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General Information about the Software:Technical Assessment:Additional comments:
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Fill out this survey to the best of your knowledge about any perfusion software you have used and/or developed. If someone else has listed the software platform, feel free to relist software again with your own comments and personal experience.
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Software Name:Developers:User/provider:
(name and email)		Is this open-sourced?
(y/n)		Is it commercial? (y/n)Programming Language
(e.g. C++, Python, Matlab, etc.)		Operating System:
(e.g. MacOS, Windows, Linux)		License?
(e.g. BSD, MIT, CC, proprietary, etc.)		Source:
(e.g. website, GitHub, etc.)		Installer / Pre-compiled tool?
(y/n)		Additional Requirements:
(e.g. open-source compiler, dependent on proprietary software like specific Matlab toolboxes?)		Perfusion method:
(e.g. ASL, DCE, DSC, etc.)		Clinical and/or preclinical Software Type:
plug-in for larger framework (e.g. Osirix/3D slicer etc.) or stand-alone?		Input Data Type:
(e.g. DICOM, csv-file, v5 file, Matlab, etc.):		Output Data Type:
(e.g. DICOM, nrrd, nifti, csv, pdf, etc.):		Graphical user interface
(GUI) ? (y/n)		Supports automatization?
(y/n)		Manual?
If yes, where?		Validation?
If yes, explain (numerical/physical phantoms, healthy volunteers...).		Extendable?
(y/n)		Publications:Personal assessment:
On a scale of 1 to 5, how would you rate the tool (in terms of user-friendlieness, documentation, flexibility)?		Additional comments:
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ExploreASLHenk-Jan Mutsaertspatricia.clement@ugent.beYMatlabmultiOS??https://sites.google.com/view/exploreasl/exploreasl?authuser=0??Matlab, SPMASLclinical?Dicom, niftynifti, pdf, ...?NYhttps://sites.google.com/view/exploreasl/exploreasl/manual?authuser=0To-date, ExploreASL has been used for processing ~8000 ASL datasets from all major MRI vendors and ASL sequences, and a variety of patient populations, representing ~30 studies.??ExploreASL paper in preparation3updates are currently ongoing to improve user-friendliness
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MITK-ModelFitCharlotte Debus, Ralf Floca et alscience.debusc@gmail.comynC++MacOS, Windows, LinuxCChttps://github.com/Cdebus/MITK
yCmake, Qt, (Git),
DCEclinical & preclinicalFramework addition to MITKDICOM, nrrd, niftyDICOM, nrrd, niftyyyhttp://mitk.org/wiki/MITK-ModelFit
yes, on DROsyDebus, C., Floca, R., Ingrisch, M., Kompan, I., Maier-Hein, K.,
Abdollahi, A., & Nolden, M. (2019). MITK-ModelFit: A generic
open-source framework for model fits and their exploration in medical
imaging–design, implementation and application on the example of
DCE-MRI. BMC bioinformatics, 20(1), 31.		4.5
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The DCE ToolUniversity Health Network, Spatio-Temporal Targeting and Amplification
of Radiation Response (STTARR) and Principal Investigators referred at http://www.thedcetool.com/credits.		science.debusc@gmail.comnn?Windows (XP, Vista, Win7)own licence agreement
http://www.thedcetool.com/
yClearCanvas 2.0SP1 and MATLAB MCR 7.8DCEclinicalPlugin for ClearCanvas?Excel, CSV, Bitmapynhttp://www.thedcetool.com/userguidenn?
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UMMPerfusionFrank Zöllner et al.science.debusc@gmail.comn (?)nCMacOS BSDhttp://ikrsrv1.medma.uni-heidelberg.de/redmine/projects/ummperfusionyOsiriX 5.6DCE clinicalPlugin for OsiriXDICOMDICOM, PDF reporty(y) Possibility to loop over all models and selected tissue ROIs for the loaded Data in the UMMPerfusion user interfacehttp://ikrsrv1.medma.uni-heidelberg.de/redmine/projects/ummperfusion/wikiy (with respect to PMI)n
Zöllner, F. G.; Daab, M.; Sourbron, S. P.; Schad, L. R.; Schoenberg, S. O. and Weisser, G.
An open source software for analysis of dynamic contrast enhanced magnetic resonance images: UMMPerfusion revisited.
BMC Medical Imaging, 2016, 16(7), 1-13; Digital Object Identifier (DOI) 10.1186/s12880-016-0109-0
(F. Zöllner, G. Weisser), M. Reich, S. Kaiser, S. Schoenberg, S. Sourbron and L. Schad.
UMMPerfusion: An Open Source software tool for quantitative MRI perfusion analysis in clinical routine J Digital Imaging, 2013, 26 (2), pp.344-352; Digital Object Identifier (DOI) 10.1007/s10278-012-9510-6
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UMMPerfusionFrank Zöllner et al.frank.zoellner@medma.uni-heidelberg.deynC/c++, objective CMacOS BSDhttp://ikrsrv1.medma.uni-heidelberg.de/redmine/projects/ummperfusionyOsiriX 5.6DCE clinicalPlugin for OsiriXDICOMDICOM, PDF reporty(y) Possibility to loop over all models and selected tissue ROIs for the loaded Data in the UMMPerfusion user interfacehttp://ikrsrv1.medma.uni-heidelberg.de/redmine/projects/ummperfusion/wikiy (with respect to PMI), own DRO dataset n
Zöllner, F. G.; Daab, M.; Sourbron, S. P.; Schad, L. R.; Schoenberg, S. O. and Weisser, G.
