The DOI matches its Crossref record; 59 of the 59 references it cites were found in a registry or an index; 5 of the 9 sources its claims cite were checked for support.
MRtrix3: A fast, flexible and open software framework for medical image processing and visualisation
Open accessPublished version of a preprint
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.
Overview
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
Cites
Statistics
Verification
Claims the paper makes
74 No basis given · 3 Own method · 3 Own interpretation · 3 Own result · 2 Supported · 2 Partly supported · 1 Sources not found · 1 No full text of the sources · 1 Not checked yet · accuracy not yet measured
The cited sources support only part of this claim — read each source’s verdict below.
In the paper
“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) .”
§ MRtrix3 : A fast, flexible and open software framework for medical image processing and visualisation > 2.1 Reproducible neuroscience
What the sources say
- Partly supportedcites Gorgolewski et al., 2017 sourceExperimental — accuracy not yet measured
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)
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
- Partly supported
Every source the paper cites for this claim was checked and supports it.
In the paper
“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) .”
§ MRtrix3 : A fast, flexible and open software framework for medical image processing and visualisation > 2.1 Reproducible neuroscience
What the sources say
- Supportedcites Gorgolewski et al., 2016 source
The citation is attached to the description of BIDS as a standard for organizing and sharing neuroimaging data, not to the statement about MRtrix3’s functionality. The Abstract identifies BIDS as a standard for organizing MRI datasets, and Results > File formats says it is aimed at facilitating data sharing. (LLM, conf=0.94)
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
- Supported
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“However, when the stored data type matches the data type requested by the application, MRtrix3 commands will automatically use”
§ MRtrix3 : A fast, flexible and open software framework for medical image processing and visualisation > 3.1.1 Optimised data access
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“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.”
§ MRtrix3 : A fast, flexible and open software framework for medical image processing and visualisation > 3.1 Image access
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“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 : A fast, flexible and open software framework for medical image processing and visualisation > 3.3.1 Integrated command-line interface and documentation
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“In this case, MRtrix3 uses an alternative delayed write-back strategy, with the backend holding the data in RAM and automatically committing the data to storage when the image is closed.”
§ MRtrix3 : A fast, flexible and open software framework for medical image processing and visualisation > 3.1.1 Optimised data access
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“The framework provides native access to and seamless interaction between a range of image file formats commonly used in the medical imaging community, including native support for DICOM (read-only), Analyze , NIfTI1 , NIfTI2 , MGH , and MRtrix3 's own dedicated image 15 16 17 18 19 formats , as well as compressed versions thereof.20”
§ MRtrix3 : A fast, flexible and open software framework for medical image processing and visualisation > 3 Design aspects
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“MRtrix3 also has a flexible concept of strides , allowing the multi-dimensional image data to be stored in RAM (or file when the image format supports it) in any reasonable order (see Appendix A for details).”
§ MRtrix3 : A fast, flexible and open software framework for medical image processing and visualisation > MRtrix3
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“MRtrix3 also provides a wide range of dMRI analysis methods, outlined in the Diffusion analyses section below.”
§ MRtrix3 : A fast, flexible and open software framework for medical image processing and visualisation > MRtrix3
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“Of the supported formats, only MRtrix3 's own formats support arbitrary stride ordering, a feature that offers distinct performance advantages when processing different types of data, particularly by allowing volume-contiguous storage.”
§ MRtrix3 : A fast, flexible and open software framework for medical image processing and visualisation > MRtrix3
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
- It may state two separate claims as one. 24
- Probably not a substantial claim. 64
- The quote only partly states this claim. 1
The cited sources support only part of this claim — read each source’s verdict below.
In the paper
“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) .”
§ MRtrix3 : A fast, flexible and open software framework for medical image processing and visualisation > MRtrix3
What the sources say
- Supportedcites Veraart et al., 2016 source
The citation is attached to “image denoising,” not to the other listed methods. The Results (section 3) describe applying the paper’s proposed denoising method to dMRI images, so the source identifies the denoising method cited in the MRtrix3 list. (LLM, conf=0.91)
- Supportedcites Kellner et al., 2016 source
The Kellner et al. citation is attached specifically to “Gibbs ringing suppression,” not to the other MRtrix3 capabilities in the sentence. The Conclusions describe a method that effectively removes ringing artifacts, supporting that identification; the source need not document MRtrix3’s implementation to support the method citation. (LLM, conf=0.94)
- Not matchedcites Raffelt et al., 2017a
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
- Supported
Every source the paper cites for this claim was checked and supports it.
In the paper
“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.”
§ MRtrix3 : A fast, flexible and open software framework for medical image processing and visualisation > 3.3.4 Python scripts
What the sources say
- Supportedcites Garyfallidis et al., 2014 source
The citation identifies DiPy as a contrasting project that can manipulate image data within Python; it does not attribute the description of the MRtrix3 scripting library to DiPy. Section 5.1 (Load/save data) describes a raw 4D diffusion image held as a NumPy array and shows how to extract a sub-array in Python. (LLM, conf=0.92)
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
- Supported
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“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 : A fast, flexible and open software framework for medical image processing and visualisation > 3.2.1
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“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.”
§ MRtrix3 : A fast, flexible and open software framework for medical image processing and visualisation > MRtrix3
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“MRtrix3 includes its own fast DICOM import handling, allowing all MRtrix3 applications to seamlessly support DICOM images as input.”
§ MRtrix3 : A fast, flexible and open software framework for medical image processing and visualisation > 3.1.2 DICOM handling
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“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”
§ MRtrix3 : A fast, flexible and open software framework for medical image processing and visualisation > 3 Design aspects
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“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.”
§ MRtrix3 : A fast, flexible and open software framework for medical image processing and visualisation > 3.1 Image access
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“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.”
§ MRtrix3 : A fast, flexible and open software framework for medical image processing and visualisation > 3.3.2 Build system
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“Other types of information are also extracted if found, including the EPI phase-encode direction and slice timings.”
§ MRtrix3 : A fast, flexible and open software framework for medical image processing and visualisation > 3.1.2 DICOM handling
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“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.”
§ MRtrix3 : A fast, flexible and open software framework for medical image processing and visualisation > Abstract
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“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.”
§ MRtrix3 : A fast, flexible and open software framework for medical image processing and visualisation > Abstract
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“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;”
§ MRtrix3 : A fast, flexible and open software framework for medical image processing and visualisation > 3.2.2 Multi-threading
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“All MRtrix3 applications consistently use the same coordinate system, which is identical to the scanner reference frame in the NIfTI standard.”
