tag:joss.theoj.org,2005:/papers/tagged/fMRIJournal of Open Source Software2023-09-17T18:20:22ZJournal of Open Source Softwarehttps://joss.theoj.orgtag:joss.theoj.org,2005:Paper/45632023-09-17T18:20:22Z2023-09-18T00:01:06ZSimulated Diffusion in Realistic Imaging Features of Tissue (Sim-DRIFT)acceptedv1.0.02023-06-25 16:14:13 UTC892023-09-17 18:20:22 UTC820235621JacobBlumWashington University in St. Louis, USA0000-0002-4156-4094KainenL.UttWashington University in St. Louis, USA0000-0002-8555-900010.21105/joss.05621https://doi.org/10.5281/zenodo.8351982Pythonhttps://joss.theoj.org/papers/10.21105/joss.05621.pdfDiffusion MRI, Diffusion Tensor Imaging, Biophysics, Monte-Carlo Simulation, CUDAtag:joss.theoj.org,2005:Paper/42622023-05-11T08:31:02Z2023-05-12T00:01:06ZfRAT: an interactive, Python-based tool for region-of-interest summaries of functional imaging dataaccepted1.0.02023-02-24 14:54:52 UTC852023-05-11 08:31:02 UTC820235200ElliotHowleySchool of Psychology, University of Nottingham, Nottingham, United Kingdom0000-0002-3868-2516SusanFrancisSir Peter Mansfield Imaging Centre, University of Nottingham, Nottingham, United Kingdom, NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham, United Kingdom0000-0003-0903-7507DenisSchluppeckSchool of Psychology, University of Nottingham, Nottingham, United Kingdom0000-0002-0634-771310.21105/joss.05200https://doi.org/10.5281/zenodo.7877605Python, JavaScripthttps://joss.theoj.org/papers/10.21105/joss.05200.pdffMRI, Neuroscience, Nipype, Pipelinetag:joss.theoj.org,2005:Paper/39612023-01-30T10:25:42Z2023-01-31T12:33:59ZFijiRelax: Fast and noise-corrected estimation of MRI relaxation maps in 3D + tacceptedv4.0.22022-10-14 14:29:38 UTC812023-01-30 10:25:42 UTC820234981RomainFernandezCIRAD, UMR AGAP Institut, F-34398 Montpellier, France, AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France.0000-0003-3670-044XCedricMoisyIFV, French Institute of Vine and Wine, UMT Géno-Vigne, UMR AGAP, F-34398 Montpellier, France.0000-0003-4637-471310.21105/joss.04981https://doi.org/10.5281/zenodo.7554691Java, MATLAB, Pythonhttps://joss.theoj.org/papers/10.21105/joss.04981.pdfFiji, Image analysis, MRI, Relaxometry, Phenotypingtag:joss.theoj.org,2005:Paper/34632022-08-05T18:36:00Z2022-08-06T02:57:34ZOpen-Source Hypothalamic-ForniX (OSHy-X) Atlases and Segmentation Tool for 3T and 7Tacceptedv0.32022-04-11 01:36:26 UTC762022-08-05 18:36:00 UTC720224368JerynChangSchool of Biomedical Sciences, The University of Queensland0000-0002-6659-365XFrederikSteynSchool of Biomedical Sciences, The University of Queensland, Department of Neurology, Royal Brisbane and Women's Hospital, Australia, Wesley Medical Research, The Wesley Hospital, UQ Centre for Clinical Research, The University of Queensland0000-0002-4782-3608ShyuanNgoDepartment of Neurology, Royal Brisbane and Women's Hospital, Australia, Wesley Medical Research, The Wesley Hospital, UQ Centre for Clinical Research, The University of Queensland, Australian Institute of Bioengineering and Nanotechnology, The University of Queensland0000-0002-1388-2108RobertHendersonDepartment of Neurology, Royal Brisbane and Women's Hospital, Australia, Wesley Medical Research, The Wesley Hospital, UQ Centre for Clinical Research, The University of Queensland0000-0002-2820-8183ChristineGuoActiGraph, LLC, Pensacola, FL, USASteffenBollmannCentre for Advanced Imaging, The University of Queensland, School of Information Technology and Electrical Engineering, The University of Queensland0000-0002-2909-0906JurgenFrippCSIRO Health and Biosecurity, The Australian eHealth Research Centre, Brisbane, Australia0000-0001-9705-0079MarkusBarthCentre for Advanced Imaging, The University of Queensland, School of Information Technology and Electrical Engineering, The University of Queensland0000-0002-0520-1843ThomasShawDepartment of Neurology, Royal Brisbane and Women's Hospital, Australia, Centre for Advanced Imaging, The University of Queensland, School of Information Technology and Electrical Engineering, The University of