; page not provided) lists an MRtrix3 connectome app for diffusion-weighted imaging, supporting the point that MRtrix3 is represented among BIDS Apps. It does not describe MRtrix3 importing or exporting gradient encoding or other metadata in JSON or BIDS bvec/bval format; searches for those terms found no such passage. (LLM, conf=0.87)

      Experimental — accuracy not yet measured
  • Findingcitation

    MRtrix3 provides functionalities for handling data in the Brain Imaging Data Structure (BIDS).

    “In addition, MRtrix3 provides the requisite functionalities for handling data in the Brain Imaging Data Structure (BIDS) , a recent standard for organising and sharing neuroimaging data (Gorgolewski et 2 al., 2016) .”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites Gorgolewski et al., 2016 source
  • Findingreasoning

    When the stored data type matches the data type requested by the application, MRtrix3 commands automatically use direct IO access, where data are accessed as a native array in memory, avoiding the overhead of function calls otherwise necessary for conversion.

    “However, when the stored data type matches the data type requested by the application, MRtrix3 commands will automatically use”
    Quote in the paperSubstantial claim
  • Findingreasoning

    MRtrix3 handles coordinates consistently across file formats.

    “MRtrix3 handles coordinates consistently across file formats and in addition, the native MRtrix3 image format allows automated handling and storage of coordinate system dependent information such as the dMRI gradient table in the image header to ensure this information remains consistent throughout the analysis pipeline.”
    Quote in the paperSubstantial claim
  • Findingnone given

    MRtrix3 provides a framework for simultaneously documenting, specifying and retrieving command-line arguments and options, all centralised within a single function for each application.

    “MRtrix3 provides a framework for simultaneously documenting, specifying and retrieving command-line arguments and options, all centralised within a single function for each application.”
    Quote in the paperNot a substantial claim
  • May combine two claims. 24
  • Classified as probably not a substantial claim. 64
  • The quote only partly states this claim. 1

  • May combine two claims.

    Findingcitation

    MRtrix3 offers image analysis methods less specific to dMRI, including image filtering and calculation, statistics, image denoising, Gibbs ringing suppression, intensity normalisation, and diffeomorphic image registration.

    “MRtrix3 also offers image analysis methods less specific to dMRI such as image filtering and calculation, statistics, image denoising (Veraart et al., 2016) and Gibbs ringing suppression (Kellner et al., 2016) , intensity normalisation (Raffelt et al., 2017a) and diffeomorphic image registration (Raffelt et al., 2011) .”
    Quote in the paperNot a substantial claim2 of 3 sources checked
    • cites Veraart et al., 2016 source
    • cites Kellner et al., 2016 source
    • cites Raffelt et al., 2017a

      Couldn’t be matched to a paper in Crossref, so it can’t be checked.

  • May combine two claims.

    Findingcitation

    The MRtrix3 Python scripting library does not provide functionality to manipulate raw image data within Python itself, but provides functionality to invoke and manage external high-performance executables to perform the actual computations.

    “In contrast to projects such as DiPy (Garyfallidis et al., 2014) , this library does not provide functionality to manipulate raw image data within Python itself, but provides functionality to invoke and manage external high-performance executables to perform the actual computations.”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites Garyfallidis et al., 2014 source

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Findingnone given

    MRtrix3 allows temporary images to be created in RAM for use as scratch buffers within applications and also passed between applications via Unix pipes.

    “MRtrix3 allows temporary images to be created in RAM for use as scratch buffers within applications and also passed between applications via Unix pipes.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingnone given

    The MRtrix3 platform incorporates features tailored to the orientational nature of dMRI data within each imaging voxel, such as a representation using spherical harmonics basis functions, and a bespoke file format for 3D streamlines.

    “The platform incorporates a number of features tailored to the orientational nature of dMRI data within each imaging voxel, such as a representation using spherical harmonics basis functions, and a bespoke file format for 3D streamlines.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingnone given

    MRtrix3 includes its own fast DICOM import handling, allowing all MRtrix3 applications to seamlessly support DICOM images as input.