§ MRtrix3 : A fast, flexible and open software framework for medical image processing and visualisation > 3.1 Image access
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: fails — The paper may give no reason why it holds.
Probably not a substantial claim. The paper may give no reason why it holds. It may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“In MRtrix3 , multi-threaded processing is principally achieved through the use of one of two Application Programming Interfaces (APIs):”
§ MRtrix3 : A fast, flexible and open software framework for medical image processing and visualisation > 3.2.2 Multi-threading
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: fails — The paper may give no reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. The paper may give no reason why it holds. The quote only partly states this claim.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“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.”
§ MRtrix3 : A fast, flexible and open software framework for medical image processing and visualisation > 3.1.2 DICOM handling
hedgeddirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The software includes a bespoke system to manage configuring and building the software.It is comprised of two Python scripts: configure and build .”
§ MRtrix3 : A fast, flexible and open software framework for medical image processing and visualisation > 3.3.2 Build system
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
None of the sources cited for this claim have been checked yet.
In the paper
“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”
§ MRtrix3 : A fast, flexible and open software framework for medical image processing and visualisation > MRtrix3
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“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 : A fast, flexible and open software framework for medical image processing and visualisation > Abstract
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. It may state two separate claims as one.
In the paper
“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.”
§ MRtrix3 : A fast, flexible and open software framework for medical image processing and visualisation > MRtrix3
What the sources say
- Not checked — no full text of the sourcecites Tournier et al., 2012 source
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“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.”
§ MRtrix3 : A fast, flexible and open software framework for medical image processing and visualisation > Abstract
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“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.”
§ MRtrix3 : A fast, flexible and open software framework for medical image processing and visualisation > 1 Introduction
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“When desired, applications can also explicitly request”
§ MRtrix3 : A fast, flexible and open software framework for medical image processing and visualisation > 3.1.1 Optimised data access
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“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”
§ MRtrix3 : A fast, flexible and open software framework for medical image processing and visualisation > 2.1 Reproducible neuroscience
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“In MRtrix3 , almost all commands have been multi-threaded, by default running with the maximum utilization of CPU processors to achieve high computing performance.”
§ MRtrix3 : A fast, flexible and open software framework for medical image processing and visualisation > 3.2.2 Multi-threading
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: fails — The paper may give no reason why it holds.
Probably not a substantial claim. The paper may give no reason why it holds. It may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“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.”
§ MRtrix3 : A fast, flexible and open software framework for medical image processing and visualisation > 1 Introduction
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“MRtrix3 has been designed as an open-source, modular software platform for medical image analysis and visualization.”
§ MRtrix3 : A fast, flexible and open software framework for medical image processing and visualisation > 1 Introduction
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“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.”
§ MRtrix3 : A fast, flexible and open software framework for medical image processing and visualisation > 3 Design aspects
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“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.”
§ MRtrix3 : A fast, flexible and open software framework for medical image processing and visualisation > 2.1 Reproducible neuroscience
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“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.”
§ MRtrix3 : A fast, flexible and open software framework for medical image processing and visualisation > 1 Introduction
boosted- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“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.”
§ MRtrix3 : A fast, flexible and open software framework for medical image processing and visualisation > 3.3.3 External contributions MRtrix3
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“In addition, MRtrix3 offers support for external modules that can be built and distributed independently.”
§ MRtrix3 : A fast, flexible and open software framework for medical image processing and visualisation > 1 Introduction
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“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 : A fast, flexible and open software framework for medical image processing and visualisation > 3 Design aspects
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: fails — The paper may give no reason why it holds.
Probably not a substantial claim. The paper may give no reason why it holds. It may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“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;”
§ MRtrix3 : A fast, flexible and open software framework for medical image processing and visualisation > 3.2.2 Multi-threading
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“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.”
§ MRtrix3 : A fast, flexible and open software framework for medical image processing and visualisation > 3.1.2 DICOM handling
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“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.”
§ MRtrix3 : A fast, flexible and open software framework for medical image processing and visualisation > 1 Introduction
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“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.”
§ MRtrix3 : A fast, flexible and open software framework for medical image processing and visualisation > Abstract
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: fails — The paper may give no reason why it holds.
Probably not a substantial claim. The paper may give no reason why it holds.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“By default, image access is achieved via memory-mapping with on-the-fly data type conversion.”
§ MRtrix3 : A fast, flexible and open software framework for medical image processing and visualisation > 3.1.1 Optimised data access
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“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.”
§ MRtrix3 : A fast, flexible and open software framework for medical image processing and visualisation > 3.1 Image access
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. It may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“Most of the functionality is written using C++ templates, providing high runtime performance by allowing the compiler to optimise away any redundant overhead.”
§ MRtrix3 : A fast, flexible and open software framework for medical image processing and visualisation > 3 Design aspects
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“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.”
§ MRtrix3 : A fast, flexible and open software framework for medical image processing and visualisation > 1 Introduction
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“The relatively simple examples below demonstrate stand-alone commands that compile / execute with MRtrix3 without modification.”
§ MRtrix3 : A fast, flexible and open software framework for medical image processing and visualisation > Additional information
boosted- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“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).”
§ MRtrix3 : A fast, flexible and open software framework for medical image processing and visualisation > 4 MRView
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“MRtrix3 command names follow a convention to reflect the purpose of the command and aid discoverability.”
§ MRtrix3 : A fast, flexible and open software framework for medical image processing and visualisation > 5 Image processing tools and analyses
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“The loop construct automatically duplicates instances of the Functor class as required, one for each executing thread (two in this case).”
§ MRtrix3 : A fast, flexible and open software framework for medical image processing and visualisation > 9.2.2 Terminal usage:
plaindirectn = 2- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“Consistent command-line interface, including checking validity of input parameters at the parsing stage”
§ MRtrix3 : A fast, flexible and open software framework for medical image processing and visualisation > Additional information
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“Compatibility with any image file format supported by the library”
§ MRtrix3 : A fast, flexible and open software framework for medical image processing and visualisation > Additional information
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: fails — The paper may give no reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. The paper may give no reason why it holds.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“MRView is also capable of displaying slice-wise information at arbitrary oblique cuts through the data.”
§ MRtrix3 : A fast, flexible and open software framework for medical image processing and visualisation > MRView
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“Symbolic strides provide a simply means to specify the voxel ordering in a manner that is independent of the dimensions of the image.”
