DiffusionKit: A light one-stop solution for diffusion MRI data analysis
•DiffusionKit has a full pipeline for (pre-)processing and visualization of diffusion MRI data.•DiffusionKit has cross-platform support and a small installation size without 3rd party dependency.•DiffusionKit has both a GUI interface and command-line functions that enable easy operation and batch pr...
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| Veröffentlicht in: | Journal of neuroscience methods 2016-11, Vol.273, p.107-119 |
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| container_title | Journal of neuroscience methods |
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| creator | Xie, Sangma Chen, Liangfu Zuo, Nianming Jiang, Tianzi |
| description | •DiffusionKit has a full pipeline for (pre-)processing and visualization of diffusion MRI data.•DiffusionKit has cross-platform support and a small installation size without 3rd party dependency.•DiffusionKit has both a GUI interface and command-line functions that enable easy operation and batch processing.
Diffusion magnetic resonance imaging (dMRI) techniques are receiving increasing attention due to their ability to characterize the arrangement map of white matter in vivo. However, the existing toolkits for dMRI analysis that have accompanied this surge possess noticeable limitations, such as large installation size, an incomplete pipeline, and a lack of cross-platform support.
In this work, we developed a light, one-stop, cross-platform solution for dMRI data analysis, called DiffusionKit. It delivers a complete pipeline, including data format conversion, dMRI preprocessing, local reconstruction, white matter fiber tracking, fiber statistical analyses and various visualization schemes. Furthermore, DiffusionKit is a self-contained executable toolkit, without the need to install any other software.
The DiffusionKit package is implemented in C/C++ and Qt/VTK, is freely available at http://diffusion.brainnetome.org and https://www.nitrc.org/projects/diffusionkit. The website of DiffusionKit includes test data, a complete tutorial and a series of tutorial examples. A mailing list has also been established for update notification and questions and answers.
DiffusionKit provides a full-function pipeline for dMRI data analysis, including data processing, modeling and visualization. Additionally, it provides both a graphical user interface (GUI) and command-line functions, which are helpful for batch processing. The standalone installation package has a small size and cross-platform support.
DiffusionKit provides a complete pipeline with cutting-edge methods for dMRI data analysis, including both a GUI interface and command-line functions. The rich functions for both data analysis and visualization will facilitate and benefit dMRI research. |
| doi_str_mv | 10.1016/j.jneumeth.2016.08.011 |
| format | Article |
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Diffusion magnetic resonance imaging (dMRI) techniques are receiving increasing attention due to their ability to characterize the arrangement map of white matter in vivo. However, the existing toolkits for dMRI analysis that have accompanied this surge possess noticeable limitations, such as large installation size, an incomplete pipeline, and a lack of cross-platform support.
In this work, we developed a light, one-stop, cross-platform solution for dMRI data analysis, called DiffusionKit. It delivers a complete pipeline, including data format conversion, dMRI preprocessing, local reconstruction, white matter fiber tracking, fiber statistical analyses and various visualization schemes. Furthermore, DiffusionKit is a self-contained executable toolkit, without the need to install any other software.
The DiffusionKit package is implemented in C/C++ and Qt/VTK, is freely available at http://diffusion.brainnetome.org and https://www.nitrc.org/projects/diffusionkit. The website of DiffusionKit includes test data, a complete tutorial and a series of tutorial examples. A mailing list has also been established for update notification and questions and answers.
DiffusionKit provides a full-function pipeline for dMRI data analysis, including data processing, modeling and visualization. Additionally, it provides both a graphical user interface (GUI) and command-line functions, which are helpful for batch processing. The standalone installation package has a small size and cross-platform support.
