From 388c599d4af8f42f84c7443a804ee2c1921a3ff7 Mon Sep 17 00:00:00 2001 From: Luis Torres Date: Sat, 6 Jun 2026 16:55:46 -0400 Subject: [PATCH 1/5] migrate content from ismrm webpage --- docs/about.md | 71 +++++++++++++++++ docs/aslliterature.md | 64 +++++++++++++++ docs/contributors.md | 168 +++++++++++++++++++++++++++++++++++++++ docs/dceliterature.md | 57 +++++++++++++ docs/dscliterature.md | 76 ++++++++++++++++++ docs/emb.md | 53 ++++++++++++ docs/getting-started.md | 18 +++-- docs/gsoc.md | 48 +++++++++++ docs/index.md | 6 +- docs/ismrmabstracts.md | 22 +++++ docs/news.md | 91 +++++++++++++++++++++ docs/osipipapers.md | 20 +++++ docs/overrides/home.html | 2 +- docs/publications.md | 15 ++++ docs/strategy-board.md | 21 +++++ docs/taskforces.md | 97 ++++++++++++++++++++-- docs/tf/tf1-1.md | 26 ++++++ docs/tf/tf1-2.md | 17 ++++ docs/tf/tf2-2.md | 23 ++++++ docs/tf/tf2-3.md | 33 ++++++++ docs/tf/tf2-4.md | 25 ++++++ docs/tf/tf3-1.md | 6 ++ docs/tf/tf3-2.md | 17 ++++ docs/tf/tf4-1.md | 31 ++++++++ docs/tf/tf4-2.md | 29 +++++++ docs/tf/tf5-1.md | 14 ++++ docs/tf/tf5-2.md | 32 ++++++++ docs/tf/tf6-1.md | 30 +++++++ docs/tf/tf6-2.md | 34 ++++++++ mkdocs.yml | 34 +++++++- 30 files changed, 1163 insertions(+), 17 deletions(-) create mode 100644 docs/about.md create mode 100644 docs/aslliterature.md create mode 100644 docs/contributors.md create mode 100644 docs/dceliterature.md create mode 100644 docs/dscliterature.md create mode 100644 docs/emb.md create mode 100644 docs/gsoc.md create mode 100644 docs/ismrmabstracts.md create mode 100644 docs/news.md create mode 100644 docs/osipipapers.md create mode 100644 docs/publications.md create mode 100644 docs/strategy-board.md create mode 100644 docs/tf/tf1-1.md create mode 100644 docs/tf/tf1-2.md create mode 100644 docs/tf/tf2-2.md create mode 100644 docs/tf/tf2-3.md create mode 100644 docs/tf/tf2-4.md create mode 100644 docs/tf/tf3-1.md create mode 100644 docs/tf/tf3-2.md create mode 100644 docs/tf/tf4-1.md create mode 100644 docs/tf/tf4-2.md create mode 100644 docs/tf/tf5-1.md create mode 100644 docs/tf/tf5-2.md create mode 100644 docs/tf/tf6-1.md create mode 100644 docs/tf/tf6-2.md diff --git a/docs/about.md b/docs/about.md new file mode 100644 index 0000000..43742fb --- /dev/null +++ b/docs/about.md @@ -0,0 +1,71 @@ +# About OSIPI + +The Open Science Initiative for Perfusion Imaging (ISMRM OSIPI) is an initiative of the [ISMRM Perfusion Study Group](https://www.ismrm.org/study-groups/perfusion-mr/). OSIPI develops open access resources and best practices for the analysis of perfusion imaging data and the interoperability of analysis results. + +## Why? + +At different times in our careers, we all struggled to find robust perfusion analysis software producing results of known quality, and to evaluate or implement perfusion tools. We want to make that process easier. + +## Who? + +We are an inclusive team of volunteers with the expertise and passion for perfusion analysis, open source software, and reproducible science. + +## What? + +We aim to create open access resources for perfusion imaging research to eliminate duplicate development, to improve reproducibility, and to speed up the translation of perfusion imaging for clinical practice. + +!!! info "When was OSIPI founded?" + The project was founded in the fall of 2018 by trainee representative Laura Bell and secretary Steven Sourbron. + + An initial call-to-action survey of the study group membership revealed a strong demand for an initiative around perfusion software. Over 100 members returned a questionnaire with detailed information on data, software, and other possible contributions. + + A founding board organised during and after the ISMRM 2019 and drafted more detailed plans including the project website and logo, communication channels, governance structure, and mission statement. + + The plans were accepted by the ISMRM Perfusion study group and the ISMRM president and president-elect in November 2019. The operational phase of OSIPI was launched on December 1, 2019. OSIPI has no predefined end date and is designed to evolve as the need for coordinated perfusion analysis development changes. + + Read more about the road to OSIPI in this [letter to the editor](https://doi.org/10.1002/mrm.29736) published in MRM. + +!!! note "OSIPI founding board" + Laura Bell, Patricia Clement, Charlotte Debus, Andrey Fedorov, Simon Levy, Steven Sourbron, and Frank Zoellner. + +## The six aims + +The work in OSIPI is planned around six specific aims: + +- Building a software inventory +- A library of code snippets +- A data inventory +- Reporting guidelines +- Education and exchange +- Benchmarking + +The aims are delivered by one or more [Task Forces](taskforces.md), each led by a (senior) task force co-lead and a (junior) co-lead appointed for a period of 2 years. + +## Who is leading OSIPI? + +OSIPI is led by a management team of 4 members (past chair, chair, co-chair, secretary). Each is appointed for 1 year with a rotation at the annual meeting of the ISMRM, when a new secretary is nominated by the current management team and the past chair rotates off. The current management team consists of: + +| Name | Role | +| --- | --- | +| Yuriko Suzuki | Chair | +| Petra van Houdt | Co-chair | +| Ben Dickie | Secretary | +| Henk-Jan Mutsaerts | Past-chair | + +## How can I join OSIPI? + +The ongoing workplan is summarised in the [OSIPI Roadmap 2 2023-2025](https://docs.google.com/document/d/e/2PACX-1vQqOATrWE2COIXq4qTkEe1Bix26GVr_-YTKUJbevCPXXFJf_nMKH3_Nw3DMsY2BcZHPKBG3EOg4SU4r/pub). + +We are always looking for help. If you want to contribute to a particular task force, please get in touch with the appropriate task force lead directly. The names and contact details are on the task force pages. If you want to contribute but are unsure where, or your ideas are outside the remit of any given task force, please contact a member of the OSIPI management team. + +## How is OSIPI managed? + +The task force leads together with the management team form the [Executive and Management Board (EMB)](emb.md). The EMB defines a 2-year roadmap with detailed deliverables and milestones for each of the task forces, and monitors their implementation. The EMB reports back to the ISMRM perfusion study group ahead of each study group meeting at the ISMRM. + +The mission and overall Strategic Plan of OSIPI is revised and updated on an annual basis by the [Strategy Board](strategy-board.md). The Strategy Board consists of the OSIPI management team, the governance committee of the perfusion study group, and representatives of other societies with a stake in perfusion imaging, such as the [Quantitative Imaging Biomarker Alliance (QIBA)](https://www.rsna.org/research/quantitative-imaging-biomarkers-alliance). + +For more details on the way OSIPI is organised, please refer to the [OSIPI Strategic Plan](https://drive.google.com/file/d/14XZYB59W2rn5NIMBKEwdzht23WLa3zzN/view?usp=sharing) and the [governance document](https://drive.google.com/file/d/1fH0hFBMJsUctdhhBmv1ujGI-9v5Bwe3k/view?usp=sharing). + +!!! note "Resources" + - Zenodo community: [zenodo.org/communities/ismrm-osipi](https://zenodo.org/communities/ismrm-osipi/) + - GitHub organisation: [github.com/OSIPI](https://github.com/OSIPI) diff --git a/docs/aslliterature.md b/docs/aslliterature.md new file mode 100644 index 0000000..6034fde --- /dev/null +++ b/docs/aslliterature.md @@ -0,0 +1,64 @@ +# ASL Recommended Literature + +Key manuscripts in perfusion MRI, curated by OSIPI Task Force 5.2 for those getting started. + + +## Seminal Papers + +- John A. Detre, John S. Leigh, Donald S. Williams, Alan P. Koretsky. [Perfusion Imaging](https://doi.org/10.1002/mrm.1910230106) +- Kim SG. [Quantification of relative cerebral blood flow change by flow-sensitive alternating inversion recovery (FAIR) technique: application to functional mapping.](https://doi.org/10.1002/mrm.1910340303) +- Alsop DC, Detre JA. [Reduced transit-time sensitivity in noninvasive magnetic resonance imaging of human cerebral blood flow. J Cereb Blood Flow Metab.1996; Nov;16(6):1236-49.](https://doi.org/10.1097/00004647-199611000-00019) +- Edelman RR, Chen Q. [EPISTAR MRI: multislice mapping of cerebral blood flow. Magn Reson Med. 1998 Dec;40(6):800-5.](https://doi.org/10.1002/mrm.1910400603) +- Wong EC, et al. [Velocity-selective arterial spin labeling. Magn Reson Med. 2006 Jun;55(6):1334-41.](https://doi.org/10.1002/mrm.20906) +- Buxton RB, Frank LR, Wong EC, et al. [A general kinetic model for quantitative perfusion imaging with arterial spin labeling. Magn Reson Med ; 1998; 40:383–396.](https://doi.org/10.1002/mrm.1910400308) +- Wong EC, et al. [Quantitative imaging of perfusion using a single subtraction (QUIPSS and QUIPSS II). Magn Reson Med. 1998 May;39(5):702-8.](https://doi.org/10.1002/mrm.1910390506) + +## Labeling Methods + +- Maccotta L, Detre JA, Alsop DC. [The efficiency of adiabatic inversion for perfusion imaging by arterial spin labeling. NMR Biomed 1997; 10: 216– 221](https://doi.org/10.1002/(SICI)1099-1492(199706/08)10:4/5<216::AID-NBM468>3.0.CO;2-U) +- Dai W, Garcia D, De Bazelaire C, Alsop DC. [Continuous flow-driven inversion for arterial spin labeling using pulsed radio frequency and gradient fields. Magn Reson Med 2008; 60:1488–1497](https://doi.org/10.1002/mrm.21790) +- Wong EC. [Vessel-encoded arterial spin-labeling using pseudocontinuous tagging. Magn Reson Med. 2007 Dec;58(6):1086-91.](https://doi.org/10.1002/mrm.21293) +- Jia Guo, Shaurov Das, and Luis Hernandez‐Garcia. ["Comparison of velocity‐selective arterial spin labeling schemes." Magnetic Resonance in Medicine 85.4 (2021): 2027-2039.](https://doi.org/10.1002/mrm.28572) +- Wong EC, et al. [Velocity-selective arterial spin labeling. Magn Reson Med. 2006 Jun;55(6):1334-41.](https://doi.org/10.1002/mrm.20906) +- Qin Qin, and Peter CM van Zijl. ["Velocity‐selective‐inversion prepared arterial spin labeling." Magnetic resonance in medicine 76.4 (2016): 1136-1148.](https://doi.org/10.1002/mrm.26010) + +## Readout schemes in ASL + +- Vidorreta M, Wang Z, Chang Y V, et al. [Whole-brain background-suppressed pCASL MRI with 1D-accelerated 3D RARE Stack-Of- Spirals readout. PLoS ONE 12:1–16. 2017](https://doi.org/10.1371/journal.pone.0183762) +- Okell, T. [Combined angiography and perfusion using radial imaging and arterial spin labeling." Magnetic Resonance in Medicine 81.1 (2019): 182-194.](https://doi.org/10.1002/mrm.27366) + +## Modeling + +- Buxton RB, Frank LR, Wong EC, Siewert B, Warach S, Edelman RR. [A general kinetic model for quantitative perfusion imaging with arterial spin labeling. Magn Reson Med; 1998; 40:383–396.](https://doi.org/10.1002/mrm.1910400308) +- Parkes, Laura M. ["Quantification of cerebral perfusion using arterial spin labeling: two‐compartment models." Journal of Magnetic Resonance Imaging: An Official Journal of the International Society for Magnetic Resonance in Medicine 22.6 (2005): 732-736.](https://doi.org/10.1002/jmri.20456) +- Woods, Joseph G., Michael A. Chappell, and Thomas W. Okell. ["Designing and comparing optimized pseudo-continuous arterial spin labeling protocols for measurement of cerebral blood flow." Neuroimage 223 (2020): 117246.](https://doi.org/10.1016/j.neuroimage.2020.117246) + +## The ASL White Paper + +- Alsop DC, et al. [Recommended implementation of arterial spin-labeled perfusion MRI for clinical applications: A consensus of the ISMRM perfusion study group and the european consortium for ASL in dementia. Magn Reson Med 2014; 73:102–116.](https://doi.org/10.1002/mrm.25197) + +## The ASL grey papers + +- Qin Q, et al. [Velocity-selective arterial spin labeling perfusion MRI: A review of the state of the art and recommendations for clinical implementation. Magn Reson Med. 2022;88(4):1528-1547.](https://doi.org/10.1002/mrm.29371) +- Hernandez-Garcia L, et al. [Recent Technical Developments in ASL: A Review of the State of the Art. Magn Reson Med. 2022;88(5):2021-2042](https://doi.org/10.1002/mrm.29381) +- Taso M, et al. [Update on state-of-the-art for arterial spin labeling (ASL) human perfusion imaging outside of the brain. Magn Reson Med. 2023;89(5):1754-1776.](https://doi.org/10.1002/mrm.29609) +- Lindner T, et al. [Current state and guidance on arterial spin labeling perfusion MRI in clinical neuroimaging. Magn Reson Med. 2023;89(5):2024-2047.](https://doi.org/10.1002/mrm.29572) +- Woods J, et al. [Quantitative Cerebral Perfusion MRI using Multi-timepoint Arterial Spin Labeling: Recommendations and Clinical Applications. Magn Reson Med (in review)](https://doi.org/10.1002/mrm.30091) + +## Other recommended papers and educational material + +- Wong EC. An introduction to ASL labeling techniques. J Magn Reson Imaging. 2014 Jul;40(1):1-10. Revised: +- Michael Chappell, Bradley MacIntosh, and Thomas Okell. [​​Introduction to Perfusion Quantification using Arterial Spin Labelling Oxford Neuroimaging Primers](https://doi.org/10.1093/oso/9780198793816.003.0001) +- Grade M et al. [A neuroradiologist’s guide to arterial spin labeling MRI in clinical practice. Neuroradiology. 2015 57:1181–202.](https://doi.org/10.1007/s00234-015-1571-z) +- Clement P et al. [Variability of physiological brain perfusion in healthy subjects - A systematic review of modifiers. Considerations for multi-center ASL studies. J Cereb Blood Flow Metab. 2018 Sep;38(9):1418-1437](https://doi.org/10.1177/0271678X17702156.) +- Aguirre GK, Detre J a., Wang J. [Perfusion fMRI for Functional Neuroimaging. Int Rev Neurobiol 2005; 66:213–236](https://doi.org/10.1016/S0074-7742(05)66007-2) +- Haller S, Zaharchuk G, Thomas DL, Lovblad KO, Barkhof F, Golay X. [Arterial Spin Labeling Perfusion of the Brain: Emerging Clinical Applications. Radiology. 