    “MRtrix3 includes its own fast DICOM import handling, allowing all MRtrix3 applications to seamlessly support DICOM images as input.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingreasoning

    MRtrix3 can run natively on most flavours of Unix, including GNU/Linux and macOS, as well as a range of high-performance computing (HPC) environments, and Microsoft Windows via the MSYS2 project or Windows Subsystem for Linux (WSL).

    “All of these 12 dependencies are available across a wide range of platforms, allowing MRtrix3 to run natively on most flavours of Unix, including GNU/Linux and macOS as well as a range of high-performance computing (HPC) environments, and Microsoft Windows via the MSYS2 project or Windows 13 Subsystem for Linux ( WSL ) .14”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingnone given

    The native MRtrix3 image format allows automated handling and storage of coordinate system dependent information such as the dMRI gradient table in the image header.

    “the native MRtrix3 image format allows automated handling and storage of coordinate system dependent information such as the dMRI gradient table in the image header to ensure this information remains consistent throughout the analysis pipeline.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Findingnone given

    The MRtrix3 build script scans the code to build a full dependency tree based on simple rules about file location and naming conventions, identifies outdated targets, assembles a list of tasks required to bring the targets up to date, and then launches the relevant commands in the right order and in parallel for fast build times.

    “The build script scans the code to build a full dependency tree based on simple rules about file location and naming conventions, identifies outdated targets, assembles a list of tasks required to bring the targets up to date, and then launches the relevant commands in the right order and in parallel for fast build times.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingnone given

    The DICOM import code extracts other types of information if found, including the EPI phase-encode direction and slice timings.

    “Other types of information are also extracted if found, including the EPI phase-encode direction and slice timings.”
    Quote in the paperNot a substantial claim

  • Classified as probably not a substantial claim.

    Findingreasoning

    The MRtrix3 framework enables efficient development of new applications.

    “It is implemented using a fast, modular and flexible general-purpose code framework for image data access and manipulation, enabling efficient development of new applications, whilst retaining high computational performance and a consistent command-line interface between applications.”
    Quote in the paperSubstantial claim

  • Classified as probably not a substantial claim.

    Findingreasoning

    MRtrix3 provides a consistent command-line interface between applications.

    “It is implemented using a fast, modular and flexible general-purpose code framework for image data access and manipulation, enabling efficient development of new applications, whilst retaining high computational performance and a consistent command-line interface between applications.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingnone given

    The run_queue() construct enables multi-threaded processing through use of data queue structures for tasks not native to an image grid.

    “General processing : For tasks not native to an image grid, the more general run_queue() construct enables multi-threaded processing through use of data queue structures;”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S4 (based). May combine two claims.

    Findingnone given

    All MRtrix3 applications consistently use the same coordinate system, which is identical to the scanner reference frame in the NIfTI standard.

    “All MRtrix3 applications consistently use the same coordinate system, which is identical to the scanner reference frame in the NIfTI standard.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing), S4 (based). The quote only partly states this claim.

    Findingnone given

    MRtrix3's multi-threaded processing is principally achieved through the use of one of two Application Programming Interfaces (APIs): ThreadedLoop and run_queue().

    “In MRtrix3 , multi-threaded processing is principally achieved through the use of one of two Application Programming Interfaces (APIs):”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingnone given

    If present, the DICOM import code extracts diffusion MRI encoding information for 3 major vendors (Siemens, GE, Philips) and makes it available to the application as part of the image header.

    “If present, it will also extract the diffusion MRI encoding information for 3 major vendors (Siemens, GE, Philips), and make it available to the application as part of the image header.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingown data

    The MRtrix3 software includes a bespoke system to manage configuring and building the software, comprised of two Python scripts: configure and build.