Queensland0000-0003-2490-053210.21105/joss.04368https://doi.org/10.5281/zenodo.6874987Pythonhttps://joss.theoj.org/papers/10.21105/joss.04368.pdfDocker, Apptainer, ANTs, MRI, Segmentation, Multi-atlas label fusiontag:joss.theoj.org,2005:Paper/33882022-06-27T08:46:45Z2022-06-28T00:00:45ZConnectome Mapper 3: A Flexible and Open-Source Pipeline Software for Multiscale Multimodal Human Connectome Mappingacceptedv3.0.32022-02-22 08:28:10 UTC742022-06-27 08:46:45 UTC720224248SebastienTourbierRadiology Department, Centre Hospitalier Universitaire Vaudois and University of Lausanne (CHUV-UNIL), Switzerland0000-0002-4441-899XJoanRue-QueraltRadiology Department, Centre Hospitalier Universitaire Vaudois and University of Lausanne (CHUV-UNIL), Switzerland0000-0002-9595-4557KatharinaGlombBerlin Institute of Health at Charité; Department of Neurology with Experimental Neurology, Brain Simulation Section, Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany0000-0002-4596-4386YasserAleman-GomezRadiology Department, Centre Hospitalier Universitaire Vaudois and University of Lausanne (CHUV-UNIL), Switzerland0000-0001-6067-8639EmelineMullierRadiology Department, Centre Hospitalier Universitaire Vaudois and University of Lausanne (CHUV-UNIL), Switzerland0000-0001-6209-0791AlessandraGriffaDepartment of Clinical Neurosciences, Division of Neurology, Geneva University Hospitals and Faculty of Medicine, University of Geneva, Geneva, Switzerland, Institute of Bioengineering, Center of Neuroprosthetics, École Polytechnique Fédérale De Lausanne (EPFL), Geneva, Switzerland0000-0003-1923-1653MikkelSchöttnerRadiology Department, Centre Hospitalier Universitaire Vaudois and University of Lausanne (CHUV-UNIL), Switzerland0000-0002-4521-9837JonathanWirsichEEG and Epilepsy Unit, University Hospitals and Faculty of Medicine of Geneva, University of Geneva, Geneva, Switzerland0000-0003-0588-9710M.AnılTuncelBlue Brain Project, École polytechnique fédérale de Lausanne (EPFL), Campus Biotech, Geneva, Switzerland0000-0003-0317-2556JakubJancovicFoxight, Geneva, Switzerland0000-0002-3312-3918MeritxellBachCuadraCIBM Center for Biomedical Imaging, Lausanne, Switzerland, Radiology Department, Centre Hospitalier Universitaire Vaudois and University of Lausanne (CHUV-UNIL), Switzerland0000-0003-2730-4285PatricHagmannRadiology Department, Centre Hospitalier Universitaire Vaudois and University of Lausanne (CHUV-UNIL), Switzerland0000-0002-2854-656110.21105/joss.04248https://doi.org/10.5281/zenodo.6645256Pythonhttps://joss.theoj.org/papers/10.21105/joss.04248.pdfneuroscience, pipeline, workflow, connectome, multi-scale, MRI, BIDS, BIDS App, containerized workflows, nipypetag:joss.theoj.org,2005:Paper/34172022-05-30T22:45:05Z2022-05-31T00:01:36ZDIRECT: Deep Image REConstruction Toolkitacceptedv1.0.12022-03-09 18:05:29 UTC732022-05-30 22:45:05 UTC720224278GeorgeYiasemisNetherlands Cancer Institute, University of AmsterdamNikitaMoriakovNetherlands Cancer Institute, Radboud University Medical CenterDimitriosKarkalousosAmsterdam UMC, Biomedical Engineering and PhysicsMatthanCaanAmsterdam UMC, Biomedical Engineering and PhysicsJonasTeuwenNetherlands Cancer Institute, University of Amsterdam, Radboud University Medical Center10.21105/joss.04278https://doi.org/10.5281/zenodo.6594702Pythonhttps://joss.theoj.org/papers/10.21105/joss.04278.pdfPytorch, Deep Learning, Inverse Problem Solver, Image Processing, Deep MRI reconstruction, Accelerated MRItag:joss.theoj.org,2005:Paper/24792021-10-12T08:03:44Z2021-10-13T00:01:46ZTE-dependent analysis of multi-echo fMRI with tedanaaccepted0.0.92021-03-09 18:22:31 UTC662021-10-12 08:03:44 UTC620213669ElizabethDuPreMcGill University0000-0003-1358-196XTaylorSaloFlorida International University0000-0001-9813-3167ZakiAhmedMayo Clinic0000-0001-5648-0590PeterA.BandettiniNational Institutes of Health0000-0001-9038-4746KatherineL.BottenhornFlorida International University0000-0002-7796-8795CésarCaballero-GaudesBasque Center on Cognition, Brain and Language0000-0002-9068-5810LoganT.DowdleCenter for Magnetic Resonance Research, University of Minnesota0000-0002-1879-705XJavierGonzalez-CastilloNational