2016 Nov;281(2):337-356.](https://doi.org/10.1148/radiol.2016150789.) +- Odudu A et al. [Arterial spin labelling MRI to measure renal perfusion: a systematic review and statement paper. Nephrol Dial Transplant. 2018 Sep 1;33(suppl_2):ii15-ii21](https://doi.org/10.1093/ndt/gfy180) +- Nery F et al. [Consensus-based technical recommendations for clinical translation of renal ASL MRI. MAGMA. 2020 Feb;33(1):141-161](https://doi.org/10.1007/s10334-019-00800-z) + +## Processing Tools + +- Clement P et al. [ASL-BIDS, the brain imaging data structure extension for arterial spin labeling.](https://doi.org/10.1038/s41597-022-01615-9) +- Clement P et al. [A beginner's guide to arterial spin labeling (ASL) image processing.](https://doi.org/10.3389/fradi.2022.929533) +- Mutsaerts H et al. [ExploreASL: An image processing pipeline for multi-center ASL perfusion MRI studies](https://doi.org/10.1016/j.neuroimage.2020.117031) +- Adebimpe A et al. [ASLPrep: a platform for processing of arterial spin labeled MRI and quantification of regional brain perfusion. Nat Methods 2022 Jun;19(6):683-686.](https://doi.org/10.1038/s41592-022-01458-7) diff --git a/docs/contributors.md b/docs/contributors.md new file mode 100644 index 0000000..ad78598 --- /dev/null +++ b/docs/contributors.md @@ -0,0 +1,168 @@ +# Contributors + +OSIPI is an active group of volunteers with a passion for perfusion analysis, open source software, and reproducible science. We are very grateful for all the efforts of the large group of volunteers that are or have been involved in OSIPI. + +## Do you also want to contribute? + +We always aim to make our community more open and inclusive. It is a great opportunity, particularly for PhD students and early career researchers, to expand your network. Our philosophy is that with little help from a lot of people, we can make large improvements. So even if you have only a little bit of time, your input will be very much appreciated. Please check out our [task force pages](taskforces.md) to see if something fits your interest, or contact us to have a chat about the possibilities. + +Contact us at [ismrmosipi@gmail.com](mailto:ismrmosipi@gmail.com). + +!!! note "Version" + This list is updated after every EMB meeting (current version June 2024). Please contact the management team if your affiliations are incorrect. + +## Current Contributors + +| Name | Institute | Role | Task force(s) | +| --- | --- | --- | --- | +| Ben Dickie | School of Medical Sciences, University of Manchester; Academy, Moss Ln E, Rusholme M14 4PX, United Kingdom | Chair, TF4.2 co-lead | TF4.2 | +| Jan Petr | Helmholtz-Zentrum Dresden-Rossendorf, Dresden, Germany | Co-chair, TF1.1 lead | TF1.1 | +| Lena Václavů | Leiden University Medical Center (LUMC), Leiden, the Netherlands | Secretary | TFx | +| Petra van Houdt | the Netherlands Cancer Institute | Past-chair (Chair 2024); TF5.1 co-lead (past TF 2.3 co-lead) | TF2.3, TF2.4, TF4.2 | +| Yuriko Suzuki | Wellcome Centre for Integrative Neuroimaging, FMRIB, University of Oxford, UK | Past-chair (chair 2023), (past TF4.1 co-lead) | TF4.1; TF3.1 | +| Sudipto Dolui | University of Pennsylvania, Philadelphia, PA, USA | TF1.1 co-lead | TF1.1 | +| Melissa Prah | Medical College of Wisconsin | TF1.2 lead | TF1.2 | +| Maria Mora | Childrens National Hospital, Washington DC, USA | TF2.2 lead | TF2.2 | +| Azeez Adebimpe | Bayer, Whippany, New Jersey, United States | TF2.2 co-lead | TF2.2 | +| Sirisha Tadimalla | Institute of Medical Physics, Faculty of Science, the University of Sydney, Camperdown NSW | TF2.3 lead | TF2.3 | +| Lucy Kershaw | University of Edinburgh | TF2.3 co-lead | TF2.3 | +| Oliver Gurney-Champion | Amsterdam University Medical Center, location AMC, Meibergdreef 9, 1105 AZ Amsterdam | TF2.4 lead (past TF2.3 member) | TF2.4 | +| Oscar Jalnefjord | University of Gothenburg, Gothenburg, Sweden | TF2.4 co-lead | TF2.4 | +| Aaron Oliver-Taylor | Gold Standard Phantoms; 1a Parkway Rise, Sheffield S9 4WQ, United Kingdom | TF3.1 lead | TF3.1 | +| Mu-lan Jen | University of Wisconsin-Madison, Madison, WI, USA | TF3.1 co-lead | TF3.1 | +| David Thomas | UCL Queen Square Institute of Neurology, UK | TF4.1 lead | TF4.1 | +| Patricia Clement | University of Ghent | founding member, TF4.1 co-lead | TF4.1 | +| Ben Dickie | Division of Informatics, Imaging & Data Sciences, University of Manchester, UK | TF4.2 lead | TF4.2 | +| Luis Torres | Flywheel i.o. | TF5.1 lead | TF5.1; TF2.3 | +| Luis Hernandez-Garcia | University of Michigan | TF5.2 lead | TF5.2 | +| Mariam Aboian | Yale University | TF5.2 co-lead | TF5.2 | +| Andre Paschoal | University of Sao Paulo, Brazil | TF6.1 lead | TF6.1 | +| Icaro Oliveira | University Health Network, 190 Elizabeth St, Toronto, ON M5G 2C4, Canada | TF6.1 co-lead | TF6.1 | +| Soudabeh Kargar | Memorial Sloan Kettering Cancer Center New York | TF6.2 lead | TF6.2 | +| Harrison Kim | Ohio University | TF6.2 co-lead | TF6.2 | +| Alberto Vazquez | Center for Biotechnology and Bioengineering, University of Pittsburgh | member | TF5.2 | +| Alex Alfaro Venegas | IMAGENOLOGIA DIAGNOSTICA TERAPEUTICA | member | TF5.2 | +| Amnah Mahroo | Fraunhofer MEVIS, Germany | member | TF3.1; past member 3.2 | +| Anahita Fathi Kazerooni | University of Pennsylvania | member, past TF6.2 lead (2020-2022) | TF6.2 | +| Andrew Jahn | University of Michigan | member | TF5.2 | +| Andrey Fedorov | Harvard Medical School | founding member, past TF3.2 lead | TF4.2 | +| Borna Roohani | Yale University | member | TF5.2 | +| Daan Kuppens | Amsterdam University Medical Center, location AMC, Meibergdreef 9, 1105 AZ Amsterdam | member | TF2.4 | +| David Frey | Functional Magnetic Resonance Imaging Laboratory; Bonisteel Interdisciplinary Research Building (BIRB), 2360 Bonisteel Blvd, Ann Arbor, MI 48109, United States | member | TF5.2 | +| Danny JJ Wang | University of Southern California | member | TF5.2 | +| Dannielle van Dorth | Leiden University Medical Center (LUMC) | member | TF5.2 | +| Dirk Poot | Erasmus MC, Rotterdam | member | TF4.2 | +| Elles Elschot | Faculty of Health, Medicine & Life Sciences - Maastricht University; Universiteitssingel 40, 6229 ER Maastricht | member | TF2.3 | +| Eric Peterson | SRI International, 333 Ravenswood Ave, Menlo Park, CA 94025, United States | member | TF2.4 | +| Eve Shalom | University of Leeds, UK | member | TF6.2 | +| Fatemeh Arzanforoosh | Erasmus University Medical Center | member | TF2.3 | +| Francis Botwe | Clinical Imaging Sciences Centre; Knightsgate Road, Falmer Campus, University of Sussex, Brighton, East Sussex BN1 9RR, United Kingdom | member | TF5.2 | +| Hanliang Xu | Johns Hopkins University | member | TF4.1; GSoC 2024 | +| Henk-Jan Mutsaerts | VU University medical center; De Boelelaan 1117, 1081 HV Amsterdam | past-chair (chair 2022), member | TF2.2 | +| Hongli Fan | The Johns Hopkins School of Medicine, USA | member | TF1.1 | +| Ina Kompan | German Cancer Research Centre (DKFZ), Heidelberg, Germany | member, past TF4.2 lead (2020-2022) | TF4.2 | +| Ingomar Gutmann | University of Vienna | member | TF4.2 | +| Ivan A Rashid | Lund University, Carl-Bertil Laurells gata 9, 20502 Malmö, Sweden | member | TF2.4 | +| James H Holmes | University of Iowa, Iowa City, IA, USA | member, past TF3.1 lead (2020-2022) | TF3.1 | +| Joana Pinto | university of oxford | member | TF6.1 | +| Jonathan Arvidsson | University of Gothenburg | member | TF2.3; TF4.2 | +| Joseph Woods | university of oxford | member | TF6.1 | +| Laura Bell | Genentech, South San Francisco, California | founding member, past-chair (2021) | TF6.2; TF1.2 | +| Leah Henze Bancroft | University of Wisconsin School of Medicine and Public Health | member | TF3.1 | +| Leon Jekel | Yale University | member | TF5.2 | +| Limin Zhou | UT southwestern medical center | member | TF2.2 | +| Lirong Yan | Northwestern University Feinberg School of Medicine; 420 E Superior St, Chicago, IL 60611, United States | member | TF5.2 | +| Manuel Taso | Siemens Healthcare, XJ5V+QJ Broomall, Pennsylvania, USA | member | TF4.1, past member TF2.2 | +| Mareike Buck | Fraunhofer Institute for Digital Medicine MEVIS, Bremen, Germany | member | TF3.1 | +| María A. Fernández Seara | Clinica Universidad de Navarra, Spain | member | TF4.1 | +| Marina Fernandez Garcia | CAMERA MRI Africa | member | TF5.2 | +| Martin Kozar | University of Manchester | member | TF4.2 | +| Mathieu Mach | | member | TF5.2 | +| Maurice Pasternak | University of Toronto, 2109 Medical Sciences Building, 1 King's College Cir, Toronto, ON M5S 1A8, Canada | member | TF1.1 | +| Merel van der Thiel | Maastricht University Medial Center | member | TF2.4 | +| Mia Mojica | | member | TF1.2 | +| Michael Berks | University of Manchester | member | TF2.3 | +| Michael Thrippleton | Centre for Clinical Brain Sciences, University of Edinburgh, UK | member, past TF2.3 lead (2020-2022) | TF2.3; TF4.2 | +| Mohamed Nasser | Cairo University Rd, Oula, Al Giza, Giza Governorate 3725121, Egypt | member; GSoC student | TF5.1 | +| Molly Bright | Northwestern University Feinberg School of Medicine; 420 E Superior St, Chicago, IL 60611, United States | member | TF5.2 | +| Moss Zhao | Stanford university | member | TF6.1 | +| Olivia Jones | Division of Informatics, Imaging & Data Sciences, University of Manchester, UK | member | TF4.2; TF5.2 | +| Paulien Voorter | Maastricht University Medial Center | member | TF2.4 | +| Rianne van der Heijden | Erasmus University Rotterdam | member, past TF4.2 co-lead | TF4.2; TF5.2 | +| Safa Hoodeshenas | Department of Radiology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA | member | TF6.2 | +| Sarah Jacobs | UMC Utrecht | member | TF5.2 | +| Sarah Johnson | Radiology and Imaging Sciences, University of Utah | member | TF2.4; TF3.1 | +| Siddharth Sahu | Plaksha University, India | member | TF2.2 | +| Sriranga Kashyap | Techna Institute, University Health Network, Toronto, Canada | member | TF6.1 | +| Steven Sourbron | the University of Sheffield | founding member, OSIPI chair (2020) | TF2.3; TF6.2 | +| Sudarshan Ragunathan | Hyperfine - Guilford | member | TF2.3 | +| Thomas Lindner | University Hospital Hamburg-Eppendorf, Germany | member | TF4.1 | +| Vera Keil | Amsterdam University Medical Center, the Netherlands | member | TF1.1 | +| Weiying Dai | State University of New York at Binghamton, USA | member | TF4.1 | +| Xingfeng Shao | University of Southern California, USA | member | TF4.1 | +| Yeva Prysiazhniuk | Institute of Physiology, the Czech Academy of Sciences | member | TF1.1 | +| Yifan Shuai | The Johns Hopkins University School of Medicine; 733 N Broadway, Baltimore, MD 21205, United States | member | TF2.2; GSoC 2024 | +| Yu Sun | Institute of Medical Physics, Faculty of Science, the University of Sydney, Camperdown NSW | member | TF2.3 | +| Yu-Feng (Erin) Wang | Institute of Medical Physics, Faculty of Science, the University of Sydney, Camperdown NSW | member | TF2.3 | +| Zaki Ahmed | Corewell William Beaumont University Hospital; GR85+8M Royal Oak, Michigan, USA | founding member, member | TF2.3; TF4.2; TF6.2 | +| Zhiliang Wei | The Johns Hopkins University School of Medicine; 733 N Broadway, Baltimore, MD 21205, United States | member | TF2.2 | +| Usman Akinyemi | Plaksha University, India | member | GSoC 2025 | +| Rohan Kumar Mahato | Indian Institute of Technology Guwahati, Guwahatie, Assam, India | member | GSoC 2025 | +| Tongxin (Elo) Li | Cornell Tech, New York, NY, United States | member | GSoC 2025 | + +## Past Contributors + +| Name | Institute | Role | Years | +| --- | --- | --- | --- | +| Ananth Madhuranthakam | UT Southwestern, TX, USA | past TF2.2 lead | 2020-2022 | +| Annette van der Toorn | University Medical Center Utrecht, The Netherlands | TF3.2 | 2020-2022 | +| Beatriz Asenjo Garcia | Regional University Hospital of Málaga, Spain | TF3.2 | 2020-2022 | +| Ben Ellingson | University of California, Los Angeles | TF2.3 | 2020-2022 | +| Cassandra Gould Van Praag | University of Oxford | TF6.1 | 2020-2022 | +| Chad Quarles | Barrow Neurological Institute, Phoenix, AZ | past TF3.1 lead | 2020-2022 | +| Charlotte Buchanan | University of Nottingham | TF1.1 | 2020-2022 | +| Charlotte Debus | Karlsruhe Institute of Technology | founding member, TF4.2 | 2019-2022 | +| David Buckley | University of leeds | past TF4.2 lead | 2020-2022 | +| David Clunie | PixelMed Publishing, Bangor, PA | TF4.2 | 2020-2022 | +| Diego Pineda-Ordóñez | Clínica del Country, Bogotá, Colombia | TF6.1 | 2020-2022 | +| Fábio Nery | University college London | TF2.1 | 2020-2022 | +| Federico Pineda | University of Chicago | TF2.3; TF3.2 | 2020-2022 | +| Felix Navarro | Regional University Hospital of Málaga, Spain | TF3.2 | 2020-2022 | +| Flora Kennedy McConnell | University of Nottingham | TF6.1 | 2020-2022 | +| Frank Zoellner | Ruprecht-Karls-Universität Heidelberg, Grabengasse, Heidelberg, Germany | founding member | 2019-2020 | +| Greg Cron | Harvard Medical School | past TF3.2 co-lead | 2020-2022 | +| Ives Levesque | McGill University - Faculty of Medicine | TF1.2 | 2020-2022 | +| Joao Almeida e Sousa | department of infection and immunity, the University of Sheffield, UK | TF2.1 | 2020-2022 | +| Kathleen Schmainda | biophysics, medical college of wisconsin | past TF1.2 lead | 2020-2022 | +| Li Zhao | Zhejiang University | past TF2.2 co-lead | 2020-2022 | +| Lutz Lüdemann | Universitätsklinikum Essen, Germany | TF3.2 | 2020-2022 | +| Lydiane Hirschler | Leiden University medical center | TF1.1 | 2020-2022 | +| Maria-Eleni Dounavi | department of psychiatry, university of cambridge, Herchel Smith Bldg, Robinson Way, Cambridge CB2 0SZ, United Kingdom | TF6.1 | 2020-2022 | +| Martin Craig | University of Oxford | TF2.1; TF2.3 | 2020-2022 | +| Matthias Schabel | Oregon Health & Science University, Portland, United States | TF2.1 | 2020-2021 | +| Patrick Hales | University College of London | TF2.2 | 2020-2021 | +| Pauline Hall Barrientos | MRI physics Royal Hospital for Children, NHS Greater Glasgow and Clyde | TF3.2 | 2020-2022 | +| Pieter Vandemaele | Ghent university | TF6.1 | 2020-2022 | +| Ralf Floca | German cancer research center | TF4.2 | 2020-2022 | +| Rebeca Echeverria Chasco | Universidad Pública de Navarra | TF2.1; TF2.2 | 2020-2022 | +| Reyna Patel | Northwestern University, IL | TF6.2 | 2020-2022 | +| Samuel Barnes | Loma Linda University | TF2.3 | 2020-2022 | +| Seyed Ali Nabavizadeh | Penn State Materials Research Institute | TF6.2 | 2020-2022 | +| Simon Levy | Center for Magnetic Resonance in Biology and Medicine, Aix-Marseille University | Founding member, past TF2.1 co-lead | 2019-2021 | +| Udunna Anazodo | MNI, McGill University, Montreal | past TF6.1 co-lead | 2020-2022 | +| Melissa Prah | Medical College of Wisconsin | past TF1.2 lead | 2020-2022 | +| Yiming Wang | Philips, China, Shanghai, Minhang District | TF2.2 | 2020-2023 | +| Beatriz Padrela | Amsterdam University Medical Center, location VUmc | TF1.1 | 2020-2022 | +| Enrico de Vita | St Thomas' Hospital, Westminster Bridge Road, London, SE1 7EH | TF1.1 | 2020-2022 | +| Hamidreza Saligheh Rad | Tehran University of Medical Sciences, Iran | TF6.2 | 2020-2023 | +| Hu Leland | Mayo Clinic Comprehensive Cancer Center, Phoenix Arizona | TF6.2 | 2020-2023 | +| Jochen Hirsch | Fraunhofer MEVIS, Germany | TF3.1; TF3.2 | 2020-2023 | +| Jorge Espinoza Abud | Bankaya, Mexico City | TF2.2 | 2020-2023 | +| Mueez Waqar | The University of Manchester | TF1.2 | 2023 | +| Nick Dowell | Brighton and Sussex Medical School, Clinical Imaging Sciences Centre (CISC), University of Sussex, Brighton, BN1 9RR | TF2.3 | 2023 | +| Eve Shalom | Sheffield University | TF6.2 | 2020-2023 | +| Ahmed Basem | Fayoum University | TF2.4; GSoC 2024 | 2024 | +| Mohamed Nasser | Cairo University Rd, Oula, Al Giza, Giza Governorate 3725121, Egypt | TF5.1; GSoC 2024 | 2024 | + +!!! note "OSIPI founding board" + Laura Bell, Patricia Clement, Charlotte Debus, Andrey Fedorov, Simon Levy, Steven Sourbron, and Frank Zoellner. diff --git a/docs/dceliterature.md b/docs/dceliterature.md new file mode 100644 index 0000000..80d0cea --- /dev/null +++ b/docs/dceliterature.md @@ -0,0 +1,57 @@ +# DCE Recommended Literature + +Key manuscripts in perfusion MRI, curated by OSIPI Task Force 5.2 for those getting started. + + +## Text Books + +- Editors: Hai-Ling Margaret Cheng, ‪Gustav J. Strijkers. Quantitative Perfusion MRI: Techniques, Applications and Practical Considerations. First edition. August 22, 2023. ISBN: 9780323952095 +- Editor: Paul Tofts. [Quantitative MRI of the Brain: Measuring Changes Caused by Disease, chapter 11. First published August 2003.](https://doi.org/10.1002/0470869526) +- Lippincott Williams and Wilkins. MR and CT Perfusion and Pharmacokinetic Imaging: Clinical Applications and Theoretical Principles. First Edition. May 11, 2016. ISBN-10 ‏ : ‎ 1451147155 +- Nicole Seiberlich, Vikas Gulani, Adrienne Campbell-Washburn, Steven Sourbron, Mariya Ivanova Doneva, Fernando Calamante, Houchun Harry Hu. Quantitative Magnetic Resonance Imaging. Of Series: Advances in Magnetic Resonance Technology and Applications. Section 2: Perfusion and Permeability, Chapters 11&13, Volume 1. First Edition, December 10, 2020. ISBN-10 ‏ : ‎ 0128170573 +- Donald W. McRobbie, Elizabeth A. Moore, Martin J. Graves, Martin R. Prince. [MRI from Picture to Proton. 2nd Edition. October 2009. Cambridge University Press](https://doi.org/10.1017/CBO9780511545405) +- Malcolm H. Levitt. Spin Dynamics: Basics of Nuclear Magnetic Resonance, 2nd Edition. March 2008. ISBN: 978-0-470-51117-6 + +## General Overview + +- Sourbron SP, Buckley DL. [On the scope and interpretation of the Tofts models for DCE-MRI. Magn Reson Med. 2011 Sep;66(3):735-45.](https://doi.org/10.1002/mrm.22861) +- Cuenod CA, Balvay D. [Perfusion and vascular permeability: basic concepts and measurement in DCE-CT and DCE-MRI. Diagn Interv Imaging. 2013 Dec;94(12):1187-204.](https://doi.org/10.1016/j.diii.2013.10.010) +- Khalifa F, Soliman A, El-Baz A, Abou El-Ghar M, El-Diasty T, Gimel'farb G, Ouseph R, Dwyer AC. [Models and methods for analyzing DCE-MRI: a review. Med Phys. 2014 Dec;41(12):124301.](https://doi.org/10.1118/1.4898202) +- Quarles CC, Bell LC, Stokes AM. [Imaging vascular and hemodynamic features of the brain using dynamic susceptibility contrast and dynamic contrast enhanced MRI. Neuroimage. 2019 Feb 15;187:32-55.](https://doi.org/10.1016/j.neuroimage.2018.04.069) +- Dyke JP, Aaron RK. [Noninvasive methods of measuring bone blood perfusion. Ann N Y Acad Sci. 2010 Mar;1192(1):95-102.](https://doi.org/10.1111/j.1749-6632.2009.05376.x) +- Lohrke, J., Frenzel, T., Endrikat, J., Alves, F. C., Grist, T. M., Law, M., Lee, J. M., Leiner, T., Li, K.-C., Nikolaou, K., Prince, M. R., Schild, H. H., Weinreb, J. C., Yoshikawa, K., & Pietsch, H. [25 Years of Contrast-Enhanced MRI: Developments, Current Challenges and Future Perspectives. Advances in Therapy, 33(1), 1–28.](https://doi.org/10.1007/s12325-015-0275-4) +- Koh, T. S., Bisdas, S., Koh, D. M., & Thng, C. H. [Fundamentals of tracer kinetics for dynamic contrast-enhanced MRI. Journal of Magnetic Resonance Imaging, 2011. 34(6), 1262–1276.](https://doi.org/10.1002/jmri.22795) +- Petralia, G., Summers, P. E., Agostini, A., Ambrosini, R., Cianci, R., Cristel, G., Calistri, L., & Colagrande, S. [Dynamic contrast-enhanced MRI in oncology: how we do it. Radiol Med. 2020 Dec;125(12):1288-1300.](https://doi.org/10.1007/s11547-020-01220-z) +- Hanson, L. G. [Introduction to Magnetic Resonance Imaging Techniques. 2009](https://eprints.drcmr.dk/37/) +- Hanson, L. G. [The Ups and Downs of Classical and Quantum Formulations of Magnetic Resonance. In Anthropic Awareness: The Human Aspects of Scientific Thinking in NMR Spectroscopy and Mass Spectrometry (pp. 141–171). Elsevier Inc. 2015](https://doi.org/10.1016/B978-0-12-419963-7.00003-1) + +## Seminal Papers + +- Tofts PS. [Modeling tracer kinetics in dynamic Gd-DTPA MR imaging. J Magn Reson Imaging. 1997 Jan-Feb;7(1):91-101.](https://doi.org/10.1002/jmri.1880070113) +- Tofts PS, Brix G, Buckley DL, Evelhoch JL, Henderson E, Knopp MV, Larsson HB, Lee TY, Mayr NA, Parker GJ, Port RE, Taylor J, Weisskoff RM. [Estimating kinetic parameters from dynamic contrast-enhanced T(1)-weighted MRI of a diffusable tracer: standardized quantities and symbols. J Magn Reson Imaging. 1999 Sep;10(3):223-32.](https://doi.org/10.1002/(SICI)1522-2586(199909)10:3%3C223::AID-JMRI2%3E3.0.CO;2-S) +- Brix G, Semmler W, Port R, Schad LR, Layer G, Lorenz WJ. [Pharmacokinetic parameters in CNS Gd-DTPA enhanced MR imaging. J Comput Assist Tomogr. 1991 Jul-Aug;15(4):621-8.](https://doi.org/10.1097/00004728-199107000-00018) +- Parker GJ, Roberts C, Macdonald A, Buonaccorsi GA, Cheung S, Buckley DL, Jackson A, Watson Y, Davies K, Jayson GC. [Experimentally-derived functional form for a population-averaged high-temporal-resolution arterial input function for dynamic contrast-enhanced MRI. Magn Reson Med. 2006 Nov;56(5):993-1000.](https://doi.org/10.1002/mrm.21066) +- Rohrer M, Bauer H, Mintorovitch J, Requardt M, Weinmann HJ. [Comparison of magnetic properties of MRI contrast media solutions at different magnetic field strengths. Invest Radiol. 2005 Nov;40(11):715-24.](https://doi.org/10.1097/01.rli.0000184756.66360.d3) + +## Clinical Applications + +- Dijkhoff RAP, Beets-Tan RGH, Lambregts DMJ, Beets GL, Maas M. [Value of DCE-MRI for staging and response evaluation in rectal cancer: A systematic review. Eur J Radiol. 2017 Oct;95:155-168.](https://doi.org/10.1016/j.ejrad.2017.08.009) +- Thrippleton MJ, Backes WH, Sourbron S, Ingrisch M, van Osch MJP, Dichgans M, Fazekas F, Ropele S, Frayne R, van Oostenbrugge RJ, Smith EE, Wardlaw JM. [Quantifying blood-brain barrier leakage in small vessel disease: Review and consensus recommendations. Alzheimers Dement. 2019 Jun;15(6):840-858.](https://doi.org/10.1016/j.jalz.2019.01.013) +- Dickie BR, Parker GJM, Parkes LM. [Measuring water exchange across the blood-brain barrier using MRI. Prog Nucl Magn Reson Spectrosc. 2020 Feb;116:19-39.](https://doi.org/10.1016/j.pnmrs.2019.09.002) +- O’Connor, J. P. B., Aboagye, E. O., Adams, J. E., Aerts, H. J. W. L., Barrington, S. F., Beer, A. J., Boellaard, R., Bohndiek, S. E., Brady, M., Brown, G., Buckley, D. L., Chenevert, T. L., Clarke, L. P., Collette, S., Cook, G. J., deSouza, N. M., Dickson, J. C., Dive, C., Evelhoch, J. L., … Waterton, J. C. [Imaging biomarker roadmap for cancer studies. Nat Rev Clin Oncol. 2017 Mar;14(3):169-186](https://doi.org/10.1038/nrclinonc.2016.162) +- Alonzi, R., Padhani, A.R. and Allen, C. [Dynamic contrast enhanced MRI in prostate cancer. Eur J Radiol. 2007 Sep;63(3):335-50.](https://doi.org/10.1016/j.ejrad.2007.06.028) +- Thng, C. H., Koh, T. S., Collins, D. J., & Koh, D. M. [Perfusion magnetic resonance imaging of the liver. World Journal of Gastroenterology](https://doi.org/10.3748/wjg.v16.i13.1598) +- Teo, Q. Q., Thng, C. H., Koh, T. S., & Ng, Q. S. [Dynamic Contrast-enhanced Magnetic Resonance Imaging: Applications in Oncology. Clin Oncol (R Coll Radiol). 2014 Oct;26(10):e9-20.](https://doi.org/10.1016/j.clon.2014.05.014) + +## Acquisition + +- QIBA MR Biomarker Committee, Quantitative Imaging Biomarkers Alliance. [MR DCE-MRI Quantification (DCEMRI-Q), 2020.](http://qibawiki.rsna.org/index.php/Profiles) + +## Analysis + +- Sourbron SP, Buckley DL. [Classic models for dynamic contrast-enhanced MRI. NMR Biomed. 2013 Aug;26(8):1004-27.](https://doi.org/10.1002/nbm.2940) +- Sourbron SP, Buckley DL. [Tracer kinetic modelling in MRI: estimating perfusion and capillary permeability. Phys Med Biol. 2012 Jan 21;57(2):R1-33.](https://doi.org/10.1088/0031-9155/57/2/R1) +- Ingrisch, M., Sourbron, S. [Tracer-kinetic modeling of dynamic contrast-enhanced MRI and CT: a primer. J Pharmacokinet Pharmacodyn 2013 Jun;40(3):281-300.](https://doi.org/10.1007/s10928-013-9315-3) +- Kim H. Variability in Quantitative DCE-MRI: Sources and Solutions. J Nat Sci. 2018;4(1):e484. PMID: https://pubmed.ncbi.nlm.nih.gov/29527572 +- Calamante F. [Arterial input function in perfusion MRI: a comprehensive review. Prog Nucl Magn Reson Spectrosc. 2013 Oct;74:1-32.](https://doi.org/10.1016/j.pnmrs.2013.04.002) +- Hanson, E. A., Sandmann, C., Malyshev, A., Lundervold, A., Modersitzki, J., & Hodneland, E. [Estimating the discretization dependent accuracy of perfusion in coupled capillary flow measurements. PLoS One. 2018 Jul 20;13(7):e0200521.](https://doi.org/10.1371/journal.pone.0200521) diff --git a/docs/dscliterature.md b/docs/dscliterature.md new file mode 100644 index 0000000..b0a4ad9 --- /dev/null +++ b/docs/dscliterature.md @@ -0,0 +1,76 @@ +# DSC Recommended Literature + +Key manuscripts in perfusion MRI, curated by OSIPI Task Force 5.2 for those getting started. + + +## Text books + +- Editor: Paul Tofts. [Quantitative MRI of the Brain: Measuring Changes Caused by Disease, chapter 11. First published August 2003.](https://doi.org/10.1002/0470869526) +- Peter B. Barker, Xavier Golay and Gregory Zaharchuk. [Clinical Perfusion MRI: Techniques and Applications. Cambridge University Press. Online publication date May 2013.](https://doi.org/10.1017/CBO9781139004053) +- Saremi, Farhood. Perfusion Imaging in Clinical Practice: A Multimodality Approach to Tissue Perfusion Analysis. Lippincott Williams & Wilkins (LWW). First edition. 2015 ISBN: 9781451193169 +- Editors: Hai-Ling Margaret Cheng, ‪Gustav J. Strijkers. Quantitative Perfusion MRI: Techniques, Applications and Practical Considerations. First edition. August 22, 2023. ISBN: 9780323952095 + +## Review papers + +- Zaharchuk G. [Theoretical basis of hemodynamic MR imaging techniques to measure cerebral blood volume, cerebral blood flow, and permeability. AJNR Am J Neuroradiol. 2007 Nov-Dec;28(10):1850-8.](https://doi.org/10.3174/ajnr.A0831) +- Calamante F. [Perfusion MRI using dynamic-susceptibility contrast MRI: quantification issues in patient studies. Top Magn Reson Imaging. 2010 Apr;21(2):75-85.](https://doi.org/10.1097/RMR.0b013e31821e53f5) +- McGehee BE, Pollock JM, Maldjian JA. [Brain perfusion imaging: How does it work and what should I use? J Magn Reson Imaging. 2012 Dec;36(6):1257-72.](https://doi.org/10.1002/jmri.23645) +- Willats L, Calamante F. [The 39 steps: evading error and deciphering the secrets for accurate dynamic susceptibility contrast MRI. NMR in Biomedicine. 2013.](https://doi.org/10.1002/nbm.2833) +- Essig M, Shiroishi MS, Nguyen TB, Saake M, Provenzale JM, Enterline D, Anzalone N, Dörfler A, Rovira A, Wintermark M, Law M. [Perfusion MRI: the five most frequently asked technical questions. AJR Am J Roentgenol. 2013 Jan;200(1):24-34.](https://doi.org/10.2214/AJR.12.9543) +- Jahng GH, Li KL, Ostergaard L, Calamante F. [Perfusion magnetic resonance imaging: a comprehensive update on principles and techniques. Korean J Radiol. 