Software for PET data analysis

Cyclotron

Comprehensive list of free software for image processing and analysis can be found from the site I do imaging. The author of the site, Andrew Crabb, organized and taught an excellent hands-on course at the XIII and XIV PET Symposium, and kindly shares the course material; please find the time to check out the contents!

Some software for PET image analysis are listed in instructions for drawing ROIs.

Software developed in TPC

Carimas™ can be used for cardiac analyses, and also as a general tool for image processing and data analysis, even for small animal studies (Nesterov et al., 2022; Rainio et al., 2023).

Human Emotion Systems Laboratory offers some of their software on their web page. Integrated brain image processing pipeline, MAGIA pipeline (Karjalainen et al., 2019), can be installed from GitHub.

Wide variety of tools with command-line interface (CLI) (TPCCLIB, written in C) for data processing and analysis are available for Windows and Linux. Binary packages can be downloaded from seafile.utu.fi, Dropbox or OneDrive folder. TPCCLIB source codes are available in gitlab.utu.fi/vesoik/tpcclib. Library documentation can be found here, and list of applications in here. Instructions for installing the applications can be found here.

Some older CLI tools are not yet included in TPCCLIB, but are still available elsewhere.

In addition, there are a few small CLI tools written in C# and Matlab:

Scripts for pre-processing input function data are available in gitlab.utu.fi/vesoik/inputbatch.

IT group has collected information on their services in Turku University Hospital intranet site https://klipintra.mednet.fi/itpalvelu/Sivut/default.aspx. Additionally, the quality system SOPs contain important instructions regarding local IT infrastructure.

PET ERP

PET ERP is a management system for PET centres, containing PET scheduler, GMP compliant LIMS, stock management, and data management developed by Atostek.

Licensing

Excluding Carimas, all other software developed in Turku PET Centre is free to use and OpenSource licensed, as recommended or requested by many publishers, including Nature (Eglen et al., 2017).


See also:


Literature

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Funck T, Larcher K, Toussaint PJ, Evans AC, Thiel A. APPIAN: Automated Pipeline for PET Image Analysis. Front Neuroinform. 2018; 12: 64. doi: 10.3389/fninf.2018.00064.

Hawe D, Fernández FRH, O'Suilleabháin L, Huang J, Wolsztynski E, O'Sullivan F. Kinetic analysis of dynamic positron emission tomography data using open-source image processing and statistical inference tools. WIREs Comput Stat. 2012; 4: 316-322. doi: 10.1002/wics.1196.

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Loening AM, Gambhir SS. AMIDE: a free software tool for multimodality medical image analysis. Mol Imaging 2003; 2(3): 131-137. doi: 10.1162/15353500200303133.

López-González FJ, Paredes-Pacheco J, Thurnhofer-Hemsi K, Rossi C, Enciso M, Toro-Flores D, Murcia-Casas B, Gutiérrez-Cardo AL, Roé-Vellvé N. QModeling: a multiplatform, easy-to-use and open-source toolbox for PET kinetic analysis. Neuroinformatics 2019; 17(1): 103-114. doi: 10.1007/s12021-018-9384-y.

Markiewicz PJ, Ehrhardt MJ, Erlandsson K, Noonan PJ, Barnes A, Schott JM, Atkinson D, Arridge SR, Hutton BF, Ourselin S. NiftyPET: a high-throughput software platform for high quantitative accuracy and precision PET imaging and analysis. Neuroinformatics 2018; 16(1): 95-115. doi: 10.1007/s12021-017-9352-y.

Matheson GJ, Plavén-Sigray P, Tuisku J, Rinne J, Matuskey D, Cervenka S. Clinical brain PET research must embrace multi-centre collaboration and data sharing or risk its demise. Eur J Nucl Med Mol Imaging 2020; 47: 502-504. doi: 10.1007/s00259-019-04541-y.

Merisaari H, Tuisku J, Joutsa J, Hirvonen J, Tuominen L. Statistical Toolbox for automated brain PET data processing. 2014, Poster presentation. figshare.

Merisaari H. Batch processing with Matlab and in-house software. Powerpoint presentation in XIII Turku PET Symposium, 2014. figshare.

Muzic RF Jr, Cornelius S. COMKAT: compartmental model kinetic analysis tool. J Nucl Med. 2001; 42(4): 636-645.

Nagy P. Open Source in imaging informatics. J Digit Imaging 2007; 20(Suppl 1): 1-10. doi: 10.1007/s10278-007-9056-1.

de la Prieta R (2012). Free Software for PET Imaging, Positron Emission Tomography - Current Clinical and Research Aspects, Dr. Chia-Hung Hsieh (Ed.), ISBN: 978-953-307-824-3, InTech. Available from here.

Rainio O, Han C, Teuho J, Nesterov SV, Oikonen V, Piirola S, Laitinen T, Tättäläinen M, Knuuti J, Klén R. Carimas: an extensive medical imaging data processing tool for research. J Digit Imaging 2023 (in press). doi: 10.1007/s10278-023-00812-1.

Ratib O, Rosset A, Heuberger J. Open Source software and social networks: disruptive alternatives for medical imaging. Eur J Radiol. 2011; 78: 259-265. doi: 10.1016/j.ejrad.2010.05.004.

Savio AM, Schutte M, Graña M, Yakushev I. Pypes: workflows for processing multimodal neuroimaging data. Front Neuroinform. 2017; 11: 25. doi: 10.3389/fninf.2017.00025.

Tjerkaski J, Cervenka S, Farde L, Matheson GJ. Kinfitr - an open-source tool for reproducible PET modelling: validation and evaluation of test-retest reliability. EJNMMI Res. 2020; 10(1): 77. doi: 10.1186/s13550-020-00664-8.

Veronese M, Rizzo G, Turkheimer FE, Bertoldo A. SAKE: a new quantification tool for positron emission tomography studies. Comput Methods Progr Biomed. 2013; 111: 199-213. doi: 10.1016/j.cmpb.2013.03.016.

Tabelow K, Clayden JD, de Micheaux PL, Polzehl J, Schmid VJ, Whitcher B. Image analysis and statistical inference in neuroimaging with R. Neuroimage 2011; 55: 1686-1693. doi: 10.1016/j.neuroimage.2011.01.013.



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Updated at: 2023-05-10
Created at: 2014-04-25
Written by: Vesa Oikonen