Institutes of Health0000-0002-6520-5125StephanHeunisEindhoven University of Technology0000-0003-3503-9872PrantikKunduMount Sinai Hospital0000-0001-9367-3068AngelaR.LairdFlorida International University0000-0003-3379-8744RossMarkelloMcGill University0000-0003-1057-1336ChristopherJ.MarkiewiczStanford University0000-0002-6533-164XStefanoMoiaBasque Center on Cognition, Brain and Language0000-0002-2553-3327IslaStadenThought Machine0000-0002-0795-1154JoshuaB.TevesNational Institutes of Health0000-0002-7767-0067EnekoUruñuelaBasque Center on Cognition, Brain and Language0000-0001-6849-9088MaryamVaziri-PashkamNational Institutes of Health0000-0003-1830-2501KirstieWhitakerAlan Turing Institute0000-0001-8498-4059DanielA.HandwerkerNational Institutes of Health0000-0001-7261-404210.21105/joss.03669https://doi.org/10.5281/zenodo.5541689Pythonhttps://joss.theoj.org/papers/10.21105/joss.03669.pdffMRI, neuroimagingtag:joss.theoj.org,2005:Paper/28192021-10-07T16:51:02Z2021-10-08T00:03:15ZMadym: A C++ toolkit for quantitative DCE-MRI analysisacceptedv4.15.02021-06-24 13:38:50 UTC662021-10-07 16:51:02 UTC620213523MichaelBerksQuantitative Biomedical Imaging Laboratory, Division of Cancer Sciences, Manchester, UK0000-0003-4727-2006GeoffJ mParkerCentre for Medical Image Computing, University College London, London, UK, Bioxydyn Ltd, Manchester, UK0000-0003-2934-2234RossLittleQuantitative Biomedical Imaging Laboratory, Division of Cancer Sciences, Manchester, UKSueCheungQuantitative Biomedical Imaging Laboratory, Division of Cancer Sciences, Manchester, UK10.21105/joss.03523https://doi.org/10.5281/zenodo.5554771C++, Chttps://joss.theoj.org/papers/10.21105/joss.03523.pdfDCE-MRI, tracer-kinetic models, pharmacokineticstag:joss.theoj.org,2005:Paper/28272021-10-07T15:41:14Z2021-10-08T00:03:14ZRadial Interstices Enable Speedy Low-volume Imagingacceptedv0.42021-06-29 14:32:59 UTC662021-10-07 15:41:14 UTC620213500TobiasC.WoodDepartment of Neuroimaging, King's College London0000-0001-7640-5520EmilLjungbergDepartment of Neuroimaging, King's College London0000-0003-1456-7967FlorianWiesingerDepartment of Neuroimaging, King's College London, GE Healthcare0000-0002-5597-605710.21105/joss.03500https://doi.org/10.5281/zenodo.5552973C++, Python, Matlabhttps://joss.theoj.org/papers/10.21105/joss.03500.pdfmri, reconstruction, ZTE, cpptag:joss.theoj.org,2005:Paper/25582021-08-04T22:32:12Z2021-08-05T00:02:46ZFURY: advanced scientific visualizationacceptedmaster2021-04-08 17:33:10 UTC642021-08-04 22:32:12 UTC620213384EleftheriosGaryfallidisDepartment of Intelligent Systems Engineering, Luddy School of Informatics, Computing and Engineering, Indiana University, Bloomington, IN, USA0000-0002-3991-2774SergeKoudoroDepartment of Intelligent Systems Engineering, Luddy School of Informatics, Computing and Engineering, Indiana University, Bloomington, IN, USA0000-0002-9819-9884JavierGuajeDepartment of Intelligent Systems Engineering, Luddy School of Informatics, Computing and Engineering, Indiana University, Bloomington, IN, USA0000-0003-3534-3794Marc-AlexCôtéMicrosoft Research, Montreal, Canada0000-0002-5147-7859SohamBiswasDepartment of Computer Science and Engineering, Institute of Engineering and Management, Kolkata, India0000-0002-8449-2107DavidReaganAdvanced Visualization Lab, University Information Technology Services, Indiana University, Bloomington, IN, USA0000-0002-8359-7580NasimAnoushehDepartment of Intelligent Systems Engineering, Luddy School of Informatics, Computing and Engineering, Indiana University, Bloomington, IN, USA0000-0002-5931-7753FilipiSilvaNetwork Science Institute, Indiana University, Bloomington, IN, USA0000-0002-9151-6517GeoffreyFoxDepartment of Intelligent Systems Engineering, Luddy School of Informatics, Computing and Engineering, Indiana University, Bloomington, IN, USA0000-0003-1017-1391FuryContributorsAnywhere in the Universe10.21105/joss.03384https://doi.org/10.5281/zenodo.5160945PowerShell, Python, GLSLhttps://joss.theoj.org/papers/10.21105/joss.03384.pdfscientific visualization, 3D rendering, Shaders, Vulkan