DiffusionKit provides a complete pipeline with cutting-edge methods for dMRI data analysis, including both a GUI interface and command-line functions. The rich functions for both data analysis and visualization will facilitate and benefit dMRI research.</description><identifier>ISSN: 0165-0270</identifier><identifier>EISSN: 1872-678X</identifier><identifier>DOI: 10.1016/j.jneumeth.2016.08.011</identifier><identifier>PMID: 27568099</identifier><language>eng</language><publisher>Netherlands: Elsevier B.V</publisher><subject>Algorithms ; Anatomical connectivity ; Anisotropy ; Brain - diagnostic imaging ; Connectome ; Diffusion Magnetic Resonance Imaging ; Diffusion MRI ; DiffusionKit ; DTI ; HARDI ; Humans ; Image Processing, Computer-Assisted ; Models, Neurological ; Nerve Fibers, Myelinated - physiology ; White Matter - diagnostic imaging</subject><ispartof>Journal of neuroscience methods, 2016-11, Vol.273, p.107-119</ispartof><rights>2016 Elsevier B.V.</rights><rights>Copyright © 2016 Elsevier B.V. All rights reserved.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c421t-a86e1ded0330bda87ca2852f088ec5932dcad4c834724078b94425c3c7af898b3</citedby><cites>FETCH-LOGICAL-c421t-a86e1ded0330bda87ca2852f088ec5932dcad4c834724078b94425c3c7af898b3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://dx.doi.org/10.1016/j.jneumeth.2016.08.011$$EHTML$$P50$$Gelsevier$$H</linktohtml><link.rule.ids>314,780,784,3541,27915,27916,45986</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/27568099$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Xie, Sangma</creatorcontrib><creatorcontrib>Chen, Liangfu</creatorcontrib><creatorcontrib>Zuo, Nianming</creatorcontrib><creatorcontrib>Jiang, Tianzi</creatorcontrib><title>DiffusionKit: A light one-stop solution for diffusion MRI data analysis</title><title>Journal of neuroscience methods</title><addtitle>J Neurosci Methods</addtitle><description>•DiffusionKit has a full pipeline for (pre-)processing and visualization of diffusion MRI data.•DiffusionKit has cross-platform support and a small installation size without 3rd party dependency.•DiffusionKit has both a GUI interface and command-line functions that enable easy operation and batch processing.
Diffusion magnetic resonance imaging (dMRI) techniques are receiving increasing attention due to their ability to characterize the arrangement map of white matter in vivo. However, the existing toolkits for dMRI analysis that have accompanied this surge possess noticeable limitations, such as large installation size, an incomplete pipeline, and a lack of cross-platform support.
In this work, we developed a light, one-stop, cross-platform solution for dMRI data analysis, called DiffusionKit. It delivers a complete pipeline, including data format conversion, dMRI preprocessing, local reconstruction, white matter fiber tracking, fiber statistical analyses and various visualization schemes. Furthermore, DiffusionKit is a self-contained executable toolkit, without the need to install any other software.
The DiffusionKit package is implemented in C/C++ and Qt/VTK, is freely available at http://diffusion.brainnetome.org and https://www.nitrc.org/projects/diffusionkit. The website of DiffusionKit includes test data, a complete tutorial and a series of tutorial examples. A mailing list has also been established for update notification and questions and answers.
DiffusionKit provides a full-function pipeline for dMRI data analysis, including data processing, modeling and visualization. Additionally, it provides both a graphical user interface (GUI) and command-line functions, which are helpful for batch processing. The standalone installation package has a small size and cross-platform support.
DiffusionKit provides a complete pipeline with cutting-edge methods for dMRI data analysis, including both a GUI interface and command-line functions. The rich functions for both data analysis and visualization will facilitate and benefit dMRI research.</description><subject>Algorithms</subject><subject>Anatomical connectivity</subject><subject>Anisotropy</subject><subject>Brain - diagnostic imaging</subject><subject>Connectome</subject><subject>Diffusion Magnetic Resonance Imaging</subject><subject>Diffusion MRI</subject><subject>DiffusionKit</subject><subject>DTI</subject><subject>HARDI</subject><subject>Humans</subject><subject>Image Processing, Computer-Assisted</subject><subject>Models, Neurological</subject><subject>Nerve Fibers, Myelinated - physiology</subject><subject>White Matter - diagnostic imaging</subject><issn>0165-0270</issn><issn>1872-678X</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2016</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFkE1LxDAQhoMoun78hSVHL62T9Cv1pPixioogCt5Cmkw1pW3WJhX231vZXa-ehmGed4Z5CJkziBmw_KyJmx7HDsNnzKc-BhEDYztkxkTBo7wQ77tkNg2yCHgBB-TQ-wYA0hLyfXLAiywXUJYzsri2dT166_oHG87pJW3tx2egrsfIB7ek3rVjmKa0dgM1W5Y-vdxTo4Kiqlftylt_TPZq1Xo82dQj8nZ783p1Fz0-L-6vLh8jnXIWIiVyZAYNJAlURolCKy4yXoMQqLMy4UYrk2qRpAVPoRBVmaY804kuVC1KUSVH5HS9dzm4rxF9kJ31GttW9ehGL5lIsozleZJOaL5G9eC8H7CWy8F2alhJBvJXomzkVqL8lShByEniFJxvboxVh-YvtrU2ARdrAKdPvy0O0muLvUZjB9RBGmf_u_EDN5qGQA</recordid><startdate>20161101</startdate><enddate>20161101</enddate><creator>Xie, Sangma</creator><creator>Chen, Liangfu</creator><creator>Zuo, Nianming</creator><creator>Jiang, Tianzi</creator><general>Elsevier