§ MRtrix3 : A fast, flexible and open software framework for medical image processing and visualisation > 8.1 Symbolic strides
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“MRtrix3 provides a suite of commands for performing various common manipulations of image data.”
§ MRtrix3 : A fast, flexible and open software framework for medical image processing and visualisation > 5.1 Basic image operations
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“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.”
§ MRtrix3 : A fast, flexible and open software framework for medical image processing and visualisation > 3.3.4 Python scripts
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“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.”
§ MRtrix3 : A fast, flexible and open software framework for medical image processing and visualisation > Additional information
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“Multi-threaded processing can be terminated by any class at any time via the return value of the corresponding functor.”
§ MRtrix3 : A fast, flexible and open software framework for medical image processing and visualisation > 9.2.2 Terminal usage:
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: fails — The paper may give no reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. The paper may give no reason why it holds.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“first, MRView accepts input from Unix pipes (as illustrated in the example in section 3.2.1);”
§ MRtrix3 : A fast, flexible and open software framework for medical image processing and visualisation > 4 MRView
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“MRView can also handle higher-dimensional images, currently up to 5D.”
§ MRtrix3 : A fast, flexible and open software framework for medical image processing and visualisation > MRView
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Note that the documentation matches the information provided by the developer in the 'usage()' function (see code listing in 9.1.1).”
§ MRtrix3 : A fast, flexible and open software framework for medical image processing and visualisation > Additional information
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“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).”
§ MRtrix3 : A fast, flexible and open software framework for medical image processing and visualisation > MRView
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“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.”
§ MRtrix3 : A fast, flexible and open software framework for medical image processing and visualisation > 5.2 Diffusion analyses
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“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.”
§ MRtrix3 : A fast, flexible and open software framework for medical image processing and visualisation > 6 Conclusion and future directions
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“Automated self-documentation that is consistent with all MRtrix3 commands.”
§ MRtrix3 : A fast, flexible and open software framework for medical image processing and visualisation > Additional information
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: fails — The paper may give no reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. The paper may give no reason why it holds.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“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.”
§ MRtrix3 : A fast, flexible and open software framework for medical image processing and visualisation > 6 Conclusion and future directions
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“It is also designed from the 30 outset for interactive use from the command-line.”
§ MRtrix3 : A fast, flexible and open software framework for medical image processing and visualisation > 4 MRView
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“and second, it is quick to launch and display (through a number of design decisions, including the use of memory-mapping for”
§ MRtrix3 : A fast, flexible and open software framework for medical image processing and visualisation > 4 MRView
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“Such queues are used extensively in MRtrix3 to process non-image data, such as streamlines”
§ MRtrix3 : A fast, flexible and open software framework for medical image processing and visualisation > 9.2.2 Terminal usage:
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“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.”
§ MRtrix3 : A fast, flexible and open software framework for medical image processing and visualisation > 4 MRView
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“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 : A fast, flexible and open software framework for medical image processing and visualisation > 6 Conclusion and future directions
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: fails — The paper may give no reason why it holds.
Probably not a substantial claim. The paper may give no reason why it holds.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“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 : A fast, flexible and open software framework for medical image processing and visualisation > 5 Image processing tools and analyses
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“The MRtrix3 viewer, MRView , was written to be cross-platform, high performance, convenient to use, and extensible.”
§ MRtrix3 : A fast, flexible and open software framework for medical image processing and visualisation > 4 MRView
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“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.”
§ MRtrix3 : A fast, flexible and open software framework for medical image processing and visualisation > MRView
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“Continuous integration testing is managed by TravisCI (for Linux and macOS) and AppVeyor (for Microsoft Windows).”
§ MRtrix3 : A fast, flexible and open software framework for medical image processing and visualisation > 3.3 Developer tools
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“Most MRtrix3 commands have tests to ensure the output remains consistent with 22 expectation throughout the development cycle.”
§ MRtrix3 : A fast, flexible and open software framework for medical image processing and visualisation > 3.3 Developer tools
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“Furthermore, MRtrix3 also incorporates continuous integration testing to detect and avoid adverse effects of code changes between versions.”
§ MRtrix3 : A fast, flexible and open software framework for medical image processing and visualisation > 2.1 Reproducible neuroscience
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
None of the sources cited for this claim could be matched to a paper in Crossref, so there is nothing to check it against.
In the paper
“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)”
§ MRtrix3 : A fast, flexible and open software framework for medical image processing and visualisation > MRtrix3
What the sources say
- Not matchedcites Johansen-Berg and Behrens, 2013
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
- Not matchedcites Jones, 2010
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
- Not matched
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“This allows for efficient access and maximises CPU cache reuse, in some cases improving performance considerably.”
§ MRtrix3 : A fast, flexible and open software framework for medical image processing and visualisation > MRtrix3
plainconditional- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“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.”
§ MRtrix3 : A fast, flexible and open software framework for medical image processing and visualisation > 6 Conclusion and future directions
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim.
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.”
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.
Rated minor: it would not touch a result — a value no result rests on, a p-value that stays on the same side of the significance level, or a conflict that is clerical, resolved elsewhere in the paper, or outside its own findings.
In the paper
§ MRtrix3 : A fast, flexible and open software framework for medical image processing and visualisation > 6 Conclusion and future directions
“MRtrix3 supports arbitrary data strides for all supported formats, and for data held in RAM.”
§ MRtrix3 : A fast, flexible and open software framework for medical image processing and visualisation > MRtrix3
“Of the supported formats, only MRtrix3 's own formats support arbitrary stride ordering, a feature that offers distinct performance advantages when processing different types of data, particularly by allowing volume-contiguous storage.”
Rated minor: it would not touch a result — a value no result rests on, a p-value that stays on the same side of the significance level, or a conflict that is clerical, resolved elsewhere in the paper, or outside its own findings.
In the paper
§ MRtrix3 : A fast, flexible and open software framework for medical image processing and visualisation > 3.1 Image access
“all MRtrix3 applications can read and write all supported image formats directly”
§ MRtrix3 : A fast, flexible and open software framework for medical image processing and visualisation > 3 Design aspects
“including native support for DICOM (read-only), Analyze , NIfTI1 , NIfTI2 , MGH , and MRtrix3 's own dedicated image 15 16 17 18 19 formats , as well as compressed versions thereof.”
