DiffusionKit: A light one-stop solution for diffusion MRI data analysis

Xie, Shaolei; Chen, Liangfu; Zuo, Nianming; Jiang, Tianzi

doi:10.1016/j.jneumeth.2016.08.011

Cited by 50 publications

(35 citation statements)

References 46 publications

(70 reference statements)

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“…5A) after standard preprocessing steps, including Eddy current distortion, with the freely available software tool DiffusionKit (http://diffusionkit. readthedocs.io) [16]. After fiber reconstruction using the manually segmented thalamus as seed and excluding vertically and posteriorly projecting bundles using appropriate exclusion planes (Fig.…”

Section: Imaging Of and Volumetry Datamentioning

confidence: 99%

Anatomical and physiological basis of continuous spike–wave of sleep syndrome after early thalamic lesions

Leal

Calado

Vieira

et al. 2018

Epilepsy & Behavior

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Unilateral selective thalamic-cortical disconnection is a common feature in our patients and is associated with both a focal pattern of CSWS and a pathological type of frequency-dependent excitability (peak: 10-20Hz). We propose that this excitability represents an abnormal synaptic plasticity previously described as the augmenting response. This synaptic plasticity has been described as absent in the corticocortical interactions in healthy experimental animals, emerging after ablation of the thalamus and producing a frequency-dependent potentiation with a peak at 10-20Hz. Because this response is potentiated by sleep states of reduced brainstem activation and by appropriate stimulating rhythms, such as sleep spindles, the simultaneous occurrence of these two factors in nonrapid-eye-movement sleep is proposed as an explanation for CSWS in our patients.

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Section: Imaging Of and Volumetry Datamentioning

confidence: 99%

Anatomical and physiological basis of continuous spike–wave of sleep syndrome after early thalamic lesions

Leal

Calado

Vieira

et al. 2018

Epilepsy & Behavior

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“…This distortion can be corrected by registering the diffusion weighted images to the b0 image with an affine transformation. DCP achieve this transformation by calling bneddy command in DiffusionKit (Xie et al, 2016).…”

Section: Methodsmentioning

confidence: 99%

“…Such as FMRIB Software Library (FSL) (Smith et al, 2004), it can only be run on Linux Operating System. For users unfamiliar with Linux, it is not convenient to use; DTI-studio (Jiang et al, 2006) and DiffusionKit (Xie et al, 2016) are run on the Windows Operating System, but they are operated step by step which is same as FSL. When there are a large number of data, not only the operation is complicated but also is easy to make a mistake.…”

Section: Introductionmentioning

confidence: 99%

DCP: a pipeline toolbox for diffusion connectome

Huang

Shu

2020

Preprint

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The brain structure network constructed by diffusion tensor imaging (DTI) reflects the anatomical connections between brain regions, so the brain structure network can quantitatively describes the anatomical connectivity pattern of the entire brain. The structure network based diffusion tensor imaging is widely used in scientific research. While a number of post processing packages have been developed, fully automated processing of DTI datasets on Windows Operating System remains challenging. Here, we developed a MATLAB toolbox named "Diffusion Connectome Pipeline" (DCP) for fully automated constructing brain structure network. The processing modules of a few developed packages, including Diffusion Toolkit, DiffusionKit, SPM and MRIcron, were employed in DCP. Using any number of raw DTI datasets from different subjects, in either DICOM or NIfTI format, DCP can automatically perform a series of steps to construct network. In addition, DCP has a friendly graphical user interface (GUI) running on the Windows Operating System, allowing the user to be interactive and to adjust the input/output settings, as well as the processing parameters. As an open-source package, DCP is freely available at https://www.nitrc.org/projects/dcp. This novel toolbox is expected to substantially simplify the image processing of DTI datasets and facilitate human brain structural connectome studies.

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“…DiffusionKit is a diffusion-weighted imaging data processing and fiber-visualizing software compiled with C++ (Xie et al, 2016 ) ( http://diffusion.brainnetome.org ). The current version of DiffusionKit is designed to process data one by one with manual input from an input interface, while across-subject batch processing requires terminal scripts.…”

Section: Methodsmentioning

confidence: 99%

BRANT: A Versatile and Extendable Resting-State fMRI Toolkit

Liu

Zhan

et al. 2018

Front. Neuroinform.

Self Cite

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Data processing toolboxes for resting-state functional MRI (rs-fMRI) have provided us with a variety of functions and user friendly graphic user interfaces (GUIs). However, many toolboxes only cover a certain range of functions, and use exclusively designed GUIs. To facilitate data processing and alleviate the burden of manually drawing GUIs, we have developed a versatile and extendable MATLAB-based toolbox, BRANT (BRAinNetome fmri Toolkit), with a wide range of rs-fMRI data processing functions and code-generated GUIs. During the implementation, we have also empowered the toolbox with parallel computing techniques, efficient file handling methods for compressed file format, and one-line scripting. In BRANT, users can find rs-fMRI batch processing functions for preprocessing, brain spontaneous activity analysis, functional connectivity analysis, complex network analysis, statistical analysis, and results visualization, while developers can quickly publish scripts with code-generated GUIs.

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DiffusionKit: A light one-stop solution for diffusion MRI data analysis

Cited by 50 publications

References 46 publications

Anatomical and physiological basis of continuous spike–wave of sleep syndrome after early thalamic lesions

Anatomical and physiological basis of continuous spike–wave of sleep syndrome after early thalamic lesions

DCP: a pipeline toolbox for diffusion connectome

BRANT: A Versatile and Extendable Resting-State fMRI Toolkit

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