2014 Sep-Oct;15(5):554-77.](https://doi.org/10.3348/kjr.2014.15.5.554) +- Welker K, Boxerman J, Kalnin A, Kaufmann T, Shiroishi M, Wintermark M. [ASFNR recommendations for clinical performance of MR dynamic susceptibility contrast perfusion imaging of the brain. American Society of Functional Neuroradiology MR Perfusion Standards and Practice Subcommittee of the ASFNR Clinical Practice Committee. AJNR Am J Neuroradiol. 2015 Jun;36(6):E41-51.](https://doi.org/10.3174/ajnr.A4341) +- Chakravorty A, Steel T, Chaganti J. [Accuracy of percentage of signal intensity recovery and relative cerebral blood volume derived from dynamic susceptibility-weighted, contrast-enhanced MRI in the preoperative diagnosis of cerebral tumours. Neuroradiol J. 2015 Dec;28(6):574-83.](https://doi.org/10.1177/1971400915611916) +- Shiroishi MS, Castellazzi G, Boxerman JL, D'Amore F, Essig M, Nguyen TB, Provenzale JM, Enterline DS, Anzalone N, Dörfler A, Rovira À, Wintermark M, Law M. [Principles of T2 *-weighted dynamic susceptibility contrast MRI technique in brain tumor imaging. J Magn Reson Imaging. 2015 Feb;41(2):296-313.](https://doi.org/10.1002/jmri.24648) +- Fu R, Szidonya L, Barajas RF Jr, Ambady P, Varallyay C, Neuwelt EA. [Diagnostic performance of DSC perfusion MRI to distinguish tumor progression and treatment-related changes: a systematic review and meta-analysis. Neurooncol Adv. 2022 Mar 1;4(1):vdac027.](https://doi.org/10.1093/noajnl/vdac027) + +## Acquisition and image readout strategies for DSC + +- Simonsen CZ, Ostergaard L, Smith DF, Vestergaard-Poulsen P, Gyldensted C. [Comparison of gradient- and spin-echo imaging: CBF, CBV, and MTT measurements by bolus tracking. J Magn Reson Imaging. 2000 Sep;12(3):411-6.](https://doi.org/10.1002/1522-2586(200009)12:3%3C411::AID-JMRI6%3E3.0.CO;2-5) +- Skinner JT, Robison RK, Elder CP, Newton AT, Damon BM, Quarles CC. [Evaluation of a multiple spin- and gradient-echo (SAGE) EPI acquisition with SENSE acceleration: applications for perfusion imaging in and outside the brain. Magn Reson Imaging. 2014 Dec;32(10):1171-80.](https://doi.org/10.1016/j.mri.2014.08.032) +- Stokes AM, Quarles CC. [A Simplified Spin and Gradient Echo Approach for Brain Tumor Perfusion Imaging. MRM. 2016.](https://doi.org/10.1002/mrm.25591) +- Bell LC, Does MD, Stokes AM, Baxter LC, Schmainda KM, Dueck AC, Quarles CC. [Optimization of DSC MRI Echo Times for CBV Measurements Using Error Analysis in a Pilot Study of High-Grade Gliomas. AJNR Am J Neuroradiol. 2017 Sep;38(9):1710-1715.](https://doi.org/10.3174/ajnr.A5295) +- Schmainda KM, Prah MA, Hu LS, Quarles CC, Semmineh N, Rand SD, Connelly JM, Anderies B, Zhou Y, Liu Y, Logan B, Stokes A, Baird G, Boxerman JL. [Moving Toward a Consensus DSC-MRI Protocol: Validation of a Low-Flip Angle Single-Dose Option as a Reference Standard for Brain Tumors. AJNR Am J Neuroradiol. 2019 Apr;40(4):626-633.](https://doi.org/10.3174/ajnr.A6015) +- Boxerman JL, Quarles CC, Hu LS, Erickson BJ, Gerstner ER, Smits M, Kaufmann TJ, Barboriak DP, Huang RH, Wick W, Weller M, Galanis E, Kalpathy-Cramer J, Shankar L, Jacobs P, Chung C, van den Bent MJ, Chang S, Al Yung WK, Cloughesy TF, Wen PY, Gilbert MR, Rosen BR, Ellingson BM, Schmainda KM. [Consensus recommendations for a dynamic susceptibility contrast MRI protocol for use in high-grade gliomas. Neuro Oncol. 2020 Sep 29;22(9):1262-1275.](https://doi.org/10.1093/neuonc/noaa141) +- Han M, Yang B, Fernandez B, Lafontaine M, Alcaide-Leon P, Jakary A, Burns BL, Morrison MA, Villanueva-Meyer JE, Chang SM, Banerjee S, Lupo JM. [Simultaneous multi-slice spin- and gradient-echo dynamic susceptibility-contrast perfusion-weighted MRI of gliomas. NMR in Biomedicine. 2021.](https://doi.org/10.1002/nbm.4399) +- Stokes AM, Bergamino M, Alhilali L, Hu LS, Karis JP, Baxter LC, Bell LC, Quarles CC. [Evaluation of single bolus, dual-echo dynamic susceptibility contrast MRI protocols in brain tumor patients. JCBFM. 2021.](https://doi.org/10.1177/0271678X211039597) +- Stokes AM, Ragunathan S, Robison RK, Fuentes A, Bell LC, Karis JP, Pipe JG, Quarles CC. [Development of a spiral spin- and gradient- echo (spiral- SAGE) approach for improved multi- parametric dynamic contrast neuroimaging. MRM. 2021.](https://doi.org/10.1002/mrm.28933) + +## (Clinical) applications of DSC imaging + +- Rempp KA, Brix G, Wenz F, Becker CR, Gückel F, Lorenz WJ. Quantification of regional cerebral blood flow and volume with dynamic susceptibility contrast-enhanced MR imaging. Radiology. 1994 Dec;193(3):637-41. +- Nasel C, Boubela R, Kalcher K, Moser E. [Normalised time-to-peak-distribution curves correlate with cerebral white matter hyperintensities – Could this improve early diagnosis? J Cereb Blood Flow Metab. 2017 Feb;37(2):444-455.](https://doi.org/10.1177/0271678X16629485) +- Law M, Young R, Babb J, Pollack E, Johnson G. Histogram Analysis versus Region of Interest Analysis of Dynamic Susceptibility Contrast Perfusion MR Imaging Data in the Grading of Cerebral Gliomas. AJNR Am J Neuroradiol. 2007 Apr;28(4):761-6. +- Schmainda KM, Zhang Z, Prah M, Snyder BS, Gilbert MR, Sorensen AG, Barboriak DP, Boxerman JL. [Dynamic susceptibility contrast MRI measures of relative cerebral blood volume as a prognostic marker for overall survival in recurrent glioblastoma: results from the ACRIN 6677/RTOG 0625 multicenter trial. Neuro Oncol. 2015 Aug;17(8):1148-56.](https://doi.org/10.1093/neuonc/nou364) +- Zhang J, Liu H, Tong H, Wang S, Yang Y, Liu G, Zhang W. [Clinical Applications of Contrast-Enhanced Perfusion MRI Techniques in Gliomas: Recent Advances and Current Challenges. Contrast Media Mol Imaging. 2017 Mar 20;2017:7064120.](https://doi.org/10.1155/2017/7064120) +- Patel P, Baradaran H, Delgado D, Askin G, Christos P, John Tsiouris A, Gupta A. [MR perfusion-weighted imaging in the evaluation of high-grade gliomas after treatment: a systematic review and meta-analysis. Neuro Oncol. 2017 Jan;19(1):118-127.](https://doi.org/10.1093/neuonc/now148) +- Hempel JM, Schittenhelm J, Klose U, Bender B, Bier G, Skardelly M, Tabatabai G, Castaneda Vega S, Ernemann U, Brendle C. [In Vivo Molecular Profiling of Human Glioma : Cross-Sectional Observational Study Using Dynamic Susceptibility Contrast Magnetic Resonance Perfusion Imaging. Clin Neuroradiol. 2019 Sep;29(3):479-491.](https://doi.org/10.1093/neuonc/nou364) +- Choi KS, Choi SH, Jeong B. [Prediction of IDH genotype in gliomas with dynamic susceptibility contrast perfusion MR imaging using an explainable recurrent neural network. Neuro Oncol. 2019 Sep 6;21(9):1197-1209.](https://doi.org/10.1093/neuonc/noz095) +- Quarles CC, Bell LC, Stokes AM. [Imaging vascular and hemodynamic features of the brain using dynamic susceptibility contrast and dynamic contrast enhanced MRI. Neuroimage. 2019 Feb 15;187:32-55.](https://doi.org/10.1016/j.neuroimage.2018.04.069) +- Chakhoyan A, Yao J, Leu K, Pope WB, Salamon N, Yong W, Lai A, Nghiemphu PL, Everson RG, Prins RM, Liau LM, Nathanson DA, Cloughesy TF, Ellingson BM. [Validation of vessel size imaging (VsI) in high-grade human gliomas using magnetic resonance imaging, image-guided biopsies, and quantitative immunohistochemistry. Sci Rep 9, 2846 (2019).](https://doi.org/10.1038/s41598-018-37564-w) +- Ozturk K, Soylu E, Cayci Z. [Correlation between dynamic susceptibility contrast perfusion MRI and genomic alterations in glioblastoma. Neuroradiology. 2021 Nov;63(11):1801-1810.](https://doi.org/10.1007/S00234-021-02674-2) +- Quan G, Zhang K, Liu Y, Ren JL, Huang D, Wang W, Yuan T. [Role of Dynamic Susceptibility Contrast Perfusion MRI in Glioma Progression Evaluation. J Oncol. 2021 Feb 9;2021:1696387.](https://doi.org/10.1155/2021/1696387) +- Anil A, Stokes AM, Chao R, Hu LS, Alhilali L, Karis JP, Bell LC, Quarles CC. [Identification of single-dose, dual-echo based CBV threshold for fractional tumor burden mapping in recurrent glioblastoma. Front Oncol. 2023 Jan 17;13:1046629.](https://doi.org/10.3389/fonc.2023.1046629) + +## Modeling of contrast agent induced MR signal changes + +- Boxerman JL, Hamberg LM, Rosen BR, Weisskoff RM. [MR contrast due to intravascular magnetic susceptibility perturbations. Magn Reson Med. 1995 Oct;34(4):555-66.](https://doi.org/10.1002/mrm.1910340412) +- Ostergaard L, Weisskoff RM, Chesler DA, Gyldensted C, Rosen BR. [High resolution measurement of cerebral blood flow using intravascular tracer bolus passages. Part I: Mathematical approach and statistical analysis. Magn Reson Med. 1996 Nov;36(5):715-25.](https://doi.org/10.1002/mrm.1910360510) +- Ostergaard L, Sorensen AG, Kwong KK, Weisskoff RM, Gyldensted C, Rosen BR. [High resolution measurement of cerebral blood flow using intravascular tracer bolus passages. Part II: Experimental comparison and preliminary results. Magn Reson Med. 1996 Nov;36(5):726-36.](https://doi.org/10.1002/mrm.1910360511) +- Kiselev VG. [On the theoretical basis of perfusion measurements by dynamic susceptibility contrast MRI. Magn Reson Med. 2001 Dec;46(6):1113-22.](https://doi.org/10.1002/mrm.1307) +- van Osch MJ, Vonken EJ, Bakker CJ, Viergever MA. [Correcting Partial Volume Artifacts of the Arterial Input Function in Quantitative Cerebral Perfusion MRI. Magn Reson Med. 2001 Mar;45(3):477-85.](https://doi.org/10.1002/1522-2594(200103)45:3%3C477::AID-MRM1063%3E3.0.CO;2-4) +- Wu O, Østergaard L, Weisskoff RM, Benner T, Rosen BR, Sorensen AG. [Tracer arrival timing-insensitive technique for estimating flow in MR perfusion-weighted imaging using singular value decomposition with a block-circulant deconvolution matrix. Magn Reson Med. 2003 Jul;50(1):164-74.](https://doi.org/10.1002/mrm.10522) +- Carroll TJ, Rowley HA, Haughton VM. [Automatic calculation of the arterial input function for cerebral perfusion imaging with MR imaging. Radiology. 2003 May;227(2):593-600.](https://doi.org/10.1148/radiol.2272020092) +- Conturo TE, Akbudak E, Kotys MS, Chen ML, Chun SJ, Hsu RM, Sweeney CC, Markham J. [Arterial Input Functions for Dynamic Susceptibility Contrast MRI: Requirements and Signal Options. J Magn Reson Imaging. 2005 Dec;22(6):697-703.](https://doi.org/10.1002/jmri.20457) +- Bleeker EJ, van Buchem MA, van Osch MJ. [Optimal location for arterial input function measurements near the middle cerebral artery in first-pass perfusion MRI. J Cereb Blood Flow Metab. 2009 Apr;29(4):840-52.](https://doi.org/10.1038/jcbfm.2008.155) +- Calamante F. [Arterial input function in perfusion MRI: a comprehensive review. Prog Nucl Magn Reson Spectrosc. 2013 Oct;74:1-32.](https://doi.org/10.1016/j.pnmrs.2013.04.002) +- Mehndiratta A, Calamante F, MacIntosh BJ, Crane DE, Payne SJ, Chappell MA. [Modeling and correction of bolus dispersion effects in dynamic susceptibility contrast MRI. Magn Reson Med. 2014 Dec;72(6):1762-74.](https://doi.org/10.1002/mrm.25077) +- Newton AT, Pruthi S, Stokes AM, Skinner JT, Quarles CC. [Improving Perfusion Measurement in DSC–MR Imaging with Multiecho Information for Arterial Input Function Determination. AJNR Am J Neuroradiol. 2016 Jul;37(7):1237-43.](https://doi.org/10.3174/ajnr.A4700) + +## Processing and analyzing DSC images + +- Boxerman JL, Schmainda KM, Weisskoff RM. Relative cerebral blood volume maps corrected for contrast agent extravasation significantly correlate with glioma tumor grade, whereas uncorrected maps do not. AJNR Am J Neuroradiol. 2006 Apr;27(4):859-67. +- Jochimsen TH, Newbould RD, Skare ST, Clayton DB, Albers GW, Moseley ME, Bammer R. [Identifying systematic errors in quantitative dynamic-susceptibility contrast perfusion imaging by high-resolution multi-echo parallel EPI. NMR Biomed. 2007 Jun;20(4):429-38.](https://doi.org/10.1002/nbm.1107) +- Quarles CC, Gochberg DF, Gore JC, Yankeelov TE. [A theoretical framework to model DSC-MRI data acquired in the presence of contrast agent extravasation. Phys Med Biol. 2009 Oct 7;54(19):5749-66.](https://doi.org/10.1088/0031-9155/54/19/006) +- Bjørnerud A, Emblem KE. [A fully automated method for quantitative cerebral hemodynamic analysis using DSC-MRI. J Cereb Blood Flow Metab. 2010 May;30(5):1066-78.](https://doi.org/10.1038/jcbfm.2010.4) +- Bell LC, Stokes AM, Quarles CC. [Analysis of postprocessing steps for residue function dependent dynamic susceptibility contrast (DSC)-MRI biomarkers and their clinical impact on glioma grading for both 1.5 and 3T. J. Magn. Reson. Imaging (2019), 51: 547-553.](https://doi.org/10.1002/jmri.26837) +- Hovden IT, Geier OM, Digernes I, Fuster-Garcia E, Løvland G, Vik-Mo E, Meling TR, Emblem KE. [The impact of EPI-based distortion correction of dynamic susceptibility contrast MRI on cerebral blood volume estimation in patients with glioblastoma. Eur J Radiol. 