Citations
Cites
Advances in functional and structural MR image analysis and implementation as FSL
Smith, S. M., Jenkinson, M., Woolrich, M. W., Beckmann, C. F., Behrens, T. E. J., Johansen-Berg, H., Bannister, P. R., De Luca, M., Drobnjak, I., Flitney, D. E., et al. (2004) · NeuroImage · doi:10.1016/j.neuroimage.2004.07.051 · Cited by 13,630
Jenkinson, M., Beckmann, C. F., Behrens, T. E. J., Woolrich, M. W., & Smith, S. M. (2012) · NeuroImage · doi:10.1016/j.neuroimage.2011.09.015 · Cited by 11,314
AFNI: Software for analysis and visualization of functional magnetic resonance neuroimages
Cox, R. W. (1996) · Computers and Biomedical Research · doi:10.1006/cbmr.1996.0014 · Cited by 10,913
Fischl, B. (2012) · NeuroImage · doi:10.1016/j.neuroimage.2012.01.021 · Cited by 9,526
Zhang, Y., Brady, M., & Smith, S. M. (2001) · IEEE Transactions on Medical Imaging · doi:10.1109/42.906424 · Cited by 7,628
N4ITK: Improved N3 Bias Correction
Tustison, N. J., Avants, B., Cook, P. A., Zheng, Y., Egan, A., Yushkevich, P. A., & Gee, J. C. (2010) · IEEE Transactions on Medical Imaging · doi:10.1109/tmi.2010.2046908 · Cited by 6,413
MR diffusion tensor spectroscopy and imaging
Basser, P. J., Mattiello, J., & LeBihan, D. (1994) · Biophysical Journal · doi:10.1016/s0006-3495(94)80775-1 · Cited by 5,970
SMITH, S., & NICHOLS, T. (2009) · NeuroImage · doi:10.1016/j.neuroimage.2008.03.061 · Cited by 5,250
Permutation inference for the general linear model
Winkler, A. M., Ridgway, G. R., Webster, M. A., Smith, S. M., & Nichols, T. E. (2014) · NeuroImage · doi:10.1016/j.neuroimage.2014.01.060 · Cited by 3,563
Andersson, J. L. R., Skare, S., & Ashburner, J. (2003) · NeuroImage · doi:10.1016/s1053-8119(03)00336-7 · Cited by 3,469
Research works printed but not linked: 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
Items 101–200 of 2,972
Structural-functional brain network coupling predicts human cognitive ability
Popp, J. L., Thiele, J. A., Faskowitz, J., Seguin, C., Sporns, O., & Hilger, K. (2024) · NeuroImage · doi:10.1016/j.neuroimage.2024.120563 · Cited by 71
A graph neural network framework for causal inference in brain networks
Wein, S., Malloni, W. M., Tomé, A. M., Frank, S., Henze, G., Wüst, S., Greenlee, M. W., & Lang, E. W. (2021) · Scientific Reports · doi:10.1038/s41598-021-87411-8 · Cited by 66
An open resource combining multi-contrast MRI and microscopy in the macaque brain
Howard, A. F. D., Huszár, I. N., Smart, A., Cottaar, M., Daubney, G., Hanayik, T., Khrapitchev, A. A., Mars, R. B., Mollink, J., Scott, C., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-39916-1 · Cited by 68
Structural connectome and connectivity lateralization of the multimodal vestibular cortical network
Indovina, I., Bosco, G., Riccelli, R., Maffei, V., Lacquaniti, F., Passamonti, L., & Toschi, N. (2020) · NeuroImage · doi:10.1016/j.neuroimage.2020.117247 · Cited by 63
Zamani, A., Walker, A. K., Rollo, B., Ayers, K. L., Farah, R., O'Brien, T. J., & Wright, D. K. (2022) · Translational Neurodegeneration · doi:10.1186/s40035-022-00291-4 · Cited by 60
Perceptual coupling and decoupling of the default mode network during mind-wandering and reading
Zhang, M., Bernhardt, B. C., Wang, X., Varga, D., Krieger‐Redwood, K., Royer, J., Rodríguez‐Cruces, R., de Wael, R. V., Margulies, D. S., Smallwood, J., et al. (2022) · eLife · doi:10.7554/elife.74011 · Cited by 67
Healthcare Data Quality Assessment for Cybersecurity Intelligence
Li, Y., Yang, J., Zhang, Z., Wen, J., & Kumar, P. (2022) · IEEE Transactions on Industrial Informatics · doi:10.1109/tii.2022.3190405 · Cited by 64
Connectomes for 40,000 UK Biobank participants: A multi-modal, multi-scale brain network resource
Sina Mansour, L., Biase, M. A. D., Smith, R. E., Zalesky, A., & Seguin, C. (2023) · NeuroImage · doi:10.1016/j.neuroimage.2023.120407 · Cited by 66
Self-citationde Almeida, J. S., Meskaldji, D. E., Loukas, S., Lordier, L., Gui, L., Lazeyras, F., & Hüppi, P. S. (2020) · NeuroImage · doi:10.1016/j.neuroimage.2020.117440 · Cited by 61
Schilling, K. G., Tax, C. M. W., Rheault, F., Hansen, C. B., Yang, Q., Yeh, F.-C. F., Cai, L. Y., Anderson, A. W., & Landman, B. A. (2021) · NeuroImage · doi:10.1016/j.neuroimage.2021.118451 · Cited by 66
Infants’ cortex undergoes microstructural growth coupled with myelination during development
Natu, V. S., Rosenke, M., Wu, H., Querdasi, F. R., Kular, H., Lopez-Alvarez, N., Grotheer, M., Berman, S., Mezer, A., & Kalanit Grill-spector, A. (2021) · Communications Biology · doi:10.1038/s42003-021-02706-w · Cited by 58
Zhang, S., Larsen, B., Sydnor, V. J., Zeng, T., An, L., Yan, X., Kong, R., Kong, X., Gur, R. C., Gur, R. E., et al. (2024) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2318641121 · Cited by 67
Structural and functional connectivity reconstruction with CATO - A Connectivity Analysis TOolbox
de Lange, S. C., Helwegen, K., & van den Heuvel, M. P. (2023) · NeuroImage · doi:10.1016/j.neuroimage.2023.120108 · Cited by 54