B.V</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope></search><sort><creationdate>20161101</creationdate><title>DiffusionKit: A light one-stop solution for diffusion MRI data analysis</title><author>Xie, Sangma ; Chen, Liangfu ; Zuo, Nianming ; Jiang, Tianzi</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c421t-a86e1ded0330bda87ca2852f088ec5932dcad4c834724078b94425c3c7af898b3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2016</creationdate><topic>Algorithms</topic><topic>Anatomical connectivity</topic><topic>Anisotropy</topic><topic>Brain - diagnostic imaging</topic><topic>Connectome</topic><topic>Diffusion Magnetic Resonance Imaging</topic><topic>Diffusion MRI</topic><topic>DiffusionKit</topic><topic>DTI</topic><topic>HARDI</topic><topic>Humans</topic><topic>Image Processing, Computer-Assisted</topic><topic>Models, Neurological</topic><topic>Nerve Fibers, Myelinated - physiology</topic><topic>White Matter - diagnostic imaging</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Xie, Sangma</creatorcontrib><creatorcontrib>Chen, Liangfu</creatorcontrib><creatorcontrib>Zuo, Nianming</creatorcontrib><creatorcontrib>Jiang, Tianzi</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><jtitle>Journal of neuroscience methods</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Xie, Sangma</au><au>Chen, Liangfu</au><au>Zuo, Nianming</au><au>Jiang, Tianzi</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>DiffusionKit: A light one-stop solution for diffusion MRI data analysis</atitle><jtitle>Journal of neuroscience methods</jtitle><addtitle>J Neurosci Methods</addtitle><date>2016-11-01</date><risdate>2016</risdate><volume>273</volume><spage>107</spage><epage>119</epage><pages>107-119</pages><issn>0165-0270</issn><eissn>1872-678X</eissn><abstract>•DiffusionKit has a full pipeline for (pre-)processing and visualization of diffusion MRI data.•DiffusionKit has cross-platform support and a small installation size without 3rd party dependency.•DiffusionKit has both a GUI interface and command-line functions that enable easy operation and batch processing.
Diffusion magnetic resonance imaging (dMRI) techniques are receiving increasing attention due to their ability to characterize the arrangement map of white matter in vivo. However, the existing toolkits for dMRI analysis that have accompanied this surge possess noticeable limitations, such as large installation size, an incomplete pipeline, and a lack of cross-platform support.
In this work, we developed a light, one-stop, cross-platform solution for dMRI data analysis, called DiffusionKit. It delivers a complete pipeline, including data format conversion, dMRI preprocessing, local reconstruction, white matter fiber tracking, fiber statistical analyses and various visualization schemes. Furthermore, DiffusionKit is a self-contained executable toolkit, without the need to install any other software.
The DiffusionKit package is implemented in C/C++ and Qt/VTK, is freely available at http://diffusion.brainnetome.org and https://www.nitrc.org/projects/diffusionkit. The website of DiffusionKit includes test data, a complete tutorial and a series of tutorial examples. A mailing list has also been established for update notification and questions and answers.
DiffusionKit provides a full-function pipeline for dMRI data analysis, including data processing, modeling and visualization. Additionally, it provides both a graphical user interface (GUI) and command-line functions, which are helpful for batch processing. The standalone installation package has a small size and cross-platform support.
DiffusionKit provides a complete pipeline with cutting-edge methods for dMRI data analysis, including both a GUI interface and command-line functions. The rich functions for both data analysis and visualization will facilitate and benefit dMRI research.</abstract><cop>Netherlands</cop><pub>Elsevier B.V</pub><pmid>27568099</pmid><doi>10.1016/j.jneumeth.2016.08.011</doi><tpages>13</tpages></addata></record> |
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| ispartof | Journal of neuroscience methods, 2016-11, Vol.273, p.107-119 |
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| source | MEDLINE; ScienceDirect Journals (5 years ago - present) |
| subjects | Algorithms Anatomical connectivity Anisotropy Brain - diagnostic imaging Connectome Diffusion Magnetic Resonance Imaging Diffusion MRI DiffusionKit DTI HARDI Humans Image Processing, Computer-Assisted Models, Neurological Nerve Fibers, Myelinated - physiology White Matter - diagnostic imaging |
| title | DiffusionKit: A light one-stop solution for diffusion MRI data analysis |
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