2020 Nov;132:109278.](https://doi.org/10.1016/j.ejrad.2020.109278) diff --git a/docs/emb.md b/docs/emb.md new file mode 100644 index 0000000..04f45ed --- /dev/null +++ b/docs/emb.md @@ -0,0 +1,53 @@ +# Executive & Management Board + +The Executive and Management Board (EMB) of OSIPI is the central body responsible for the execution of the strategic plan and ongoing management of OSIPI. + +## Structure and responsibilities + +The EMB consists of 4 members: past chair, chair, co-chair, secretary. Each is appointed for 1 year with a rotation at the annual meeting of the ISMRM, when a new secretary is nominated and the past chair rotates off. + +The EMB defines a Roadmap that sets out deliverables and milestones, monitors its implementation, and reports back to the [ISMRM Perfusion Study Group](https://www.ismrm.org/study-groups/perfusion-mr/) ahead of the annual ISMRM meeting. + +The EMB consists of the OSIPI leadership team and the (co-)leads of each task force. Meetings are held quarterly. A link to the [meeting minutes](https://drive.google.com/open?id=1zjiT6dmbC7t1Svii_HG6NpYE8iS8bnR-GIf_-m02Fhc) is available. + +!!! info "OSIPI Roadmaps" + - [Roadmap 1 2020-2022](https://docs.google.com/document/d/e/2PACX-1vRbxX9ywttwQfd2hyj62h676RjEZ3YHZBIBTkUmEb2nqOmrRVd-PlWeL6nAsJ79akQpXHmtBIizJiOK/pub) + - [Roadmap 2 2023-2025](https://docs.google.com/document/d/e/2PACX-1vQqOATrWE2COIXq4qTkEe1Bix26GVr_-YTKUJbevCPXXFJf_nMKH3_Nw3DMsY2BcZHPKBG3EOg4SU4r/pub) + - Roadmap 3: work in progress + +## Current EMB members (June 2025) + +| Name | Role | +| --- | --- | +| Ben Dickie | OSIPI chair | +| Jan Petr | OSIPI co-chair | +| Lena Václavů | OSIPI secretary | +| Petra van Houdt | OSIPI past chair | +| Jan Petr | OSIPI Task Force 1.1 Lead | +| Sudipto Dolui | OSIPI Task Force 1.1 Co-lead | +| Maria Mora | OSIPI Task Force 2.2 Lead | +| Azeez Adebimpe | OSIPI Task Force 2.2 Lead | +| Sirisha Tadimalla | OSIPI Task Force 2.3 Lead | +| Lucy Kershaw | OSIPI Task Force 2.3 Co-lead | +| Oliver Gurney-Champion | OSIPI Task Force 2.4 Lead | +| Oscar Jalnefjord | OSIPI Task Force 2.4 Co-lead | +| Aaron Oliver-Taylor | OSIPI Task Force 3.1 Lead | +| Mu-lan Jen | OSIPI Task Force 3.1 Co-lead | +| David Thomas | OSIPI Task Force 4.1 Lead | +| Patricia Clement | OSIPI Task Force 4.1 Co-lead | +| Ben Dickie | OSIPI Task Force 4.2 Lead | +| Luis Torres | OSIPI Task Force 5.1 Lead | +| Luis Hernandez-Garcia | OSIPI Task Force 5.2 Lead | +| Andre Paschoal | OSIPI Task Force 6.1 Lead | +| Icaro Oliveira | OSIPI Task Force 6.1 Co-lead | +| Soudabeh Kargar | OSIPI Task Force 6.2 Lead | +| Harrison Kim | OSIPI Task Force 6.2 Co-lead | + +## Past Leadership + +| Name | Role | +| --- | --- | +| Yuriko Suzuki | OSIPI chair 2023 | +| Henk-Jan Mutsaerts | OSIPI chair 2022 | +| Laura C Bell | OSIPI chair 2021 | +| Steven Sourbron | OSIPI chair 2020 | diff --git a/docs/getting-started.md b/docs/getting-started.md index 88f1173..97029da 100644 --- a/docs/getting-started.md +++ b/docs/getting-started.md @@ -1,9 +1,9 @@ # Getting Started -Welcome to the **OSIPI Documentation Hub** +Welcome to **OSIPI**, the Open Science Initiative for Perfusion Imaging. !!! info "What is OSIPI?" - **OSIPI** (Open Science Initiative for Perfusion Imaging) is an initiative of the ISMRM, aiming to improve transparency, standardization, and reproducibility in perfusion MRI. This site hosts documentation for lexicons, tools, and code repositories developed by OSIPI task forces. + **OSIPI** (Open Science Initiative for Perfusion Imaging) is an initiative of the ISMRM Perfusion Study Group, aiming to improve transparency, standardization, and reproducibility in perfusion MRI. OSIPI develops shared resources — lexicons, code libraries, data inventories, challenges, and education materials — through volunteer task forces. See [About OSIPI](about.md) for the mission, history, and how the initiative is organized. ## Who is this for? @@ -18,12 +18,18 @@ Welcome to the **OSIPI Documentation Hub** ## Start here !!! tip "Explore the key sections" - - 📚 **Lexicons** + - ℹ️ **[About OSIPI](about.md)** + Mission, founding history, leadership, and how the initiative is governed + - 🧭 **[Task Forces](taskforces.md)** + The working groups behind OSIPI's six aims, with leads and ongoing projects + - 📚 **[Lexicons](lexicons.md)** Standardized terminology for ASL and contrast-agent based perfusion MRI - - 🧪 **Code Repositories** + - 🧪 **[Code Repositories](pyCode.md)** Python and MATLAB tools for DCE, DSC, ASL, and IVIM analysis - - 🛠️ **Tools** - Web-based utilities for dataset validation and artifact reporting + - 🛠️ **[Tools](tools.md)** + Web-based utilities for dataset validation and artifact reporting + - 📰 **[News](news.md)** + Announcements, challenges, events, and Google Summer of Code ## Get involved diff --git a/docs/gsoc.md b/docs/gsoc.md new file mode 100644 index 0000000..2956b6c --- /dev/null +++ b/docs/gsoc.md @@ -0,0 +1,48 @@ +# Google Summer of Code + +OSIPI participates in the Google Summer of Code (GSoC) program to expand its contributor base and make its perfusion imaging resources more accessible and easier to use. + +!!! info "About the program" + [Google Summer of Code](https://summerofcode.withgoogle.com/) is an online program that supports junior software developers to contribute to open source software development. + + OSIPI has participated twice in GSoC (2024 and 2025). Many resources have been developed within OSIPI, but they are still in a preliminary state. The current goal is to make these resources more accessible and user-friendly for anyone working with perfusion imaging. This requires input from various professions, from imaging scientists to physicians to software engineers. The OSIPI community currently consists predominantly of scientists and clinicians; by joining GSoC, OSIPI aims to expand its talent pool with summer students who can help solve software-technical challenges, so that OSIPI software works more easily, more robustly, and in a more user-friendly way. + + In 2024, four contributors were matched to OSIPI. This motivated participation again in 2025, when five contributors began working on a variety of projects in May. + +## 2024 Project Reports + +### Methods section generator for ASL + +**Hanliang Xu** created a tool that automatically extracts and generates "ASL parameters" from DICOM and BIDS images. This tool is designed to assist researchers in easily describing standardized imaging parameters in their scientific publications. This work is related to TF4.1. + +See the [tool here](https://osipi.ismrm.org/task-forces/tf4-1/asl-methods-generator/). [Read the full report](https://github.com/Hanliang-Xu/Hanliang-Xu.github.io/blob/main/README.md). + +### Setting up a framework for large-scale development + +**Mohamed Nasser Hussein**'s project prepared OSIPI for large-scale collaborative development and streamlined the integration of various developers' contributions. This work was related to TF2.3, but will have a wider impact for all OSIPI repositories in the future. + +[Read the full report](https://medium.com/@nassermohamed3222/my-google-summer-of-code-2024-journey-with-the-osipi-foundation-b4ad4d738e2d). + +### Translation of ASL code snippets into python + +**Yifan Shuai** worked on the aggregation and translation of existing ASL code snippets to develop a library that is both robust for developers and accessible for users. This work is related to the efforts of TF2.2. + +[Read the full report](https://github.com/Trico01/pyasl/wiki/PyASL_GSoC'24-Final-Report). + +### Interactive visualization dashboard + +**Ahmed Bassem** worked on the development of a data visualization dashboard that serves as an interface to visualize the differences between collected IVIM code snippets. This work is related to ongoing efforts in TF2.4. + +[Read the full report](https://gist.github.com/AhmedBasem20/76c37422dcbd7aab5922b96897188daf). + +## 2025 Projects + +Five projects were granted by GSoC for the 2025 program. Over the summer these contributors are working on the following projects: + +- **Melissa Lange** will work on an addition to the Python package for blood brain barrier analysis (mentors: Ben Dickie, Jan Petr) +- **Elo** will work on the extension of the ASL module for the OSIPI Python package (mentors: Maria Mora, Zhiliang Wei) +- **Ibrahim Abdelazim** will work on the ASL parameter generator (mentors: David Thomas, Jan Petr) +- **Rohan Kumar Mahato** will improve the structure and visibility of the documentation pages of all OSIPI resources (mentors: Luis Torres, Petra van Houdt) +- **Usman Akinyemi** will develop a dockerized data processing pipeline for image analysis (mentors: Eric Peterson, Luis Torres) + +See the [news announcement](https://osipi.ismrm.org/gsoc-2025-5-projects-selected/) for details. diff --git a/docs/index.md b/docs/index.md index 572466b..05bd307 100644 --- a/docs/index.md +++ b/docs/index.md @@ -1,9 +1,9 @@ --- template: home.html -title: OSIPI Documentation Hub +title: OSIPI — Open Science Initiative for Perfusion Imaging social: cards_layout_options: - title: Documentation for OSIPI Repositories + title: Open Science Initiative for Perfusion Imaging --- -Welcome to OSIPI Documentation Hub. +Welcome to OSIPI, the Open Science Initiative for Perfusion Imaging. diff --git a/docs/ismrmabstracts.md b/docs/ismrmabstracts.md new file mode 100644 index 0000000..a615846 --- /dev/null +++ b/docs/ismrmabstracts.md @@ -0,0 +1,22 @@ +# ISMRM Abstracts + +OSIPI-related abstracts presented at ISMRM annual meetings, grouped by year and labeled by the contributing task force. + +## 2021 + +- TF1.1 — ASL software inventory. [ISMRM 2021, abstract 2713](https://cds.ismrm.org/protected/21MProceedings/PDFfiles/2713.html) +- TF6.1 — ISMRM-OSIPI ASL MRI Challenge. [ISMRM 2021, abstract 2714](https://cds.ismrm.org/protected/21MProceedings/PDFfiles/2714.html) +- TF6.2 — DSC/DCE-MRI challenges. [ISMRM 2021, abstract 1094](https://cds.ismrm.org/protected/21MProceedings/PDFfiles/1094.html) + +## 2022 + +- TF2.2 — ASL code collection. [ISMRM 2022, abstract 0914](https://cds.ismrm.org/protected/22MProceedings/PDFfiles/0914.html) +- TF6.1 — ISMRM-OSIPI ASL MRI Challenge. [ISMRM 2022, abstract 0910](https://cds.ismrm.org/protected/22MProceedings/PDFfiles/0910.html) +- TF6.2 — DSC/DCE-MRI challenges. [ISMRM 2022, abstract 0047](https://cds.ismrm.org/protected/22MProceedings/PDFfiles/0047.html) + +## Presentations + +- Petr J. ASL-BIDS and OSIPI Pipeline Inventory. MRI Together, 2022. +- Petr J. OSIPI Inventory of ASL Pipelines. ISMRM Workshop on Perfusion MRI: From Head to Toe, 2022. +- Tadimalla S. OSIPI Experience on Scientific. [MRI Together 2021](https://www.youtube.com/watch?v=yGBiDGBtJGY). +- Berks M. Open Science Initiative for Perfusion Imaging (OSIPI): a global collaboration of researchers committed to improving software in their field. [SeptembRSE 2021](https://youtube.com/watch?v=dk9SzgCCH4s). diff --git a/docs/news.md b/docs/news.md new file mode 100644 index 0000000..bdd575b --- /dev/null +++ b/docs/news.md @@ -0,0 +1,91 @@ +# News + +Updates from the OSIPI community: project launches, Google Summer of Code, workshops, and publications. + +## GSoC 2025: 5 projects selected + +*May 8, 2025* + +Five projects were granted by Google Summer of Code for the 2025 program. Over the summer these contributors will work on the following projects: + +- **Melissa Lange** will work on an addition to the Python package for blood brain barrier analysis (mentors: Ben Dickie, Jan Petr) +- **Elo** will work on the extension of the ASL module for the OSIPI Python package (mentors: Maria Mora, Zhiliang Wei) +- **Ibrahim Abdelazim** will work on the ASL parameter generator (mentors: David Thomas, Jan Petr) +- **Rohan Kumar Mahato** will improve the structure and visibility of the documentation pages of all OSIPI resources (mentors: Luis Torres, Petra van Houdt) +- **Usman Akinyemi** will develop a dockerized data processing pipeline for image analysis (mentors: Eric Peterson, Luis Torres) + +OSIPI received a large number of excellent proposals this year and thanks all candidates for their efforts and interest in the community. + +Read more about the projects on [Program Organization | Google Summer of Code](https://summerofcode.withgoogle.com/), and see the [Google Summer of Code](gsoc.md) page for full project history. + +[Original article](https://osipi.ismrm.org/gsoc-2025-5-projects-selected/) + +## AURA: A Perfusion Imaging Artefact Database + +*March 28, 2025* + +AURA is a new OSIPI project dedicated to building an inventory of perfusion imaging artifacts. The goal is to better understand and address common and perfusion-specific artifacts, ultimately improving imaging quality for the community. + +!!! info "Call for contributions" + Do you work with ASL, DSC, or DCE imaging? If you have examples of artifacts in your perfusion images, you are invited to submit them. To participate, use this link: + +**The AURA team:** Annelie Haek, Patricia Clement, Soetkin Beun, Henk-Jan Mutsaerts, Luis Hernandez-Garcia, Jan Petr, David Thomas + +See also the [Perfusion Artifact Database](tools.md) tool. + +[Original article](https://osipi.ismrm.org/new-aura-a-perfusion-imaging-artefact-database/) + +## OSIPI in Pamplona + +*March 19, 2025* + +OSIPI was well represented at the ISMRM perfusion workshop in Pamplona. Two master students presented their work for the first time at an international workshop: + +- **Annelie Haek** (Ghent University) presented a perfusion imaging artefact database: AURA +- **Mohamed Nasser** (GSoC 2024 student, Egypt) presented the start of the OSIPI Python package + +The IVIM code repository from TF2.4 and the ASL parameter generator (from Hanliang Xu's GSoC 2024 project) were presented in the power pitches. Yuriko presented on standardization and open science in perfusion imaging, including OSIPI in her talk. + +The OSIPI secret session at the end of the official program produced many new ideas that will be used for drafting the third roadmap. + +[Original article](https://osipi.ismrm.org/osipi-in-pamplona/) + +## Google Summer of Code 2024 finished! + +*September 27, 2024* + +The Google Summer of Code 2024 program is complete. Four software engineers worked on projects related to ongoing activities in the task forces, in OSIPI's first experience with the program. + +Read more about the projects and results on the [Google Summer of Code](gsoc.md) page. + +[Original article](https://osipi.ismrm.org/google-summer-of-code-2024-finished/) + +## First OSIPI papers published in MRM! + +*July 5, 2024* + +The first set of OSIPI papers is published as a dedicated section in the May edition of Magnetic Resonance in Medicine. They are also