Binette, A. P., Theaud, G., Rheault, F., Roy, M., Collins, D. L., Levin, J., Mori, H., Lee, J. H., Farlow, M. R., Schofield, P. R., et al. (2021) · eLife · doi:10.7554/elife.62929 · Cited by 60
Park, B., Paquola, C., Bethlehem, R. A. I., Benkarim, O. M., Mišić, B., Smallwood, J., Bullmore, E. T., Bernhardt, B. C., Bullmore, E. T., Dolan, R. J., et al. (2022) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2116673119 · Cited by 56
Enhancing Fine-Tuning based Backdoor Defense with Sharpness-Aware Minimization
Zhu, M., Wei, S., Shen, L., Fan, Y., & Wu, B. (2023) · IEEE/CVF International Conference on Computer Vision (ICCV) · doi:10.1109/iccv51070.2023.00412 · Cited by 72
Hypothalamic deep brain stimulation augments walking after spinal cord injury
Cho, N., Squair, J. W., Aureli, V., James, N. D., Bole-Feysot, L., Dewany, I., Hankov, N., Baud, L., Leonhartsberger, A., Sveistyte, K., et al. (2024) · Nature Medicine · doi:10.1038/s41591-024-03306-x · Cited by 62
The human corticocortical vestibular network
Raiser, T. M., Flanagin, V. L., Duering, M., Ombergen, A. V., Ruehl, R. M., & zu Eulenburg, P. (2020) · NeuroImage · doi:10.1016/j.neuroimage.2020.117362 · Cited by 65
Ball, G., Seidlitz, J., O’Muircheartaigh, J., Dimitrova, R., Fenchel, D., Makropoulos, A., Christiaens, D., Schuh, A., Passerat‐Palmbach, J., Hutter, J. M., et al. (2020) · PLoS Biology · doi:10.1371/journal.pbio.3000976 · Cited by 54
Self-citationMiddle Frontal Gyrus and Area 55b: Perioperative Mapping and Language Outcomes
Hazem, S., Awan, M., Lavrador, J., Patel, S., Wren, H., Lucena, O., Semedo, C., Irzan, H., Melbourne, A., Ourselin, S., et al. (2021) · Frontiers in Neurology · doi:10.3389/fneur.2021.646075 · Cited by 49
Fetal whole heart blood flow imaging using 4D cine MRI
Roberts, T. A., van Amerom, J. F. P., Uus, A. U., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-18790-1 · Cited by 55
Self-citationExtensive Connections of the Canine Olfactory Pathway Revealed by Tractography and Dissection
Andrews, E. F., Paşcalău, R., Horowitz, A., Lawrence, G. M., & Johnson, P. J. (2022) · Journal of Neuroscience · doi:10.1523/jneurosci.2355-21.2022 · Cited by 59
Statistical power in network neuroscience
Helwegen, K., Libedinsky, I., & van den Heuvel, M. P. (2023) · Trends in Cognitive Sciences · doi:10.1016/j.tics.2022.12.011 · Cited by 59
MR cell size imaging with temporal diffusion spectroscopy
Jiang, X., Li, H., Devan, S. P., Gore, J. C., & Xu, J. (2020) · Magnetic Resonance Imaging · doi:10.1016/j.mri.2020.12.010 · Cited by 54
Structural white matter connectometry of reading and dyslexia
Sihvonen, A. J., Virtala, P., Thiede, A., Laasonen, M. R., & Kujala, T. (2021) · NeuroImage · doi:10.1016/j.neuroimage.2021.118411 · Cited by 62
Multiscale communication in cortico-cortical networks
Bazinet, V., de Wael, R. V., Hagmann, P., Bernhardt, B. C., & Mišić, B. (2021) · NeuroImage · doi:10.1016/j.neuroimage.2021.118546 · Cited by 53
Multi-shell Diffusion MRI Models for White Matter Characterization in Cerebral Small Vessel Disease
Konieczny, M. J., Dewenter, A., ter Telgte, A., Gesierich, B. G., Wiegertjes, K., Finsterwalder, S., Kopczak, A., Hübner, M., Malik, R., Tuladhar, A. M., et al. (2020) · Neurology · doi:10.1212/wnl.0000000000011213 · Cited by 52
The variability of MR axon radii estimates in the human white matter
Veraart, J., Raven, E. P., Edwards, L., Weiskopf, N., & Jones, D. K. (2021) · Human Brain Mapping · doi:10.1002/hbm.25359 · Cited by 50
Mitochondrial DNA variation in Alzheimer’s disease reveals a unique microprotein called SHMOOSE
Miller, B., Kim, S., Mehta, H. H., Cao, K., Kumagai, H., Thumaty, N., Leelaprachakul, N., Braniff, R. G., Jiao, H., Vaughan, J. M., et al. (2022) · Molecular Psychiatry · doi:10.1038/s41380-022-01769-3 · Cited by 55
Network Localisation of White Matter Damage in Cerebral Small Vessel Disease
Petersen, M., Frey, B. M., Schlemm, E., Mayer, C., Hanning, U. M. P., Engelke, K., Fiehler, J., Borof, K., Jagodzinski, A., Gerloff, C. P., et al. (2020) · Scientific Reports · doi:10.1038/s41598-020-66013-w · Cited by 53
DNA methylation in relation to gestational age and brain dysmaturation in preterm infants
Wheater, E., Galdi, P., McCartney, D. L., Blesa, M., Sullivan, G., Stoye, D. Q., Lamb, G. J., Sparrow, S. A., Murphy, L., Wrobel, N., et al. (2022) · Brain Communications · doi:10.1093/braincomms/fcac056 · Cited by 53
Comparative brain structure and visual processing in octopus from different habitats
Chung, W., Kurniawan, N. D., & Marshall, N. J. (2021) · Current Biology · doi:10.1016/j.cub.2021.10.070 · Cited by 50
Rosen, B. Q., & Halgren, E. (2022) · PLoS Biology · doi:10.1371/journal.pbio.3001575 · Cited by 55
Macroscale and microcircuit dissociation of focal and generalized human epilepsies