    “The software includes a bespoke system to manage configuring and building the software.It is comprised of two Python scripts: configure and build .”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingcitation

    MRtrix3 was historically developed with a particular emphasis on investigating brain white matter using diffusion-weighted MRI (dMRI).

    “MRtrix3 was historically developed with a particular emphasis on investigating brain white matter using diffusion-weighted MRI (dMRI), a medical imaging modality that can act as an indirect probe of neural microstructure, by measuring local hindrance of water diffusion”
    Quote in the paperNot a substantial claim

  • Classified as probably not a substantial claim. May combine two claims.

    Findingnone given

    MRtrix3 is an open-source, cross-platform software package for medical image processing, analysis and visualization, with a particular emphasis on the investigation of the brain using diffusion MRI.

    “MRtrix3 is an open-source, cross-platform software package for medical image processing, analysis and visualization, with a particular emphasis on the investigation of the brain using diffusion MRI.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingcitation

    MRtrix3 derives from the now deprecated MRtrix 0.2.x software package.

    “It derives from the now deprecated MRtrix 0.2.x software package (Tournier et al., 2012) , which was itself started circa 2003, when few packages existed for the analysis of diffusion MRI data.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Tournier et al., 2012 source

  • Classified as probably not a substantial claim.

    Findingnone given

    MRtrix3 is implemented using a fast, modular and flexible general-purpose code framework for image data access and manipulation.

    “It is implemented using a fast, modular and flexible general-purpose code framework for image data access and manipulation, enabling efficient development of new applications, whilst retaining high computational performance and a consistent command-line interface between applications.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingnone given

    MRtrix3 provides convenient multi-threading primitives.

    “This includes a lightweight framework for application development that facilitates efficient image access and manipulation, convenient multi-threading primitives, and support for a broad range of image file formats.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingreasoning

    MRtrix3 applications can explicitly request direct IO access to image data.

    “When desired, applications can also explicitly request”
    Quote in the paperNot a substantial claim

  • Classified as probably not a substantial claim.

    Findingnone given

    MRtrix3 is published under the terms of the open source Mozilla Public Licence 2.0.

    “The software is published under the terms of the open source Mozilla Public Licence 2.0 , which permits 1 third-party modification, distribution and commercial use as long as the source code is disclosed”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S4 (based). May combine two claims.

    Findingnone given

    In MRtrix3, almost all commands have been multi-threaded, by default running with the maximum utilization of CPU processors to achieve high computing performance.

    “In MRtrix3 , almost all commands have been multi-threaded, by default running with the maximum utilization of CPU processors to achieve high computing performance.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingnone given

    MRtrix3 supports a broad range of image file formats.

    “This includes a lightweight framework for application development that facilitates efficient image access and manipulation, convenient multi-threading primitives, and support for a broad range of image file formats.”
    Quote in the paperNot a substantial claim

  • Classified as probably not a substantial claim.

    Findingnone given

    MRtrix3 has been designed as an open-source, modular software platform for medical image analysis and visualization.

    “MRtrix3 has been designed as an open-source, modular software platform for medical image analysis and visualization.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingnone given

    MRtrix3 focuses primarily on command-line applications to provide a wide range of functionalities that can be combined and scripted to form complex automated workflows.

    “It focuses primarily on command-line applications to provide a wide range of functionalities that can be combined and scripted to form complex automated workflows.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingnone given

    MRtrix3 offers automatic history tracking in the output file header, archiving the pipeline of operations used to generate each output image, as well as the exact version tag of each invoked command.

    “Finally, MRtrix3 also offers automatic history tracking in the output file header, archiving the pipeline of operations used to generate each output image, as well as the exact version tag of each invoked command.”
    Quote in the paperSubstantial claim

  • Classified as probably not a substantial claim.

    Findingreasoning

    All MRtrix3 components are designed with a strong focus on performance and memory efficiency.

    “All components are designed with a strong focus on performance and memory efficiency, which are essential features for dealing with these often very large datasets.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingreasoning

    MRtrix3's build system provides a convenient primitive for external modules that enables developers to build their own applications, linked to the core MRtrix3 library and leveraging its image access and multi-threading primitives.

