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| Home > Publications database > HeuDiConv — flexible DICOM conversion into structured directory layouts > print |
| 001 | 1031830 | ||
| 005 | 20250203133212.0 | ||
| 024 | 7 | _ | |a 10.21105/joss.05839 |2 doi |
| 024 | 7 | _ | |a 10.34734/FZJ-2024-05845 |2 datacite_doi |
| 037 | _ | _ | |a FZJ-2024-05845 |
| 082 | _ | _ | |a 004 |
| 100 | 1 | _ | |a Halchenko, Yaroslav O. |0 P:(DE-HGF)0 |b 0 |e Corresponding author |
| 245 | _ | _ | |a HeuDiConv — flexible DICOM conversion into structured directory layouts |
| 260 | _ | _ | |a [Erscheinungsort nicht ermittelbar] |c 2024 |b [Verlag nicht ermittelbar] |
| 336 | 7 | _ | |a article |2 DRIVER |
| 336 | 7 | _ | |a Output Types/Journal article |2 DataCite |
| 336 | 7 | _ | |a Journal Article |b journal |m journal |0 PUB:(DE-HGF)16 |s 1729499623_25924 |2 PUB:(DE-HGF) |
| 336 | 7 | _ | |a ARTICLE |2 BibTeX |
| 336 | 7 | _ | |a JOURNAL_ARTICLE |2 ORCID |
| 336 | 7 | _ | |a Journal Article |0 0 |2 EndNote |
| 500 | _ | _ | |a Open Source Initiative8605 Santa Monica Blvd PMB 63639West Hollywood, CA 90069-4109United StatesThe Open Source Initiative’s IRS Tax ID Number (TIN) is 91-2037395.The Open Source Initiative’s EU Transparency Register Number 672028337929-77 |
| 520 | _ | _ | |a In order to support efficient processing, data must be formatted according to standards thatare prevalent in the field and widely supported among actively developed analysis tools. TheBrain Imaging Data Structure (BIDS) (Gorgolewski et al., 2016) is an open standard designedfor computational accessibility, operator legibility, and a wide and easily extendable scopeof modalities — and is consequently used by numerous analysis and processing tools as thepreferred input format in many fields of neuroscience. HeuDiConv (Heuristic DICOM Converter)enables flexible and efficient conversion of spatially reconstructed neuroimaging data fromthe DICOM format (quasi-ubiquitous in biomedical image acquisition systems, particularlyin clinical settings) to BIDS, as well as other file layouts. HeuDiConv provides a multi-stageoperator input workflow (discovery, manual tuning, conversion) where a manual tuning step isoptional and the entire conversion can thus be seamlessly integrated into a data processingpipeline. HeuDiConv is written in Python, and supports the DICOM specification for input parsing, and the BIDS specification for output construction. The support for these standardsis extensive, and HeuDiConv can handle complex organization scenarios that arise for specificdata types (e.g., multi-echo sequences, or single-band reference volumes). In addition togenerating valid BIDS outputs, additional support is offered for custom output layouts. Thisis obtained via a set of built-in fully functional or example heuristics expressed as simplePython functions. Those heuristics could be taken as a template or as a base for developingcustom heuristics, thus providing full flexibility and maintaining user accessibility. HeuDiConvfurther integrates with DataLad (Halchenko et al., 2021), and can automatically preparehierarchies of DataLad datasets with optional obfuscation of sensitive data and metadata,including obfuscating patient visit timestamps in the git version control system. As a result,given its extensibility, large modality support, and integration with advanced data managementtechnologies, HeuDiConv has become a mainstay in numerous neuroimaging workflows, andconstitutes a powerful and highly adaptable tool of potential interest to large swathes of theneuroimaging community. |