An open source software for analysis of dynamic contrast enhanced magnetic resonance images: UMMPerfusion revisited.
BMC Medical Imaging, 2016, 16(7), 1-13; Digital Object Identifier (DOI) 10.1186/s12880-016-0109-0
(F. Zöllner, G. Weisser), M. Reich, S. Kaiser, S. Schoenberg, S. Sourbron and L. Schad.
UMMPerfusion: An Open Source software tool for quantitative MRI perfusion analysis in clinical routine J Digital Imaging, 2013, 26 (2), pp.344-352; Digital Object Identifier (DOI) 10.1007/s10278-012-9510-6		4,5
in house certified, documentation of certification process published on website, software documentation on website (wiki), issue tracker
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RocketshipBarnes S, Ng T et al.science.debusc@gmail.comynMatlabMacOS, Windows, LinuxGNUGPLhttps://github.com/petmri/ROCKETSHIPnMatlab + TB: curve fitting, parallel, statistics, image processing, optimizationDCEclinicalstand-alone Matlab PipelineDICOM, Analyze, NIFTI, Raw data, Matlab dataMatlab datay
yhttps://github.com/petmri/ROCKETSHIPnyNg et al. ROCKETSHIP: a flexible and modular software tool for the planning, processing and analysis of dynamic MRI studies. BMC Med Img 2015
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3D Slicer / PkModelinghttps://github.com/QIICR/PkModeling/graphs/contributorsandrey.fedorov@gmail.comynC++MacOS, Windows, Linux3D Slicer license https://github.com/QIICR/PkModeling/blob/master/License.txt https://github.com/QIICR/PkModelingyThis is a 3D Slicer extensionDCEno constraints per seextension for 3D SlicerDICOM, NRRD, NIfTIany ITK-readable 3D volume formatyyhttps://www.slicer.org/wiki/Documentation/Nightly/Modules/PkModelingphantom, clinical datayHuang, W., Li, X., Chen, Y., Li, X., Chang, M.-C., Oborski, M. J., … Kalpathy-Cramer, J. (2014). Variations of dynamic contrast-enhanced magnetic resonance imaging in evaluation of breast cancer therapy response: a multicenter data analysis challenge. Translational Oncology, 7(1), 153–66. doi:10.1593/tlo.13838 http://dx.doi.org/10.1593/tlo.13838abstain
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IB NeuroImaging Biometricslaura.bell@barrowneuro.orgnyn/aMacOShttps://www.imagingbiometrics.com/what-we-offer/product-services/ib-neuro/
DSConly have experience so far with clinicalPlugin for OsiriXDICOMDICOMyn
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DCEMRI.jlDavid Smith, Vanderbilt U.andrey.fedorov@gmail.comnJulianot platform-specificMIT
https://github.com/davidssmith/DCEMRI.jl
nDCEno constraints per sestand-aloneMatlabMatlabny
https://github.com/davidssmith/DCEMRI.jl
phantom, clinical dataySmith DS, Li X, Arlinghaus LR, Yankeelov TE, Welch EB. 2015. DCEMRI.jl: a fast, validated, open source toolkit for dynamic contrast enhanced MRI analysis. PeerJ 3:e909https://doi.org/10.7717/peerj.909
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DCE@urLabJ.E. Ortuñoandrey.fedorov@gmail.comynIDLRequires IDL (commercial environment)not specifiedhttp://www2.die.upm.es/im/archives/DCEurLAB/?requires IDL, Windows only??GUI??y?http://www2.die.upm.es/im/archives/DCEurLAB/??Ortuño, J. E., Ledesma-Carbayo, M. J., Simões, R. V., Candiota, A. P., Arús, C. & Santos, A. DCE@urLAB: a dynamic contrast-enhanced MRI pharmacokinetic analysis tool for preclinical data. BMC Bioinformatics 14, 316 (2013).
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dcemriS4andrey.fedorov@gmail.comR
https://cran.r-project.org/web/packages/dcemriS4/index.html
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pydcemriandrey.fedorov@gmail.compython
https://github.com/welcheb/pydcemri
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DSC-MRI toolboxMarco CastellaroYNMatLabMultiOShttps://github.com/marcocastellaro/dsc-mri-toolbox?MatlabDSCBothStand alone MatLab scriptsNiftiNiftiYYNoY simulations and clinica dataYNot yet
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QuantiphyseQuBiC group, Nottingam (formerly Oxford)martin.craig@eng.ox.ac.uk
michael.chappell@eng.ox.ac.uk
YPotentially via Oxford University InnovationPythonCross platformApache 2 for core application and generic plugins. Specialised plugins licensed under 'free for non commercial use' academic licensehttps://github.com/ibme-qubic/quantiphyseYes, via Oxford University Innovation (however lags behind current version)Some components (including perfusion tools) require FSL, although core application does notASL, DCE, DSC, qBOLDNo constraintsCore application with pluginsNifti. Limited DICOM importNiftiYYquantiphyse.readthedocs.ioSome limited validation for DCE using digital phantomsYCEST plugin described in:
Croal, Paula & Msayib, Yunus & Ray, Kevin & Craig, Martin & Chappell, Michael. (2018). QuantiCEST: Bayesian Model-based Analysis of CEST MRI.
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