    “Therefore, the MRtrix3 build system provides a convenient primitive for external modules that enables developers to build their own applications, linked to the core MRtrix3 library and leveraging its image access and multi-threading primitives.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingnone given

    MRtrix3 offers support for external modules that can be built and distributed independently.

    “In addition, MRtrix3 offers support for external modules that can be built and distributed independently.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S4 (based). May combine two claims.

    Findingnone given

    MRtrix3 has been designed from the outset to facilitate the development of high-performance applications concerned with the processing and analysis of medical image datasets, and to offer a consistent and simple command-line interface.

    “MRtrix3 has been designed from the outset to facilitate the development of high-performance applications concerned with the processing and analysis of medical image datasets, and to offer a consistent and simple command-line interface.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingnone given

    The ThreadedLoop construct performs a multi-threaded traversal of images when subsets of an image can be processed independently.

    “Image processing : When subsets (e.g.voxels, slices, volumes) of an image (or set of images) can be processed independently, the ThreadedLoop construct performs a multi-threaded traversal of the image(s), with the only requisite that the programmer define the function to be executed for each image location;”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Findingnone given

    The DICOM import code handles data stored using the recent DICOM multi-frame standard, as well as the standard multi-file storage, including Siemens mosaics.

    “The DICOM import code handles data stored using the recent DICOM multi-frame standard, as well as the standard multi-file storage, including Siemens mosaics.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Findingnone given

    End-user applications provided with MRtrix3 include general-purpose image conversion and manipulation tools and the visualisation tool MRView tailored to multi-dimensional (3D+) medical image data.

    “End-user applications provided with MRtrix3 include general-purpose image conversion and manipulation tools and the visualisation tool MRView tailored to multi-dimensional (3D+) medical image data.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S4 (based).

    Findingreasoning

    MRtrix3 retains high computational performance.

    “It is implemented using a fast, modular and flexible general-purpose code framework for image data access and manipulation, enabling efficient development of new applications, whilst retaining high computational performance and a consistent command-line interface between applications.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingnone given

    By default, MRtrix3 image access is achieved via memory-mapping with on-the-fly data type conversion.

    “By default, image access is achieved via memory-mapping with on-the-fly data type conversion.”
    Quote in the paperNot a substantial claim

  • Classified as probably not a substantial claim. May combine two claims.

    Findingnone given

    Functionality for image input/output is provided by the core MRtrix3 library, so that all MRtrix3 applications can read and write all supported image formats directly, with no requirement to convert the data to and from specific image formats.

    “Functionality for image input/output is provided by the core MRtrix3 library, so that all MRtrix3 applications can read and write all supported image formats directly: there is no requirement to convert the data to and from specific image formats.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingreasoning

    Most of MRtrix3's functionality is written using C++ templates, providing high runtime performance by allowing the compiler to optimise away any redundant overhead.

    “Most of the functionality is written using C++ templates, providing high runtime performance by allowing the compiler to optimise away any redundant overhead.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingnone given

    MRtrix3 includes a lightweight framework for application development that facilitates efficient image access and manipulation.

    “This includes a lightweight framework for application development that facilitates efficient image access and manipulation, convenient multi-threading primitives, and support for a broad range of image file formats.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingnone given

    The stand-alone example commands compile and execute with MRtrix3 without modification.

    “The relatively simple examples below demonstrate stand-alone commands that compile / execute with MRtrix3 without modification.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Findingreasoning

    MRView uses the high-performance industry-standard OpenGL 3.3 API and the widely supported and open-source Qt toolkit to manage interface elements.

    “To meet these aims, MRView uses the high-performance industry-standard OpenGL 3.3 API to leverage the graphics capabilities of modern systems, and the widely supported 29 and open-source Qt toolkit to manage the interface elements (widgets).”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingnone given

    MRtrix3 command names follow a convention to reflect the purpose of the command and aid discoverability.

