HeuDiConv - flexible DICOM conversion into structured directory layouts

Yaroslav O Halchenko¹, Mathias Goncalves², Satrajit Ghosh³, Pablo Velasco⁴, Matteo Visconti di Oleggio Castello⁵, Taylor Salo⁶, John T Wodder 2nd¹, Michael Hanke^{7

8}, Patrick Sadil⁹, Krzysztof Jacek Gorgolewski¹⁰, Horea-Ioan Ioanas¹, Chris Rorden¹¹, Timothy J Hendrickson^{12

13}, Michael Dayan¹⁴, Sean Dae Houlihan^{1

15}, James Kent¹⁶, Ted Strauss¹⁷, John Lee¹⁸, Isaac To¹, Christopher J Markiewicz², Darren Lukas¹⁹, Ellyn R Butler²⁰, Todd Thompson¹⁵, Maite Termenon^{21

22}, David V Smith²³, Austin Macdonald¹, David N Kennedy²⁴

Affiliations

¹ Center for Open Neuroscience, Department of Psychological and Brain Sciences, Dartmouth College, Hanover, NH, USA.
² Department of Psychology, Stanford University, CA, USA.
³ McGovern Institute, Massachusetts Institute of Technology, Cambridge, MA, USA.
⁴ Flywheel Exchange LLC, Minneapolis, MN, USA.
⁵ University of California, Berkeley, Berkeley, CA, USA.
⁶ Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
⁷ Institute of Neuroscience and Medicine, Brain & Behaviour (INM-7), Research Center Jülich, Jülich, Germany.
⁸ Institute of Systems Neuroscience, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
⁹ Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
¹⁰ Emeritus of Department of Psychology, Stanford University, CA, USA.
¹¹ Department of Psychology, University of South Carolina, Columbia, SC, USA.
¹² Masonic Institute for the Developing Brain, University of Minnesota, Minneapolis, MN, USA.
¹³ Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN, USA.
¹⁴ Human Neuroscience Platform, Fondation Campus Biotech Geneva, Geneva, Switzerland.
¹⁵ Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA.
¹⁶ Department of Psychology, University of Texas at Austin, Austin, TX, USA.
¹⁷ McConnell Brain Imaging Centre, McGill University, Montreal, QC, Canada.
¹⁸ Data Science and Sharing Team, National Institute of Mental Health, Bethesda, MD, USA.
¹⁹ Institute for Glycomics, Griffith University, QLD, Australia.
²⁰ Department of Psychology, Northwestern University, Evanston, IL, USA.
²¹ Biomedical Engineering Department, Faculty of Engineering, Mondragon University, Mondragon, Spain.
²² BCBL, Basque center on Cognition, Brain and Language, San Sebastian, Spain.
²³ Department of Psychology and Neuroscience, Temple University, Philadelphia, PA, USA.
²⁴ Departments of Psychiatry and Radiology, University of Massachusetts Chan Medical School, Worcester, MA, USA.

PMID: 39323511
PMCID: PMC11423922
DOI: 10.21105/joss.05839

HeuDiConv - flexible DICOM conversion into structured directory layouts

Yaroslav O Halchenko et al. J Open Source Softw. 2024.

. 2024;9(99):5839.

doi: 10.21105/joss.05839. Epub 2024 Jul 3.

Authors

Affiliations

¹ Center for Open Neuroscience, Department of Psychological and Brain Sciences, Dartmouth College, Hanover, NH, USA.
² Department of Psychology, Stanford University, CA, USA.
³ McGovern Institute, Massachusetts Institute of Technology, Cambridge, MA, USA.
⁴ Flywheel Exchange LLC, Minneapolis, MN, USA.
⁵ University of California, Berkeley, Berkeley, CA, USA.
⁶ Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
⁷ Institute of Neuroscience and Medicine, Brain & Behaviour (INM-7), Research Center Jülich, Jülich, Germany.
⁸ Institute of Systems Neuroscience, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
⁹ Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
¹⁰ Emeritus of Department of Psychology, Stanford University, CA, USA.
¹¹ Department of Psychology, University of South Carolina, Columbia, SC, USA.
¹² Masonic Institute for the Developing Brain, University of Minnesota, Minneapolis, MN, USA.
¹³ Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN, USA.
¹⁴ Human Neuroscience Platform, Fondation Campus Biotech Geneva, Geneva, Switzerland.
¹⁵ Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA.
¹⁶ Department of Psychology, University of Texas at Austin, Austin, TX, USA.
¹⁷ McConnell Brain Imaging Centre, McGill University, Montreal, QC, Canada.
¹⁸ Data Science and Sharing Team, National Institute of Mental Health, Bethesda, MD, USA.
¹⁹ Institute for Glycomics, Griffith University, QLD, Australia.
²⁰ Department of Psychology, Northwestern University, Evanston, IL, USA.
²¹ Biomedical Engineering Department, Faculty of Engineering, Mondragon University, Mondragon, Spain.
²² BCBL, Basque center on Cognition, Brain and Language, San Sebastian, Spain.
²³ Department of Psychology and Neuroscience, Temple University, Philadelphia, PA, USA.
²⁴ Departments of Psychiatry and Radiology, University of Massachusetts Chan Medical School, Worcester, MA, USA.