Weng, Y., Larivière, S., Caciagli, L., de Wael, R. V., Rodríguez‐Cruces, R., Royer, J., Xu, Q., Bernasconi, N., Bernasconi, A., Yeo, B. T. T., et al. (2020) · Communications Biology · doi:10.1038/s42003-020-0958-5 · Cited by 46
Frey, B. M., Petersen, M., Schlemm, E., Mayer, C., Hanning, U. M. P., Engelke, K., Fiehler, J., Borof, K., Jagodzinski, A., Gerloff, C. P., et al. (2020) · Human Brain Mapping · doi:10.1002/hbm.25301 · Cited by 51
Koops, E. A., & van Dijk, P. (2020) · Hearing Research · doi:10.1016/j.heares.2020.108158 · Cited by 50
Maffei, C., Girard, G., Schilling, K. G., Aydogan, D. B., Adluru, N., Zhylka, A., Wu, Y., Mancini, M., Hamamcı, A., Sarica, A., et al. (2022) · NeuroImage · doi:10.1016/j.neuroimage.2022.119327 · Cited by 49
Skin cancer detection using dual optimization based deep learning network
Gomathi, E., Jayasheela, M., Thamarai, M., & Geetha, M. (2023) · Biomedical Signal Processing and Control · doi:10.1016/j.bspc.2023.104968 · Cited by 49
MRIcroGL: voxel-based visualization for neuroimaging
Rorden, C. (2025) · Nature Methods · doi:10.1038/s41592-025-02763-7 · Cited by 49
The solitary nucleus connectivity to key autonomic regions in humans
Forstenpointner, J., Maallo, A. M. S., Elman, I., Holmes, S. A., Freeman, R. L., Baron, R., & Borsook, D. (2022) · European Journal of Neuroscience · doi:10.1111/ejn.15691 · Cited by 48
The inferior fronto-occipital fasciculus: bridging phylogeny, ontogeny and functional anatomy
Giampiccolo, D., Herbet, G., & Duffau, H. (2025) · Brain · doi:10.1093/brain/awaf055 · Cited by 60
Lehman, V. T., Lee, K. H., Klassen, B. T., et al. (2020) · Neurosurgical FOCUS · doi:10.3171/2020.4.focus20170 · Cited by 48
A unified framework for multimodal structure–function mapping based on eigenmodes
Deslauriers‐Gauthier, S., Zucchelli, M., Frigo, M., & Rachid Deriche, B. (2020) · Medical Image Analysis · doi:10.1016/j.media.2020.101799 · Cited by 45
Jitsuishi, T., & Yamaguchi, A. (2022) · Scientific Reports · doi:10.1038/s41598-022-08231-y · Cited by 47
Linking cortical atrophy to white matter hyperintensities of presumed vascular origin
Mayer, C., Frey, B. M., Schlemm, E., Petersen, M., Engelke, K., Hanning, U. M. P., Jagodzinski, A., Borof, K., Fiehler, J., Gerloff, C. P., et al. (2020) · Journal of Cerebral Blood Flow & Metabolism · doi:10.1177/0271678x20974170 · Cited by 42
Glymphatic System Dysfunction Underlying Schizophrenia Is Associated With Cognitive Impairment
Tu, Y., Fang, Y., Li, G., Xiong, F., & Gao, F. (2024) · Schizophrenia Bulletin · doi:10.1093/schbul/sbae039 · Cited by 46
Benchmarking methods for mapping functional connectivity in the brain
Liu, Z.-Q., Luppi, A. I., Hansen, J. Y., Tian, Y., Zalesky, A., Yeo, B. T. T., Fulcher, B., & Mišić, B. (2025) · Nature Methods · doi:10.1038/s41592-025-02704-4 · Cited by 55
Yeh, C., Smith, R. E., Dhollander, T., Calamante, F., & Connelly, A. (2019) · NeuroImage · doi:10.1016/j.neuroimage.2019.05.005 · Cited by 45
Self-citationTozzi, L., Staveland, B. R., Holt-Gosselin, B., Chesnut, M., Chang, S. E., Choi, D., Shiner, M., Wu, H., Lerma‐Usabiaga, G., Sporns, O., et al. (2020) · NeuroImage · doi:10.1016/j.neuroimage.2020.116715 · Cited by 48
Pham, L., Wright, D. K., O’Brien, W. T., Bain, J., Huang, C., Sun, M., Casillas-Espinosa, P. M., Shah, A. D., Schittenhelm, R. B., Sobey, C. G., et al. (2020) · Neurobiology of Disease · doi:10.1016/j.nbd.2020.105151 · Cited by 44
Cai, L. Y., Yang, Q., Kanakaraj, P., Nath, V., Newton, A. T., Edmonson, H. A., Luci, J. J., Conrad, B. N., Price, G. R., Hansen, C. B., et al. (2021) · Magnetic Resonance in Medicine · doi:10.1002/mrm.28926 · Cited by 50
Interleukin-8 dysregulation is implicated in brain dysmaturation following preterm birth
Sullivan, G., Galdi, P., Blesa, M., Borbye‐Lorenzen, N., Stoye, D. Q., Lamb, G. J., Evans, M. J., Quigley, A. J., Thrippleton, M. J., Skogstrand, K., et al. (2020) · Brain Behavior and Immunity · doi:10.1016/j.bbi.2020.09.007 · Cited by 44
Soman, S. M., Vijayakumar, N., Thomson, P., Ball, G., Hyde, C. E., & Silk, T. J. (2023) · Human Brain Mapping · doi:10.1002/hbm.26288 · Cited by 47
Learning how network structure shapes decision-making for bio-inspired computing
Schirner, M., Deco, G., & Ritter, P. (2023) · Nature Communications · doi:10.1038/s41467-023-38626-y · Cited by 55
Liang, X., Sun, L., Liao, X., Lei, T., Xia, M., Duan, D., Zeng, Z., Li, Q., Xu, Z., Men, W., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-44863-6 · Cited by 42
Tau follows principal axes of functional and structural brain organization in Alzheimer’s disease
Ottoy, J., Kang, M. S., Tan, J. X. M., Boone, L., de Wael, R. V., Park, B., Bezgin, G., Lussier, F. Z., Pascoal, T. A., Rahmouni, N., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-49300-2 · Cited by 56
Separate lanes for adding and reading in the white matter highways of the human brain
Grotheer, M., Zhen, Z., Lerma‐Usabiaga, G., & Kalanit Grill-spector, A. (2019) · Nature Communications · doi:10.1038/s41467-019-11424-1 · Cited by 44