    “MRtrix3 command names follow a convention to reflect the purpose of the command and aid discoverability.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingnone given

    The ThreadedLoop construct automatically duplicates instances of the Functor class as required, one for each executing thread.

    “The loop construct automatically duplicates instances of the Functor class as required, one for each executing thread (two in this case).”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingnone given

    MRtrix3 provides a consistent command-line interface, including checking the validity of input parameters at the parsing stage.

    “Consistent command-line interface, including checking validity of input parameters at the parsing stage”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing), S4 (based).

    Findingnone given

    MRtrix3 is compatible with any image file format supported by the library.

    “Compatibility with any image file format supported by the library”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingnone given

    MRView can display slice-wise information at arbitrary oblique cuts through the data.

    “MRView is also capable of displaying slice-wise information at arbitrary oblique cuts through the data.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingnone given

    Symbolic strides allow the voxel ordering of an image to be specified in a manner independent of the image dimensions.

    “Symbolic strides provide a simply means to specify the voxel ordering in a manner that is independent of the dimensions of the image.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingnone given

    MRtrix3 provides a suite of commands for performing various common manipulations of image data.

    “MRtrix3 provides a suite of commands for performing various common manipulations of image data.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingnone given

    MRtrix3 contains a dedicated Python scripting library to aid the development of more complex applications and processing pipelines involving multiple MRtrix3 (or other) commands.

    “MRtrix3 also contains a dedicated Python scripting library to aid the development of more complex applications and processing pipelines involving multiple MRtrix3 (or other) commands.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingnone given

    The help page of the demo_script is formatted identically to the demo_binary command help page.

    “The help page of the demo_script listed in 9.2.1 is formatted identically to the demo_binary command help page listed in 9.1.3.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing), S4 (based).

    Findingnone given

    Multi-threaded processing can be terminated by any class at any time via the return value of the corresponding functor.

    “Multi-threaded processing can be terminated by any class at any time via the return value of the corresponding functor.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingnone given

    MRView accepts input from Unix pipes.

    “first, MRView accepts input from Unix pipes (as illustrated in the example in section 3.2.1);”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingnone given

    MRView can handle higher-dimensional images, currently up to 5D.

    “MRView can also handle higher-dimensional images, currently up to 5D.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingown data

    The documentation produced by a compiled command matches the information provided by the developer in the usage() function.

    “Note that the documentation matches the information provided by the developer in the 'usage()' function (see code listing in 9.1.1).”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingnone given

    MRView provides a number of different viewing modes, including single-slice; orthoview; lightbox; and volume render.

    “MRView provides a number of different viewing modes , including single-slice; orthoview (a montage of 3 orthogonal slices), lightbox (a grid montage of adjacent slices or volumes); and volume render (3D rendering using ray-tracing).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingnone given

    MRtrix3 includes tools to undertake different types of diffusion analyses from start to finish, including state-of-the-art tools for pre-processing, voxel-level modelling, fibre tracking and connectomics, and groupwise analysis.

    “MRtrix3 includes tools to undertake different types of diffusion analyses from start to finish.In particular, it includes state-of-the-art tools for pre-processing, voxel-level modelling, fibre tracking and connectomics, and groupwise analysis.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingreasoning

    MRtrix3 supports arbitrary data strides for all supported image formats and for data held in RAM.

    “To allow for all these different storage conventions and to enhance performance of the various analyses to be performed, MRtrix3 supports arbitrary data strides for all supported formats, and for data held in RAM.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing), S4 (based).

    Findingnone given

    MRtrix3 provides automated self-documentation that is consistent with all MRtrix3 commands.

    “Automated self-documentation that is consistent with all MRtrix3 commands.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Findingnone given

    MRtrix3 is designed to be compatible with the broadest range of applications possible, although its historical focus has been diffusion MRI analysis.