PMID: 39323511
PMCID: PMC11423922
DOI: 10.21105/joss.05839

No abstract available

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Figures

**Figure 1:. HeuDiConv automates the keystone conversion step in reproducible data handling, without compromising operator flexibility.**
The showcased set-up depicts a 2-machine infrastructure, with heudiconv operating on the same machine as subsequent analysis steps for data in a standardized and shareable representation. For more advanced usage at institutions with dedicated infrastructure, HeuDiConv can operate on an additional third machine, which then interfaces between the depicted two machines and is dedicated to data repositing, versioning, and backup.

**Figure 2:. HeuDiConv conversion and layout is controlled via heuristics (custom or provided built-ins) either with manual tune up of proposed filenames or fully automated.**
The heudiconv application can be used with the -c none parameter to generate by heuristic a list of filenames for the user to edit, before invoking the conversion to be performed via the -c dcm2niix option to use the dcm2niix tool. The process is idempotent, and specifying the -c dcm2niix option can automatically convert without seeking user tune up of proposed filenames.

Figure 3:. Downloads experienced an initial sharp rise after the ReproNim HeuDiconv training event at OHBM in mid 2018, and have subsequently followed a positive trend along with the usage — exceeding 1000 sessions per week — in the data collection interval.
Depicted are weekly download and confirmed session estimates, averaged per month, with a 95% confidence interval. User session estimates for July and August 2022 are linearly extrapolated from the nearest neighbour. Download counts are sourced from PyPI, the Python community repository; whereas user session counts are sourced from Etelemetry, an infrastructure for verifiable research impact, which end-users can disable to protect privacy.

See this image and copyright information in PMC

References

1. Gorgolewski KJ, Auer T, Calhoun VD, Craddock RC, Das S, Duff EP, Flandin G, Ghosh SS, Glatard T, Halchenko YO, Handwerker DA, Hanke M, Keator D, Li X, Michael Z, Maumet C, Nichols BN, Nichols TE, Pellman J, … Poldrack RA (2016). The brain imaging data structure, a format for organizing and describing outputs of neuroimaging experiments. Scientific Data, 3, 160044. 10.1038/sdata.2016.44 - DOI - PMC - PubMed
1. Gorgolewski KJ, Burns CD, Madison C, Clark D, Halchenko YO, Waskom ML, & Ghosh SS (2011). Nipype: A flexible, lightweight and extensible neuroimaging data processing framework in python. Frontiers in Neuroinformatics, 5. 10.3389/fninf.2011.00013 - DOI - PMC - PubMed
1. Halchenko Y, Meyer K, Poldrack B, Solanky D, Wagner A, Gors J, MacFarlane D, Pustina D, Sochat V, Ghosh S, Mönch C, Markiewicz C, Waite L, Shlyakhter I, Vega A. de la, Hayashi S, Häusler C, Poline J-B, Kadelka T, … Hanke M (2021). DataLad: Distributed system for joint management of code, data, and their relationship. Journal of Open Source Software, 6(63), 3262. 10.21105/joss.03262 - DOI
1. Hanke M, Baumgartner FJ, Ibe P, Kaule FR, Pollmann S, Speck O, Zinke W, & Stadler J (2014). A high-resolution 7-tesla fMRI dataset from complex natural stimulation with an audio movie. Scientific Data, 1(1). 10.1038/sdata.2014.3 - DOI - PMC - PubMed
1. Jamadar SD, Zhong S, Carey A, McIntyre R, Ward PGD, Fornito A, Premaratne M, Shah NJ, O’Brien K, Stäb D, Chen Z, & Egan GF (2021). Task-evoked simultaneous FDG-PET and fMRI data for measurement of neural metabolism in the human visual cortex. Scientific Data, 8(1). 10.1038/s41597-021-01042-2 - DOI - PMC - PubMed

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HeuDiConv - flexible DICOM conversion into structured directory layouts

Affiliations

HeuDiConv - flexible DICOM conversion into structured directory layouts

Authors

Affiliations

Figures

References

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