| 536 | _ | _ | |a 5254 - Neuroscientific Data Analytics and AI (POF4-525) |0 G:(DE-HGF)POF4-5254 |c POF4-525 |f POF IV |x 0 |
| 588 | _ | _ | |a Dataset connected to CrossRef, Journals: juser.fz-juelich.de |
| 700 | 1 | _ | |a Goncalves, Mathias |0 P:(DE-HGF)0 |b 1 |
| 700 | 1 | _ | |a Ghosh, Satrajit |0 P:(DE-HGF)0 |b 2 |
| 700 | 1 | _ | |a Velasco, Pablo |0 P:(DE-HGF)0 |b 3 |
| 700 | 1 | _ | |a Visconti di Oleggio Castello, Matteo |0 P:(DE-HGF)0 |b 4 |
| 700 | 1 | _ | |a Salo, Taylor |0 P:(DE-HGF)0 |b 5 |
| 700 | 1 | _ | |a Wodder, John T. |0 P:(DE-HGF)0 |b 6 |
| 700 | 1 | _ | |a Hanke, Michael |0 P:(DE-Juel1)177087 |b 7 |
| 700 | 1 | _ | |a Sadil, Patrick |0 P:(DE-HGF)0 |b 8 |
| 700 | 1 | _ | |a Gorgolewski, Krzysztof Jacek |0 P:(DE-HGF)0 |b 9 |
| 700 | 1 | _ | |a Ioanas, Horea-Ioan |0 P:(DE-HGF)0 |b 10 |
| 700 | 1 | _ | |a Rorden, Chris |0 P:(DE-HGF)0 |b 11 |
| 700 | 1 | _ | |a Hendrickson, Timothy J. |0 P:(DE-HGF)0 |b 12 |
| 700 | 1 | _ | |a Dayan, Michael |0 P:(DE-HGF)0 |b 13 |
| 700 | 1 | _ | |a Houlihan, Sean Dae |0 P:(DE-HGF)0 |b 14 |
| 700 | 1 | _ | |a Kent, James |0 P:(DE-HGF)0 |b 15 |
| 700 | 1 | _ | |a Strauss, Ted |0 P:(DE-HGF)0 |b 16 |
| 700 | 1 | _ | |a Lee, John |0 P:(DE-HGF)0 |b 17 |
| 700 | 1 | _ | |a To, Isaac |0 P:(DE-HGF)0 |b 18 |
| 700 | 1 | _ | |a Markiewicz, Christopher J. |0 P:(DE-HGF)0 |b 19 |
| 700 | 1 | _ | |a Lukas, Darren |0 P:(DE-HGF)0 |b 20 |
| 700 | 1 | _ | |a Butler, Ellyn R. |0 P:(DE-HGF)0 |b 21 |
| 700 | 1 | _ | |a Thompson, Todd |0 P:(DE-HGF)0 |b 22 |
| 700 | 1 | _ | |a Termenon, Maite |0 P:(DE-HGF)0 |b 23 |
| 700 | 1 | _ | |a Smith, David V. |0 P:(DE-HGF)0 |b 24 |
| 700 | 1 | _ | |a Macdonald, Austin |0 P:(DE-HGF)0 |b 25 |
| 700 | 1 | _ | |a Kennedy, David N. |0 P:(DE-HGF)0 |b 26 |
| 773 | _ | _ | |a 10.21105/joss.05839 |g Vol. 9, no. 99, p. 5839 - |0 PERI:(DE-600)2891760-1 |n 99 |p 5839 - |t The journal of open source software |v 9 |y 2024 |x 2475-9066 |
| 856 | 4 | _ | |y OpenAccess |u https://juser.fz-juelich.de/record/1031830/files/10.21105.joss.05839.pdf |
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| 910 | 1 | _ | |a Center for Open Neuroscience, Department of Psychological and Brain Sciences, Dartmouth College, Hanover, NH, USA |0 I:(DE-HGF)0 |b 0 |6 P:(DE-HGF)0 |
| 910 | 1 | _ | |a Forschungszentrum Jülich |0 I:(DE-588b)5008462-8 |k FZJ |b 7 |6 P:(DE-Juel1)177087 |
| 913 | 1 | _ | |a DE-HGF |b Key Technologies |l Natural, Artificial and Cognitive Information Processing |1 G:(DE-HGF)POF4-520 |0 G:(DE-HGF)POF4-525 |3 G:(DE-HGF)POF4 |2 G:(DE-HGF)POF4-500 |4 G:(DE-HGF)POF |v Decoding Brain Organization and Dysfunction |9 G:(DE-HGF)POF4-5254 |x 0 |
| 914 | 1 | _ | |y 2024 |
| 915 | _ | _ | |a Creative Commons Attribution CC BY 4.0 |0 LIC:(DE-HGF)CCBY4 |2 HGFVOC |
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