    “While the focus of MRtrix3 has historically been on diffusion MRI analysis, the software itself is designed to be compatible with the broadest range of applications possible.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingnone given

    MRView is designed from the outset for interactive use from the command-line.

    “It is also designed from the 30 outset for interactive use from the command-line.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingreasoning

    MRView is quick to launch and display.

    “and second, it is quick to launch and display (through a number of design decisions, including the use of memory-mapping for”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingreasoning

    Queues are used extensively in MRtrix3 to process non-image data such as streamlines.

    “Such queues are used extensively in MRtrix3 to process non-image data, such as streamlines”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingnone given

    MRView can load multiple images concurrently, allowing fast switching between them via the menu or the PageUp / PageDown keys.

    “An important aspect of MRView is its ability to load multiple images concurrently, allowing fast switching between them via the menu or the PageUp / PageDown keys.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S4 (based).

    Findingnone given

    MRtrix3 was designed from the outset as a framework for the development and dissemination of high-performance imaging research applications, guided by the principles of open and reproducible science.

    “MRtrix3 was designed from the outset as a framework for the development and dissemination of high-performance imaging research applications, guided by the principles of open and reproducible science.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Findingnone given

    MRtrix3 comes bundled with a range of end-user applications for performing general-purpose image manipulations as well as complex analyses, with a strong (although not exclusive) focus on diffusion MRI.

    “MRtrix3 comes bundled with a range of end-user applications for performing general-purpose image manipulations as well as complex analyses, with a strong (although not exclusive) focus on diffusion MRI.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Findingnone given

    MRView was written to be cross-platform, high performance, convenient to use, and extensible.

    “The MRtrix3 viewer, MRView , was written to be cross-platform, high performance, convenient to use, and extensible.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingnone given

    In MRView, content is always displayed at the correct location in scanner coordinates, not relative to the image voxel coordinates.

    “A core principle in MRView is that content is always displayed at the correct location in scanner coordinates, not relative to the image voxel coordinates.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Study design and conductnone given

    Continuous integration testing for MRtrix3 is managed by TravisCI (for Linux and macOS) and AppVeyor (for Microsoft Windows).

    “Continuous integration testing is managed by TravisCI (for Linux and macOS) and AppVeyor (for Microsoft Windows).”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductnone given

    Most MRtrix3 commands have tests to ensure the output remains consistent with expectation throughout the development cycle.

    “Most MRtrix3 commands have tests to ensure the output remains consistent with 22 expectation throughout the development cycle.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductnone given

    MRtrix3 incorporates continuous integration testing to detect and avoid adverse effects of code changes between versions.

    “Furthermore, MRtrix3 also incorporates continuous integration testing to detect and avoid adverse effects of code changes between versions.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Diffusion-weighted MRI can act as an indirect probe of neural microstructure by measuring local hindrance of water diffusion.

    “diffusion-weighted MRI (dMRI), a medical imaging modality that can act as an indirect probe of neural microstructure, by measuring local hindrance of water diffusion (Johansen-Berg and Behrens, 2013;Jones, 2010)”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites Johansen-Berg and Behrens, 2013

      Couldn’t be matched to a paper in Crossref, so it can’t be checked.

    • cites Jones, 2010

      Couldn’t be matched to a paper in Crossref, so it can’t be checked.

  • May combine two claims.

    Interpretationreasoning

    Volume-contiguous storage allows for efficient access and maximises CPU cache reuse, in some cases improving performance considerably.

    “This allows for efficient access and maximises CPU cache reuse, in some cases improving performance considerably.”
    Quote in the paperNot a substantial claim

  • Classified as probably not a substantial claim.

    Premisereasoning

    Computer hardware generally performs best when data are processed in the order they appear on file or in memory.

    “Computer hardware generally performs best when data are processed in the order they appear on file (or in memory): this avoids seek latency when reading from disk, allows burst transfers to and from the main system memory, leverages the CPU's cache prefetching engine, and maximises usage of each line of the on-board CPU cache.”
    Quote in the paperSubstantial claim
74 of 74

  • The authors state this as an assumption.