Brighi, C., Reid, L. B., Genovesi, L. A., Kojic, M., Millar, A., Bruce, Z. C., White, A. L., Day, B. W., Rose, S., Whittaker, A. K., et al. (2020) · Theranostics · doi:10.7150/thno.46468 · Cited by 44
Reduced emergent character of neural dynamics in patients with a disrupted connectome
Luppi, A. I., Mediano, P. A. M., Rosas, F. E., Allanson, J. E., Pickard, J. D., Williams, G. B., Craig, M. M., Finoia, P., Peattie, A. R. D., Coppola, P., et al. (2023) · NeuroImage · doi:10.1016/j.neuroimage.2023.119926 · Cited by 41
Schilling, K. G., Archer, D. B., Rheault, F., Lyu, I., Huo, Y., Cai, L. Y., Bunge, S. A., Weiner, K. S., Gore, J. C., Anderson, A. W., et al. (2023) · Brain Structure and Function · doi:10.1007/s00429-023-02642-x · Cited by 50
Simulation and assimilation of the digital human brain
Lu, W., Du, X., Wang, J., Zeng, L., Ye, L., Xiang, S., Zheng, Q., Zhang, J., Xu, N., Feng, J., et al. (2024) · Nature Computational Science · doi:10.1038/s43588-024-00731-3 · Cited by 50
Human Olfaction without Apparent Olfactory Bulbs
Weiss, T., Soroka, T., Gorodisky, L., Shushan, S., Snitz, K., Weissgross, R., Furman‐Haran, E., Dhollander, T., & Sobel, N. (2019) · Neuron · doi:10.1016/j.neuron.2019.11.017 · Cited by 43
Self-citationTrack-to-Learn: A general framework for tractography with deep reinforcement learning
Théberge, A., Desrosiers, C., Descoteaux, M., & Jodoin, P. (2021) · Medical Image Analysis · doi:10.1016/j.media.2021.102093 · Cited by 44
Lu, Q., Li, Y., & Ye, C. (2021) · Medical Image Analysis · doi:10.1016/j.media.2021.102094 · Cited by 43
Assortative mixing in micro-architecturally annotated brain connectomes
Bazinet, V., Hansen, J. Y., de Wael, R. V., Bernhardt, B. C., van den Heuvel, M. P., & Mišić, B. (2023) · Nature Communications · doi:10.1038/s41467-023-38585-4 · Cited by 41
Language function following preterm birth: prediction using machine learning
Valavani, E., Blesa, M., Galdi, P., Sullivan, G., Dean, B., Cruickshank, H., Sitko-Rudnicka, M., Bastin, M. E., Chin, R., MacIntyre, D. J., et al. (2021) · Pediatric Research · doi:10.1038/s41390-021-01779-x · Cited by 42
Jünemann, K., Marié, D., Worschech, F., Scholz, D. S., Grouiller, F., Kliegel, M., Ville, D. V. D., James, C. E., Krüger, T. H. C., ALTENMÜLLER, E. O., et al. (2022) · Frontiers in Aging Neuroscience · doi:10.3389/fnagi.2022.817889 · Cited by 46
Neurological Effects of Repeated Blast Exposure in Special Operations Personnel
Stone, J. R., Avants, B., Tustison, N. J., Gill, J., Wilde, E. A., Neumann, K. D., Gladney, L. A., Kilgore, M. O., Bowling, F. Y., Wilson, C. M., et al. (2023) · Journal of Neurotrauma · doi:10.1089/neu.2023.0309 · Cited by 43
Newman, B. T., Dhollander, T., Reynier, K. A., Panzer, M. B., & Druzgal, T. J. (2020) · Magnetic Resonance in Medicine · doi:10.1002/mrm.28242 · Cited by 38
Self-citationA causal role for the pulvinar in coordinating task‐independent cortico–cortical interactions
Eradath, M. K., Pinsk, M. A., & Kästner, S. (2021) · The Journal of Comparative Neurology · doi:10.1002/cne.25193 · Cited by 45
The glial framework reveals white matter fiber architecture in human and primate brains
Schurr, R., & Mezer, A. (2021) · Science · doi:10.1126/science.abj7960 · Cited by 42
Taylor, N. L., D’Souza, A., Munn, B., Lv, J., Záborszky, L., Müller, E. J., Wainstein, G., Calamante, F., & Shine, J. M. (2022) · NeuroImage · doi:10.1016/j.neuroimage.2022.119455 · Cited by 42
The Myelin‐Weighted Connectome in Parkinson's Disease
Boshkovski, T., Cohen‐Adad, J., Mišić, B., Arnulf, I., Corvol, J., Vidailhet, M., Lehéricy, S., Stikov, N., & Mancini, M. (2021) · Movement Disorders · doi:10.1002/mds.28891 · Cited by 41
Normalizing the brain connectome for communication through synchronization
Petkoski, S., & Jirsa, V. (2022) · Network Neuroscience · doi:10.1162/netn_a_00231 · Cited by 44
Deep Diffusion MRI Registration (DDMReg): A Deep Learning Method for Diffusion MRI Registration
Zhang, F., Wells, W. M., & O’Donnell, L. J. (2021) · IEEE Transactions on Medical Imaging · doi:10.1109/tmi.2021.3139507 · Cited by 42
Liebe, T., Kaufmann, J., Hämmerer, D., Betts, M. J., & Walter, M. (2022) · Molecular Psychiatry · doi:10.1038/s41380-022-01761-x · Cited by 46
ConFiG: Contextual Fibre Growth to generate realistic axonal packing for diffusion MRI simulation
Callaghan, R., Alexander, D. C., Palombo, M., & Zhang, H. G. (2020) · NeuroImage · doi:10.1016/j.neuroimage.2020.117107 · Cited by 49
Arun, A. H., Connelly, A., Smith, R., & Calamante, F. (2020) · NeuroImage · doi:10.1016/j.neuroimage.2020.117505 · Cited by 44
Self-citationCarandini, T., Mancini, M., Bogdan, I., Rae, C. L., Barritt, A. W., Sethi, A., Harrison, N. A., Rashid, W., Scarpini, E. A., Galimberti, D., et al. (2021) · NeuroImage Clinical · doi:10.1016/j.nicl.2021.102587 · Cited by 44
White matter tract signatures of fiber density and morphology in ADHD.