gathered together as a [virtual special issue](https://onlinelibrary.wiley.com/doi/toc/10.1002/(ISSN)1522-2594.OSIPI). These papers are the result of teamwork within several task forces. + +!!! info "Published papers" + **Letter to the editor by OSIPI management:** + + - [The road to the ISMRM OSIPI: A community-led initiative for reproducible perfusion MRI](https://pubmed.ncbi.nlm.nih.gov/37279059/) + + **Software and code:** + + - [ISMRM Open Science Initiative for Perfusion Imaging (OSIPI): ASL pipeline inventory](https://onlinelibrary.wiley.com/doi/10.1002/mrm.29869) — led by Hongli Fan and Jan Petr (TF1.1) + - [Contrast-agent-based perfusion MRI code repository and testing framework: ISMRM Open Science Initiative for Perfusion Imaging (OSIPI)](https://onlinelibrary.wiley.com/doi/full/10.1002/mrm.29826) — led by Petra van Houdt and Michael Thrippleton (TF2.3) + + **Two lexicons:** + + - [ASL lexicon and reporting recommendations: A consensus report from the ISMRM Open Science Initiative for Perfusion Imaging (OSIPI)](https://onlinelibrary.wiley.com/doi/full/10.1002/mrm.29815) — led by Yuriko Suzuki and David Thomas (TF4.1) + - [A community-endorsed open-source lexicon for contrast agent–based perfusion MRI: A consensus guidelines report from the ISMRM Open Science Initiative for Perfusion Imaging (OSIPI)](https://onlinelibrary.wiley.com/doi/full/10.1002/mrm.29840) — led by Ben Dickie and Ina Kompan (TF4.2) + + **Results from the first two OSIPI challenges:** + + - [Reproducibility of arterial spin labeling cerebral blood flow image processing: A report of the ISMRM open science initiative for perfusion imaging (OSIPI) and the ASL MRI challenge](https://onlinelibrary.wiley.com/doi/10.1002/mrm.30081) — led by Andre Paschoal and Udunna Anazodo (TF6.1) + - [The ISMRM Open Science Initiative for Perfusion Imaging (OSIPI): Results from the OSIPI–Dynamic Contrast-Enhanced challenge](https://onlinelibrary.wiley.com/doi/10.1002/mrm.29909) — led by Eve Shalom and Anahita Kazerooni (TF6.2) + +See also the [MRM highlights interview](https://blog.ismrm.org/2024/03/04/qa-with-the-osipi-leadership-laura-bell-ben-dickie-petra-houdt-henk-mutsaerts-and-yuriko-suzuki/). + +[Original article](https://osipi.ismrm.org/first-osipi-papers-published-in-mrm/) diff --git a/docs/osipipapers.md b/docs/osipipapers.md new file mode 100644 index 0000000..7bd8256 --- /dev/null +++ b/docs/osipipapers.md @@ -0,0 +1,20 @@ +# OSIPI Papers + +Peer-reviewed journal articles authored by OSIPI task forces, documenting the inventories, code collections, and challenges developed by the initiative. + +## Peer-reviewed papers + +- Fan H, Mutsaerts HJMM, Anazodo U, Arteaga D, Baas KPA, Buchanan C, Camargo A, Keil VC, Lin Z, Lindner T, Hirschler L, Hu J, Padrela BE, Taghvaei M, Thomas DL, Dolui S, Petr J. ISMRM Open Science Initiative for Perfusion Imaging (OSIPI): ASL pipeline inventory. Magn Reson Med. 2023. doi:[10.1002/mrm.29869](https://doi.org/10.1002/mrm.29869) +- van Houdt PJ, Ragunathan S, Berks M, Ahmed Z, Kershaw LE, Gurney-Champion OJ, Tadimalla S, Arvidsson J, Sun Y, Kallehauge J, Dickie B, Lévy S, Bell L, Sourbron S, Thrippleton MJ. Contrast-agent-based perfusion MRI code repository and testing framework: ISMRM Open Science Initiative for Perfusion Imaging (OSIPI). Magn Reson Med. 2023;1-13. doi:[10.1002/mrm.29826](https://onlinelibrary.wiley.com/doi/full/10.1002/mrm.29826) +- Shalom ES, Kim H, van der Heijden RA, Ahmed Z, Patel R, Hormuth DA 2nd, DiCarlo JC, Yankeelov TE, Sisco NJ, Dortch RD, Stokes AM, Inglese M, Grech-Sollars M, Toschi N, Sahoo P, Singh A, Verma SK, Rathore DK, Kazerouni AS, Partridge SC, LoCastro E, Paudyal R, Wolansky IA, Shukla-Dave A, Schouten P, Gurney-Champion OJ, Jiřík R, Macíček O, Bartoš M, Vitouš J, Das AB, Kim SG, Bokacheva L, Mikheev A, Rusinek H, Berks M, Hubbard Cristinacce PL, Little RA, Cheung S, O'Connor JPB, Parker GJM, Moloney B, LaViolette PS, Bobholz S, Duenweg S, Virostko J, Laue HO, Sung K, Nabavizadeh A, Saligheh Rad H, Hu LS, Sourbron S, Bell LC, Fathi Kazerooni A. The ISMRM Open Science Initiative for Perfusion Imaging (OSIPI): Results from the OSIPI-Dynamic Contrast-Enhanced challenge. Magn Reson Med. 2023 Dec 19. doi:[10.1002/mrm.29909](https://doi.org/10.1002/mrm.29909) +- Suzuki Y, Clement P, Dai W, Dolui S, Fernández-Seara MA, Lindner T, Mutsaerts HJMM, Petr J, Shao X, Taso M, Thomas DL. ASL lexicon and reporting recommendations: A consensus report from the ISMRM Open Science Initiative for Perfusion Imaging (OSIPI). Magn Reson Med. 2023;91(5):1743-1760. doi:[10.1002/mrm.29815](https://doi.org/10.1002/mrm.29815) +- Dickie BR, Ahmed Z, Arvidsson J, Bell LC, Buckley DL, Debus C, Fedorov A, Floca R, Gutmann I, van der Heijden RA, van Houdt PJ, Sourbron S, Thrippleton MJ, Quarles C, Kompan IN. A community-endorsed open-source lexicon for contrast agent–based perfusion MRI: A consensus guidelines report from the ISMRM Open Science Initiative for Perfusion Imaging (OSIPI). Magn Reson Med. 2023;91(5):1761-1773. doi:[10.1002/mrm.29840](https://doi.org/10.1002/mrm.29840) +- Paschoal AM, Woods JG, Pinto J, Bron EE, Petr J, Kennedy McConnell FA, Bell L, Dounavi ME, Gould van Praag C, Mutsaerts HJMM, Oliver Taylor A, Zhao MY, Brumer I, Chan WSM, Toner J, Hu J, Zhang LX, Domingos C, Monteiro SP, Figueiredo P, Harms AGJ, Padrela BE, Tham C, Abdalle A, Croal PL, Anazodo U. Reproducibility of arterial spin labeling cerebral blood flow image processing: A report of the ISMRM open science initiative for perfusion imaging (OSIPI) and the ASL MRI challenge. Magn Reson Med. 2024;92(2):836-852. doi:[10.1002/mrm.30081](https://doi.org/10.1002/mrm.30081) + +## Letter to the editor + +- Bell LC, Suzuki Y, van Houdt PJ, Sourbron S, Mutsaerts HJMM. The road to the ISMRM OSIPI: A community-led initiative for reproducible perfusion MRI. Magn Reson Med. 2023;91(5):1740-1742. doi:[10.1002/mrm.29736](https://doi.org/10.1002/mrm.29736) + +## In preparation / under review + +- Mora Álvarez MG, Zhou L, Wang Y, Zhao L, Dolui S, Taso M, Wang Z, Adebimpe A, Mutsaerts H, Madhuranthakam AJ. The Open Science Initiative for Perfusion Imaging (OSIPI) ASL Processing Code Library. 2023. (To be submitted to Magn Reson Med.) diff --git a/docs/overrides/home.html b/docs/overrides/home.html index 8d71733..25ce1a8 100644 --- a/docs/overrides/home.html +++ b/docs/overrides/home.html @@ -9,7 +9,7 @@
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Documentation for OSIPI Repositories

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Open Science Initiative for Perfusion Imaging

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Let's Explore diff --git a/docs/publications.md b/docs/publications.md new file mode 100644 index 0000000..8fc0144 --- /dev/null +++ b/docs/publications.md @@ -0,0 +1,15 @@ +# Publications + +OSIPI task forces produce peer-reviewed papers and conference contributions documenting their resources, code collections, inventories, and challenges. These are collected on the pages below. + +!!! abstract "OSIPI Papers" + Peer-reviewed journal articles authored by OSIPI task forces. + + 📘 [OSIPI Papers](osipipapers.md) + +!!! abstract "ISMRM Abstracts" + OSIPI-related abstracts presented at ISMRM annual meetings. + + 📘 [ISMRM Abstracts](ismrmabstracts.md) + +A collection of recommended reading is also available for [ASL](aslliterature.md), [DSC](dscliterature.md), and [DCE](dceliterature.md). diff --git a/docs/strategy-board.md b/docs/strategy-board.md new file mode 100644 index 0000000..90727f3 --- /dev/null +++ b/docs/strategy-board.md @@ -0,0 +1,21 @@ +# Strategy Board + +The Strategy Board (SB) represents the stakeholders within OSIPI and maintains the Strategic Plan outlining the mission, aims, and general approach of OSIPI. If needed, the SB will also propose changes to the OSIPI governance for approval by the ISMRM perfusion study group. + +## Composition + +The SB consists of the OSIPI leadership team and representatives from the ISMRM board, ISMRM Perfusion Study Group, and any number of advisory members representing other bodies and societies with an interest in open science and reproducibility. This could include other ISMRM study groups, other societies, or more informal networks. These are currently the perfusion committees of [QIBA RSNA](https://www.rsna.org/research/quantitative-imaging-biomarkers-alliance) (QIBA ASL committee, QIBA DSC committee, and QIBA DCE committee governing committee). + +If you are interested in joining the SB, please contact the OSIPI chair. + +!!! info "Governance documents" + - OSIPI Strategic Plan: [Current version 1.0](https://drive.google.com/file/d/14XZYB59W2rn5NIMBKEwdzht23WLa3zzN/view?usp=sharing) + - OSIPI Governance: [Current version 1.0](https://drive.google.com/open?id=1fH0hFBMJsUctdhhBmv1ujGI-9v5Bwe3k) + +## SB meetings + +| Date | Meeting | +| --- | --- | +| May 2021 | First SB meeting | +| Feb 2023 | Second SB meeting | +| Jan 2024 | Upcoming SB meeting | diff --git a/docs/taskforces.md b/docs/taskforces.md index 74c3ca4..1c7c2bc 100644 --- a/docs/taskforces.md +++ b/docs/taskforces.md @@ -2,10 +2,95 @@ OSIPI's aims are addressed through dedicated Task Forces. The objectives, time plan, leadership, and members of each task force for the years 2026-2028 are defined in the [Roadmap](https://docs.google.com/document/d/1w2JlVK3hP5dgXMcrK8da5z94ivsK8Or__NU9qUR6WRk). More details and contacts are available below. -!!! abstract "Template (TFX.X)" - Description of the Task force +To achieve OSIPI's mission, six specific aims were identified. Each aim is supported by one to three task forces (TF), generally split by non-contrast (arterial spin labeling; ASL) and contrast-agent-based (dynamic susceptibility contrast; DSC; and dynamic contrast enhanced; DCE) perfusion MRI. From the second roadmap, intravoxel incoherent motion (IVIM) was also added. - Task Force leaders: [Name](email@gmail.com), name
- Task Force members:
- [📘 Documentation](https://osipi.github.io/)
- [🧪 GitHub Repository](https://github.com/osipi) +## Aim 1 — Software Inventories + +Inventories and evaluation of available complete perfusion image analysis tools for end-users. + +!!! abstract "TF1.1 — ASL software inventory" + Inventory of publicly available ASL pipelines along with their features, compatibility, and links to manuals and source code. + + [📘 Task Force 1.1 details](tf/tf1-1.md) + +!!! abstract "TF1.2 — DCE/DSC inventory (inactive)" + Inventory of software packages for DCE/DSC image analysis. This task force is currently inactive due to insufficient members. + + [📘 Task Force 1.2 details](tf/tf1-2.md) + +## Aim 2 — Code Libraries + +Develops community-driven open-source code libraries for perfusion imaging analysis. + +!!! abstract "TF2.2 — ASL code contributions" + Code collection of open-source functions, scripts, and in-house pipelines for ASL perfusion imaging analysis. + + [📘 Task Force 2.2 details](tf/tf2-2.md) + +!!! abstract "TF2.3 — DSC/DCE code contributions" + Tested code collection of open-source Python functions for DCE/DSC perfusion imaging analysis. + + [📘 Task Force 2.3 details](tf/tf2-3.md) + +!!! abstract "TF2.4 — IVIM code contributions" + Gathered and tested code for intravoxel incoherent motion (IVIM) analysis, with model fitting code in Python and Matlab. + + [📘 Task Force 2.4 details](tf/tf2-4.md) + +## Aim 3 — Data Inventory + +Inventories with open-access (pre-)clinical or phantom data and digital reference objects (DROs). + +!!! abstract "TF3.1 — Digital Reference Objects and Phantoms" + Inventory of digital reference objects and phantom data for perfusion MRI. + + [📘 Task Force 3.1 details](tf/tf3-1.md) + +!!! abstract "TF3.2 — Clinical and preclinical data (inactive)" + Inventory of freely available clinical and preclinical perfusion MRI data. This task force is currently inactive due to insufficient members. + + [📘 Task Force 3.2 details](tf/tf3-2.md) + +## Aim 4 — Lexicons + +Develop terminology and reporting guidelines for image acquisition and perfusion image analysis. + +!!! abstract "TF4.1 — ASL Lexicon" + Standardized terminology and reporting recommendations for arterial spin labeling imaging. + + [📘 Lexicons overview](lexicons.md)
+ [📘 ASL Lexicon documentation](https://osipi.github.io/ASL-Lexicon/) + +!!! abstract "TF4.2 — DSC/DCE Lexicon (CAPLEX)" + Lexicon of definitions for quantities, models, and analysis methods used in contrast-agent-based perfusion MRI. + + [📘 Lexicons overview](lexicons.md)