    Reproducible neuroscience relies first and foremost on open source software.

    “The MRtrix3 collective believes that reproducible neuroscience relies first and foremost on open source software.”

  • The paper relies on this without support.

    The multi-shell diffusion MRI dataset used for the runtime breakdown is typical of routine clinical practice.

    “The following provides a breakdown of the time required to process a typical multi-shell diffusion MRI dataset as might be acquired in routine clinical practice.”
2 of 2

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

Each contradiction between two passages listed here was confirmed by an independent check.

  • Claim of arbitrary strides across all formats conflicts with format limitation

    Minor

    The appendix says arbitrary data strides are supported for all formats, but the image-access section says only MRtrix3's own formats support arbitrary stride ordering.

  • Claim that every supported format can be written conflicts with read-only DICOM support

    Minor

    The paper says all applications can write every supported image format directly, but identifies DICOM as read-only.

2 of 2

Cites

Flagged first, then by citations

Research works printed but not linked: 1

  1. Raffelt, 2017, Bias field correction and intensity normalisation for quantitative analysis of apparent fibre density, Proc. Intl. Soc. Mag. Reson. Med., 3541

Cited by

Sorted by citations

Related

Authors
Tournier, J.-D., Smith, R., Raffelt, D., Tabbara, R., Dhollander, T., Pietsch, M., Christiaens, D., Jeurissen, B., Yeh, C.-H., & Connelly, A.
Affiliations
  • King's College London (GB)
  • The University of Melbourne (AU)
  • Florey Institute of Neuroscience and Mental Health (AU)
  • University of Antwerp (BE)
Corresponding author
Tournier, J-Donald
ORCID
Venue
NeuroImage
Publisher
Elsevier BV
Published
2019-11
Volume
202
Pages
116137
ISSN
1053-8119 (ISSN-L)
DOI
10.1016/j.neuroimage.2019.116137
OpenAlex
W2970898057
Cited by
2,974
References
57
Citations by year
2026: 495 · 2025: 627 · 2024: 491 · 2023: 432 · 2022: 408 · 2021: 331 · 2020: 171 · 2019: 18
FWCI
139.11
Type
journal article
Language
en
Open access
Licence
Locations
  • NeuroImage (publishedVersion)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • PubMed (publishedVersion)
  • Lirias (submittedVersion, other-oa)
Funders
  • King's College London
  • Seventh Framework Programme (319456)
  • European Research Council
  • National Imaging Facility
  • National Health and Medical Research Council (1026077, 1091593, 400121, 628952)
  • Medical Research Council (MR/K006355/1)
  • Fonds Wetenschappelijk Onderzoek (12M3116N, 12M3119N)
  • Engineering and Physical Sciences Research Council
  • State Government of Victoria
  • National Institute for Health and Care Research
  • Wellcome Trust
  • Guy's and St Thomas' NHS Foundation Trust
  • King’s College London (WT 203148/Z/16/Z)
Topics
  • Health Sciences › Medicine › Radiology, Nuclear Medicine and Imaging › Advanced Neuroimaging Techniques and Applications
  • Health Sciences › Medicine › Radiology, Nuclear Medicine and Imaging › Advanced MRI Techniques and Applications
  • Life Sciences › Neuroscience › Cognitive Neuroscience › Functional Brain Connectivity Studies
Keywords
MRtrix3, diffusion MRI, neuroimaging, medical image processing, image visualization, open source software, command-line interface, software framework
MeSH terms
Humans, Image Processing, Computer-Assisted, Magnetic Resonance Imaging, Software Design, Diffusion Magnetic Resonance Imaging, Neuroimaging

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Claims read by deepseek-v4.1-flash under definition version 3 (extract-v3) on 2026-10-24.

Classified by jev-1.13-20260917 (gold-guideline-v0.2) on 2026-10-24.

Cited sources are checked by gpt-6-sol.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

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