Fuelscher, I., Hyde, C., Anderson, V., & Silk, T. (2021) · Cortex; a journal devoted to the study of the nervous system and behavior · doi:10.1016/j.cortex.2021.02.015 · Cited by 40
Physical activity and cognitive and imaging biomarkers of Alzheimer's disease in down syndrome
Fleming, V., Piro‐Gambetti, B., Patrick, A., Zammit, M. D., Alexander, A. L., Christian, B. T., Handen, B. L., Cohen, A. D., Klunk, W. E., Laymon, C. M., et al. (2021) · Neurobiology of Aging · doi:10.1016/j.neurobiolaging.2021.07.016 · Cited by 41
Mosley, P. E., Paliwal, S., Robinson, K., Coyne, T. J., Silburn, P. A., Tittgemeyer, M., Stephan, K. E., Breakspear, M. J., & Perry, A. (2019) · Brain · doi:10.1093/brain/awz327 · Cited by 44
Haber, S. N., Lehman, J. F., Maffei, C., & Yendiki, A. (2022) · Biological Psychiatry · doi:10.1016/j.biopsych.2023.01.006 · Cited by 40
Palombo, M., Valindria, V. V., Singh, S., Chiou, E., Giganti, F., Pye, H., Whitaker, H. C., Atkinson, D., Punwani, S., Alexander, D. C., et al. (2023) · Scientific Reports · doi:10.1038/s41598-023-30182-1 · Cited by 39
Griffa, A., Mach, M., Dedelley, J., Gutierrez‐Barragan, D., Gozzi, A., Allali, G., Grandjean, J., Ville, D. V. D., & Amico, E. (2023) · Nature Communications · doi:10.1038/s41467-023-43971-z · Cited by 50
Attali, D., Tiennot, T., Manuel, T. J., Daniel, M., Houdouin, A., Annic, P., Dizeux, A., Haroche, A., Dadi, G., Henensal, A., et al. (2025) · Brain stimulation · doi:10.1016/j.brs.2025.04.018 · Cited by 40
Baraković, M., Tax, C. M. W., Rudrapatna, U. S., Chamberland, M., Rafael‐Patiño, J., Granziera, C., Thiran, J., Daducci, A., Canales-Rodríguez, E. J., & Jones, D. K. (2020) · NeuroImage · doi:10.1016/j.neuroimage.2020.117617 · Cited by 39
Zöller, D., Sandini, C., Schaer, M., Eliez, S., Bassett, D. S., & Ville, D. V. D. (2021) · Human Brain Mapping · doi:10.1002/hbm.25358 · Cited by 39
Navigating the link between processing speed and network communication in the human brain
Imms, P., Domínguez D, J. F., Burmester, A., Seguin, C., Clemente, A., Dhollander, T., Wilson, P. H., Poudel, G., & Caeyenberghs, K. (2021) · Brain Structure and Function · doi:10.1007/s00429-021-02241-8 · Cited by 39
Self-citationStructural brain changes in patients with persistent headache after COVID-19 resolution
Planchuelo‐Gómez, Á., García‐Azorín, D., Peral, Á. L. G., Rodríguez, M., Aja‐Fernández, S., & de Luis-Garcı́a, R. (2022) · Journal of Neurology · doi:10.1007/s00415-022-11398-z · Cited by 40
Diffusion MRI tracks cortical microstructural changes during the early stages of Alzheimer’s disease
Spotorno, N., Strandberg, O. T., Stomrud, E., Janelidze, S., Blennow, K., Nilsson, M., van Westen, D., & Hansson, O. (2023) · Brain · doi:10.1093/brain/awad428 · Cited by 41
Microstructural Bias in the Assessment of Periventricular Flow as Revealed in Postmortem Brains
Li, S., Chen, R., Cao, Z., Zhu, Q., Ma, Y., Zhu, K., Lin, Z., Wu, D., & Initiative, A. D. N. (2025) · Radiology · doi:10.1148/radiol.250753 · Cited by 39
Leuze, C. W., Goubran, M., Baraković, M., Aswendt, M., Tian, Q., Hsueh, B., Crow, A., Weber, E. M. M., Steinberg, G. K., Zeineh, M., et al. (2020) · NeuroImage · doi:10.1016/j.neuroimage.2020.117692 · Cited by 37
Diffusion Imaging Reveals Sex Differences in the White Matter Following Sports-Related Concussion.
Wright, D. K., Symons, G. F., O’Brien, W., McDonald, S., Zamani, A., Major, B., Chen, Z.-B., Costello, D. M., Brady, R., Sun, M.-J., et al. (2021) · Cerebral Cortex · doi:10.1093/cercor/bhab095 · Cited by 39
Nonparametric D-R1-R2 distribution MRI of the living human brain
Martin, J., Reymbaut, A., Schmidt, M. A., Doerfler, A., Uder, M., Laun, F. B., & Topgaard, D. (2021) · NeuroImage · doi:10.1016/j.neuroimage.2021.118753 · Cited by 35
Sydnor, V. J., Bagautdinova, J., Larsen, B., Arcaro, M. J., Barch, D. M., Bassett, D. S., Alexander‐Bloch, A. F., Cook, P. A., Covitz, S. C., Franco, A. R., et al. (2025) · Nature Neuroscience · doi:10.1038/s41593-025-01991-6 · Cited by 57
Tornifoglio, B., Stone, A. J., Johnston, R. D., Shahid, S. S., Kerskens, C., & Lally, C. (2020) · Scientific Reports · doi:10.1038/s41598-020-77675-x · Cited by 37
Ghimire, P., Lavrador, J. P., Mirza, A. B., et al. (2021) · Brain Structure and Function · doi:10.1007/s00429-021-02274-z · Cited by 37
Autofluorescence enhancement for label-free imaging of myelinated fibers in mammalian brains
Costantini, I., Baria, E., Sorelli, M., Matuschke, F., Giardini, F., Menzel, M., Mazzamuto, G., Silvestri, L., Cicchi, R., Amunts, K., et al. (2021) · Scientific Reports · doi:10.1038/s41598-021-86092-7 · Cited by 32
Solana, E., Martínez‐Heras, E., Montal, V., Vilaplana, E., López-Soley, E., Raduà, J., Solà‐Valls, N., Montejo, C., Blanco, Y., Pulido-Valdeolivas, I., et al. (2021) · Scientific Reports · doi:10.1038/s41598-021-96132-x · Cited by 38
Metadata
- 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)
- 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
- bronze
- doi.org
- 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.
A language model drew the claims from the paper on 2026-10-24, under version 3 of the claim definition (model deepseek-v4.1-flash, prompt extract-v3).
A second model labelled each claim on 2026-10-24 (model jev-1.13-20260917, definition revision gold-guideline-v0.2).
Cited sources are checked with a language model’s help (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.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