+ [📘 CAPLEX documentation](https://osipi.github.io/OSIPI_CAPLEX/) + +## Aim 5 — Exchange and Education platform + +Dissemination of resources through website and educational activities. + +!!! abstract "TF5.1 — Website" + Develops and maintains the OSIPI website for sharing resources with the community. + + [📘 Task Force 5.1](https://osipi.ismrm.org/task-forces/task-force-5-1/) + +!!! abstract "TF5.2 — Education" + Develops educational activities and materials for perfusion imaging. + + [📘 Task Force 5.2](https://osipi.ismrm.org/task-forces/task-force-5-2/) + +## Aim 6 — Challenges + +Develop challenges that compare the performance of perfusion image analysis software. + +!!! abstract "TF6.1 — ASL challenges" + Develops challenges comparing ASL perfusion image analysis software. + + [📘 Task Force 6.1](https://osipi.ismrm.org/task-forces/task-force-6-1/) + +!!! abstract "TF6.2 — DSC/DCE challenges" + Develops challenges comparing DSC/DCE perfusion image analysis software. + + [📘 Task Force 6.2](https://osipi.ismrm.org/task-forces/task-force-6-2/) diff --git a/docs/tf/tf1-1.md b/docs/tf/tf1-1.md new file mode 100644 index 0000000..40de591 --- /dev/null +++ b/docs/tf/tf1-1.md @@ -0,0 +1,26 @@ +# TF1.1 — ASL software inventory + +This task force aims to build an ASL software inventory aimed at end-users looking for a suitable tool to process their ASL images. The inventory lists available open-source and commercial tools, providing information that will help users select a suitable tool, such as scope of application, methodology, level of validation, license policy, transparency, user-friendliness, and reviews by other users. Currently, the task force is focusing on supporting pipeline developers in implementing new features and on helping users to use the pipelines. + +## Leads + +- [Jan Petr](mailto:j.petr@hzdr.de) +- [Sudipto Dolui](mailto:sudiptod@pennmedicine.upenn.edu) + +## Ongoing projects + +This task force is currently expanding the ASL pipeline inventory by including more pipelines, especially the commercial ones, and also pipelines specifically targeted to preclinical data and body ASL other than the brain. Moreover, we are working with the education and web-page task forces on creating new tutorials and ASL-pipeline forums. Finally, we plan to connect and support pipeline developers to facilitate implementation of the ASL-BIDS standard and non-brain and pre-clinical functionality to major public ASL pipelines. If you want to know more details about our projects, please check out the [roadmap](https://docs.google.com/document/d/1FzOFMV420xew2oiSDq4Wi3tRZ45if73Rw-6at2hKNFw/edit#bookmark=id.beor3bs2cwsa). + +## Publications + +- Jan Petr. [ASL-BIDS and OSIPI Pipeline Inventory](https://www.youtube.com/live/4wsEodepyI8?si=kpfczDCG40tCbWuF). MRI Together, 2022. +- Jan Petr. OSIPI Inventory of ASL Pipelines. ISMRM Workshop on Perfusion MRI: From Head to Toe, 2022. +- ISMRM abstract 2021 — [cds.ismrm.org/protected/21MProceedings/PDFfiles/2713.html](https://cds.ismrm.org/protected/21MProceedings/PDFfiles/2713.html) +- Hongli Fan, Henk J. M. M. Mutsaerts, Udunna Anazodo, Daniel Arteaga, Koen P. A. Baas, Charlotte Buchanan, Aldo Camargo, Vera C. Keil, Zixuan Lin, Thomas Lindner, Lydiane Hirschler, Jian Hu, Beatriz E. Padrela, Mohammad Taghvaei, David L. Thomas, Sudipto Dolui, Jan Petr, ISMRM Open Science Initiative for Perfusion Imaging (OSIPI): ASL pipeline inventory, Magn Reson Med. 2023, doi: [https://doi.org/10.1002/mrm.29869](https://doi.org/10.1002/mrm.29869) + +## Resources + +!!! abstract "ASL software inventory" + The inventory contains the list of publicly available ASL pipelines along with their features, compatibility, and links to manuals and source code. + + [📘 Check out the ASL software inventory](https://docs.google.com/document/d/e/2PACX-1vQ-1GF2fmz6Q4IukuKP_-57H-xi872Xq_uBlX5P0Cwpj4RYd_t73pvZ64UqXegPaVpQJhQQrVRJRPro/pub) diff --git a/docs/tf/tf1-2.md b/docs/tf/tf1-2.md new file mode 100644 index 0000000..203e8f1 --- /dev/null +++ b/docs/tf/tf1-2.md @@ -0,0 +1,17 @@ +# TF1.2 — DCE/DSC inventory + +The goal of this task force is to develop a comprehensive inventory of software packages for DCE/DSC imaging analysis. This is aimed at end-users looking for a suitable tool to process their data. The inventory will list available tools, providing information that will help users to select a suitable tool, such as scope of application, methodology, level of validation, license policy, transparency, user-friendliness, and reviews by other users. + +!!! warning "Inactive" + The task force is currently inactive due to insufficient members. Do you have suggestions on how to continue or are you interested in getting this task force up and running again? Feel free to drop us a mail. + +## Contact + +- [Management team](mailto:ismrmosipi@gmail.com) + +## Resources + +!!! abstract "DCE/DSC-MRI software inventory" + The DCE/DSC-MRI software inventory listing available software packages for DCE and/or DSC image processing. + + [📘 Check out the inventory](https://docs.google.com/spreadsheets/d/e/2PACX-1vSOHrNIiWcwDD5BoHij1dpXKgEejtohqKF6KZQMZi3G6GzM_BP8xpuwRbjFFvDW9Q/pubhtml?gid=1031101549&single=true) diff --git a/docs/tf/tf2-2.md b/docs/tf/tf2-2.md new file mode 100644 index 0000000..e198bdf --- /dev/null +++ b/docs/tf/tf2-2.md @@ -0,0 +1,23 @@ +# TF2.2 — ASL code contributions + +The aim of TF2.2 is to develop a code collection of open-source functions, scripts, and in-house pipelines for ASL perfusion imaging analysis. This is aimed at developers of ASL perfusion methods looking for specific functionality or development templates, or who want to share their own in-house code with others. Contributions will be sourced from the community and may include individual functions and more complete pipelines in various programming languages. TF2.2 will organize these in a coherent and well documented structure. + +The code repository details are listed on the [Python Code Repositories page](../pyCode.md). + +## Leads + +- [María Mora](mailto:magumoal@gmail.com) +- [Azeez Adebimpe](mailto:azeez.adebimpe@bayer.com) + +## Ongoing projects + +For this delivery cycle, the code collection will be focused on preclinical and non-brain applications. Beginning with images of vendors' products would be the priority, including PASL and pCASL for brain imaging, and eventually incorporate reconstruction from k-space. Any functionality beyond that is reserved for future updates. + +The code will be collected and organised in two main phases. In the first phase (May 2023 – Feb 2024), a complete collection of code will be sourced from the community through a public call for contributions. The code will be classified and organised according to functionality and will undergo a minimal verification, but will not otherwise be modified, harmonised, documented or tested. In a second phase (May 2024 – Feb 2025) the code will be harmonised, tested more rigorously and documented. If you want to know more about our ongoing project, please read here our [two-year roadmap](https://docs.google.com/document/d/1FzOFMV420xew2oiSDq4Wi3tRZ45if73Rw-6at2hKNFw/edit#bookmark=id.28nk37pzp6i). + +We continuously welcome new ASL code contributions. At the moment we have a special interest in extending our repository with code for preclinical and non-brain code snippets. Contact the leads for more information on how you can contribute your code. + +## Publications + +- ISMRM abstract 2022 — [cds.ismrm.org/protected/22MProceedings/PDFfiles/0914.html](https://cds.ismrm.org/protected/22MProceedings/PDFfiles/0914.html) +- Mora Álvarez M.G., Zhou L., Wang Y., Zhao L., Dolui S., Taso M., Wang Z., Adebimpe A., Mutsaerts H., and Madhuranthakam A.J. (2023). The Open Science Initiative for Perfusion Imaging (OSIPI) ASL Processing Code Library. To be submitted to MRM. diff --git a/docs/tf/tf2-3.md b/docs/tf/tf2-3.md new file mode 100644 index 0000000..41a2b86 --- /dev/null +++ b/docs/tf/tf2-3.md @@ -0,0 +1,33 @@ +# TF2.3 — DSC/DCE code contributions + +TF2.3 has built a code collection consisting of open-source python functions for DCE/DSC perfusion imaging analysis. Contributions came from researchers across the world who wanted to share their own in-house developments with others. The code was tested, with results freely available on a website (see below). The aim was to make this tested code available for developers and scientists looking for specific functionality or development templates, so that users could have confidence in the code and avoid duplicating work already done by others. + +The main aim of the current OSIPI roadmap is to make this code user-friendly, providing users with the building blocks for DCE analysis (e.g. different kinetic models) in standard nomenclature, and the ability to link them together. We will use the lexicon notation for quantities, models and analysis developed by TF4.2 and rework the existing code to develop a new python package. + +The code repository details are listed on the [Python Code Repositories page](../pyCode.md). + +## Leads + +- [Sirisha Tadimalla](mailto:sirisha.tadimalla@sydney.edu.au) +- [Lucy Kershaw](mailto:lucy.kershaw@ed.ac.uk) + +## Ongoing projects + +There are two main strands to our ongoing work. Firstly, we aim to bring the DSC part of our code collection to a similar stage as the DCE part. In particular we need to collect extra code from contributors and define a basic minimum processing pipeline. The other piece of ongoing work is the development of our python package, adding functionality to the existing skeleton including documentation and examples. + +If you want to know more about our ongoing project, please read here our [two-year roadmap](https://docs.google.com/document/d/1FzOFMV420xew2oiSDq4Wi3tRZ45if73Rw-6at2hKNFw/edit#bookmark=id.obucmtsk8skv). + +Although we have a large number of contributions, there are still some gaps in functionality (especially for DSC) and further code contributions are welcome. Please follow the instructions on the [wiki](https://github.com/OSIPI/DCE-DSC-MRI_CodeCollection/wiki) with information about how to submit code to the collection and develop tests, or contact the leads for more information. + +## Publications + +- van Houdt PJ, Ragunathan S, Berks M, Ahmed Z, Kershaw LE, Gurney-Champion OJ, Tadimalla S, Arvidsson J, Sun Y, Kallehauge J, Dickie B, Lévy S, Bell L, Sourbron S, Thrippleton MJ. Contrast‐agent‐based perfusion MRI code repository and testing framework: ISMRM Open Science Initiative for Perfusion Imaging (OSIPI). Magn Reson Med. 2023;1-13. doi: [10.1002/mrm.29826](https://onlinelibrary.wiley.com/doi/full/10.1002/mrm.29826) (also presented at ISMRM2022 in London and at ISMRM Benelux 2022) +- TF lead Sirisha Tadimalla talking about OSIPI at MRI Together in 2021: [MRI Together 2021 – D1 (Pacific) – Hands-on: OSIPI Experience on Scientific… (S. Tadimalla)](https://www.youtube.com/watch?v=yGBiDGBtJGY) +- Berks, M. Open Science Initiative for Perfusion Imaging (OSIPI): a global collaboration of researchers committed to improving software in their field. SeptembRSE 2021 [SeptembRSE: 13th September – Afternoon](https://youtube.com/watch?v=dk9SzgCCH4s&ab_channel=SocietyofResearchSoftwareEngineering#t=22m35s…) + +## Resources + +!!! abstract "Test results website" + Test results website with information about how we tested the submitted code and the results. + + [📘 See the test results](https://osipi.github.io/DCE-DSC-MRI_TestResults/intro.html) diff --git a/docs/tf/tf2-4.md b/docs/tf/tf2-4.md new file mode 100644 index 0000000..fe3ee62 --- /dev/null +++ b/docs/tf/tf2-4.md @@ -0,0 +1,25 @@ +# TF2.4 — IVIM code contributions + +As of the start of the second OSIPI roadmap, a task force dedicated towards code contributions for intravoxel incoherent motion (IVIM) analysis was founded (TF2.4). The aim of the task force is to gather and test code relevant for IVIM analysis. In particular, model fitting code in Python and Matlab will be gathered. A test bed including automated tests as well as both simulated and in vivo data of the brain and upper abdomen will be used to evaluate the gathered code. The phantoms and tests can also serve as a benchmark for future developments. Building upon the code and resources generated in its roadmap, a long-term goal of the task force is to form a harmonized code library for IVIM-related code. + +The code repository details are listed on the [Python Code Repositories page](../pyCode.md). + +## Leads + +- [Oliver Gurney-Champion](mailto:o.j.gurney-champion@amsterdamumc.nl) +- [Oscar Jalnefjord](mailto:oscar.jalnefjord@gu.se) + +## Ongoing projects + +The task force is now focusing on extending the code contributions and test suite. The task force is currently working actively with automated presentation of test results from available code contributions. We are also writing wrapper functions, such that any contribution can be run using a simple python object in which you specify the preferred fitting method/contribution. + +If you want to know more about our ongoing project, please read here our [two-year roadmap](https://docs.google.com/document/d/1FzOFMV420xew2oiSDq4Wi3tRZ45if73Rw-6at2hKNFw/edit#bookmark=kix.bfc7493zayvq). + +If you have IVIM code you want to share, please follow the [contribution guidelines](https://github.com/OSIPI/TF2.4_IVIM-MRI_CodeCollection/blob/main/doc/guidelines_for_contributions.md), or contact the co-leads for more information. + +## Resources + +!!! abstract "DRO data" + A subfolder of the repository hosts digital phantom data which can serve as a benchmark for future developments. + + [🧪 Go to the DRO data](https://github.com/OSIPI/TF2.4_IVIM-MRI_CodeCollection/tree/main/phantoms) diff --git a/docs/tf/tf3-1.md b/docs/tf/tf3-1.md new file mode 100644 index 0000000..fe6c68f --- /dev/null +++ b/docs/tf/tf3-1.md @@ -0,0 +1,6 @@ +# TF3.1 — Digital Reference Objects and Phantoms + +The goal of this task force is to build an inventory of digital reference objects and phantom data for perfusion MRI. The inventory is aimed at researchers looking for data to test their perfusion analysis methods, and at data owners who want to share data for secondary research. The inventory developed by Task force 3.1 will include a curated list of publicly available digital reference objects (DROs), synthetic and phantom data that can serve as ground truth for perfusion analysis methods. Task force 3.1 will initially focus on identifying, listing and qualifying existing datasets. In a second phase we may identify gaps in the available data and take actions to fill them. + +!!! note "Under development" + This page is still under development, more details will be added soon! diff --git a/docs/tf/tf3-2.md b/docs/tf/tf3-2.md new file mode 100644 index 0000000..25f720a --- /dev/null +++ b/docs/tf/tf3-2.md @@ -0,0 +1,17 @@ +# TF3.2 — Clinical and preclinical data + +The goal of this task force is to build an inventory of freely available clinical and preclinical perfusion MRI data. The inventory is aimed at researchers looking for data to test their perfusion analysis methods, and at data owners who want to share data for secondary research. The inventory will provide a curated list of publicly available preclinical and clinical perfusion datasets that can be used to test algorithms in real-world conditions for robustness, reproducibility and practicality. Based on the available data we plan to perform a meta-analysis of perfusion data (e.g. field strengths, acquisitions, contrast agents, non-contrast) and evaluate the datasets for completeness. Through this we would identify pitfalls with sharing perfusion data and what is required to ensure you have curated data for sharing, which could lead to a white paper on "how to" share perfusion data. + +!!! warning "Inactive" + The task force is currently inactive due to insufficient members. If you have experience sharing data, we are actively looking for a few people to lead the next phase of the work in this task force. Drop us a mail to chat about the possibilities! + +## Contact + +- [Management team](mailto:ismrmosipi@gmail.com) + +## Resources + +!!! abstract "Data inventory" + The inventory lists currently available preclinical and clinical perfusion imaging data sets. + + [📘 Check out the inventory](https://docs.google.com/spreadsheets/d/e/2PACX-1vT74GQ4c9NfslwHhxArQqa5k_5yZfP8uZjBsbK7F8q7bt76xhq9Vbp4HgSi8pNZjC3WcFRgxzVl_arm/pubhtml) diff --git a/docs/tf/tf4-1.md b/docs/tf/tf4-1.md new file mode 100644 index 0000000..724b198 --- /dev/null +++ b/docs/tf/tf4-1.md @@ -0,0 +1,31 @@ +# TF4.1 — ASL Lexicon + +Task Force 4.1 develops a standardized lexicon and reporting recommendations for Arterial Spin Labeling (ASL) perfusion MRI. + +The guidelines developed by TF4.1 enable interoperability and facilitate the comparison of results produced by different ASL analysis tools, studies, or sites. The task force aims to harmonize and increase the detail in the description of parameters and configurations, enable encoding of the complete perfusion imaging workflow, and pave the way for consensus building. An important application is the amendment of the DICOM standard for ASL perfusion parametric maps, as well as BIDS extensions, and the development of demonstrations and use cases. + +See the [Lexicons overview](../lexicons.md) for the published ASL Lexicon and CAPLEX resources. + +!!! abstract "ASL Lexicon" + Standardized nomenclature and terminology for a broad range of ASL imaging techniques and parameters, as well as for the physiological constants required for quantitative analysis. + + [📘 ASL Lexicon](https://docs.google.com/document/d/e/2PACX-1vSWItjZWR51N5FPsGnKQd5oaLwvwWF4VkuOgWgVSg2lXmPaGwcPkI9fZkbFbuDe0vWEhMzeJNtQ6wqc/pub) + +!!! abstract "ASL Methods Section Generator" + An automatic "Methods section generator" extracts and formats key imaging parameters from DICOM and BIDS images. This tool helps researchers correctly report ASL acquisition parameters in a standardized way, contributing to the broader goal of harmonization in perfusion MRI studies. + + [📘 Methods Generator](https://osipi.ismrm.org/task-forces/tf4-1/asl-parameter-generator/) + +## Leads + +- [David Thomas](mailto:d.thomas@ucl.ac.uk) +- [Patricia Clement](mailto:patricia.clement@ugent.be) + +## Ongoing projects + +In the roadmap 2023-2025, TF4.1 is transferring the current Lexicon to a user-friendly webpage on the OSIPI website, to complement and expand on the MRM paper. The Lexicon will also be expanded to cover more ASL methods. Additionally, the task force will verify harmonization of the Lexicon with ASL-BIDS, and highlight and explain discrepancies where they are unavoidable. Finally, in collaboration with OSIPI TF5.2, the task force is developing practical introductory multimedia educational tools, using terminology from the Lexicon, for clinicians and radiographers/technicians, to help break down barriers to the use of ASL in the clinical domain. + +## Publications + +- ISMRM abstract 2022 — [cds.ismrm.org/protected/22MProceedings/PDFfiles/0908.html](https://cds.ismrm.org/protected/22MProceedings/PDFfiles/0908.html) +- Suzuki Y, Clement P, Dai W, et al. ASL lexicon and reporting recommendations: A consensus report from the ISMRM Open Science Initiative for Perfusion Imaging (OSIPI). Magn Reson Med. 2023; 1-18. doi: 10.1002/mrm.29815 diff --git a/docs/tf/tf4-2.md b/docs/tf/tf4-2.md new file mode 100644 index 0000000..11d0cbb --- /dev/null +++ b/docs/tf/tf4-2.md @@ -0,0 +1,29 @@ +# TF4.2 — DCE/DSC Lexicon (CAPLEX) + +Task Force 4.2 has developed CAPLEX, an open-source lexicon of standardized quantities, models, and analysis processes for contrast-agent based perfusion MRI (DCE and DSC-MRI). + +Over the past 3 years, TF4.2 has developed an open-source lexicon of standardized quantities, models, and analysis processes for DCE/DSC analyses, dubbed CAPLEX. The aim of CAPLEX is to standardize the way researchers report their DCE/DSC analyses in papers and other documentation by providing standard nomenclature and definitions for commonly used quantities, models, and processes. The lexicon is hosted online and the website code is open-source, with contributions welcomed. In addition to the lexicon, the task force has developed human-readable and machine-readable reporting formats to help researchers precisely report their analysis pipelines using CAPLEX terminology. + +See the [Lexicons overview](../lexicons.md) for the published ASL Lexicon and CAPLEX resources. + +!!! abstract "CAPLEX" + CAPLEX is a library of standardized definitions of quantities, models, and analysis processes commonly used in contrast-agent based perfusion MRI (DCE and DSC-MRI). + + [📘 CAPLEX website](https://osipi.github.io/OSIPI_CAPLEX/)
+ [🧪 CAPLEX code repository](https://github.com/OSIPI/OSIPI_CAPLEX) + +## Leads + +- [Ben Dickie](mailto:ben.dickie@manchester.ac.uk) + +The task force is actively looking for new members. + +## Ongoing projects + +The task force is midway through its 2nd 2-year [roadmap](https://docs.google.com/document/d/e/2PACX-1vQqOATrWE2COIXq4qTkEe1Bix26GVr_-YTKUJbevCPXXFJf_nMKH3_Nw3DMsY2BcZHPKBG3EOg4SU4r/pub). The primary aims of this roadmap are to improve user experience and documentation, with the goal of establishing CAPLEX as a key resource within the DCE/DSC field. For example, the task force aims to provide researchers with tools that incorporate lexicon terminology into materials and methods text and to provide educational tools on the lexicon structure and use. The task force is also aiming to establish links and integrate more with other standard initiatives such as DICOM and QIBA. + +## Publications + +- ISMRM abstract 2021 — [cds.ismrm.org/protected/21MProceedings/PDFfiles/1093.html](https://cds.ismrm.org/protected/21MProceedings/PDFfiles/1093.html) +- ISMRM abstract 2022 — [cds.ismrm.org/protected/22MProceedings/PDFfiles/0803.html](https://cds.ismrm.org/protected/22MProceedings/PDFfiles/0803.html) +- Dickie B.R, Ahmed Z, Arvidsson J, Bell L, Buckley DL, Debus C, Fedorov A, Floca R, Gutmann I, van der Heijden RA, van Houdt PJ, Sourbron S, Thrippleton MJ, Quarles C, Kompan I. A community-endorsed open-source lexicon for contrast-agent based perfusion MRI (CAPLEX): A consensus guidelines report from the ISMRM Open Science Initiative for Perfusion Imaging (OSIPI). Mag Resn Med, 2023. doi: 10.1002/mrm.29840 diff --git a/docs/tf/tf5-1.md b/docs/tf/tf5-1.md new file mode 100644 index 0000000..47cf562 --- /dev/null +++ b/docs/tf/tf5-1.md @@ -0,0 +1,14 @@ +# TF5.1 — Website and Technical Support + +Task Force 5.1 maintains and improves the OSIPI website and supports other task forces in disseminating their resources. + +Task Force 5.1 works to improve the website of OSIPI so that its goals and resources become more accessible, and to assist other task forces in the dissemination of their resources. This includes the migration of the current website to the ISMRM subdomain. The goal is for visitors to get the most from the website, including a concise vision/purpose, simple and organized access to resources gathered by OSIPI, and quick access to tools developed by the OSIPI community. + +## Leads + +- [Luis Torres](mailto:luistorres@flywheel.io) +- [Petra van Houdt](mailto:p.v.houdt@nki.nl) + +## Ongoing projects + +The task force is currently migrating the basic content of OSIPI's first website to the ISMRM domain. Thereafter, the task force will add other much-wanted features, such as a forum. More details are available in the [two-year roadmap](https://docs.google.com/document/d/1FzOFMV420xew2oiSDq4Wi3tRZ45if73Rw-6at2hKNFw/edit#bookmark=id.kx8yo4cql0zk). diff --git a/docs/tf/tf5-2.md b/docs/tf/tf5-2.md new file mode 100644 index 0000000..bd9901d --- /dev/null +++ b/docs/tf/tf5-2.md @@ -0,0 +1,32 @@ +# TF5.2 — Education + +Task Force 5.2 creates resources to educate newcomers to perfusion MRI, including tutorial videos, a key-manuscripts bibliography, and a database of example images and artefacts. + +The task force aims to create a set of resources to educate newcomers to perfusion MRI. These include a set of tutorial videos describing the physics and applications of perfusion imaging in all its variants. The task force also publishes a bibliography of the key seminal articles for those who wish to learn about perfusion imaging techniques and applications. A further goal is to build a database of examples of perfusion images and image artefacts associated with perfusion. + +!!! abstract "Tutorial videos" + The first videos on ASL physics have been released. + + [📘 ASL tutorials](https://youtube.com/playlist?list=PLTIlnXdb9rwhoO8afyba3GQSh8ueShJ03&si=rTJUBVXftFicno3j) + +!!! abstract "Reference list" + New to ASL, DSC, or DCE? Check out the key papers to get started. + + [📘 OSIPI's recommended reading list](https://osipi.ismrm.org/task-forces/task-force-5-2/perfusion-onboarding/) + +## Leads + +- [Luis Hernandez-Garcia](mailto:hernan@umich.edu) +- [Mariam Aboian](mailto:mariam.aboian@yale.edu) + +## Key Manuscripts in Perfusion + +The task force maintains a curated bibliography of key manuscripts in perfusion MRI for those getting started, organized by modality: + +- [ASL Recommended Literature](../aslliterature.md) +- [DSC Recommended Literature](../dscliterature.md) +- [DCE Recommended Literature](../dceliterature.md) + +## Ongoing projects + +The task force is currently working on a first set of videos explaining the concepts of perfusion imaging. At the same time, the task force is working on the bibliography. More details are available in the [two-year roadmap](https://docs.google.com/document/d/1FzOFMV420xew2oiSDq4Wi3tRZ45if73Rw-6at2hKNFw/edit#bookmark=id.kx8yo4cql0zk). diff --git a/docs/tf/tf6-1.md b/docs/tf/tf6-1.md new file mode 100644 index 0000000..73d3a5e --- /dev/null +++ b/docs/tf/tf6-1.md @@ -0,0 +1,30 @@ +# TF6.1 — ASL Challenge + +Task Force 6.1 creates challenges that serve as benchmarks for ASL perfusion analysis practices, pipelines, and software. + +The goal of this task force is to create challenges that can serve as widely recognized benchmarks for perfusion analysis practices, pipelines, and software. This involves the development of metrics that quantify the performance of a perfusion analysis tool (e.g. bias and precision on DROs, agreement with reference methods in-vivo, reproducibility on in-vivo data, processing time). The long-term objective is to establish OSIPI as an independent arbiter for software solutions in perfusion imaging. + +The ISMRM ASL MRI Challenge is the outcome of the first roadmap set by OSIPI TF6.1. Launched in February 2021, this challenge was designed to compare ASL data processing pipelines, taking into account the image analysis steps, CBF quantification accuracy, and reproducibility of the submitted pipelines. In the first roadmap challenge, the task force successfully identified and understood sources of CBF variability, particularly in cases involving motion in the data. + +!!! abstract "First ASL challenge" + This repository contains all the documentation and datasets provided for the ISMRM-OSIPI ASL Challenge. + + [📘 Go to the repository](https://osf.io/6xyu3/) + +!!! abstract "Second ASL challenge" + Work-in-progress: challenge on multi-PLD ASL. Stay tuned! Coming soon. + +## Leads + +- [Andre Paschoal](mailto:andremp@unicamp.br) +- [Icaro Oliveira](mailto:icaro.oliveira2@uhn.ca) + +## Ongoing projects + +The task force is in the process of launching the second ASL Challenge focusing on multi-PLD ASL. Challenge design and dataset definition are already completed. The task force is preparing an ISMRM abstract (2024) to share the goals of the next Challenge with the community. More details are available in the [two-year roadmap](https://docs.google.com/document/d/1FzOFMV420xew2oiSDq4Wi3tRZ45if73Rw-6at2hKNFw/edit#bookmark=kix.bc32yvh9bcd2). + +## Publications + +- ISMRM abstract 2021 — [https://cds.ismrm.org/protected/21MProceedings/PDFfiles/2714.html](https://cds.ismrm.org/protected/21MProceedings/PDFfiles/2714.html) +- ISMRM abstract 2022 — [https://cds.ismrm.org/protected/22MProceedings/PDFfiles/0910.html](https://cds.ismrm.org/protected/22MProceedings/PDFfiles/0910.html) +- (under review, submitted to MRM) — Reproducibility of ASL Cerebral Blood Flow image processing: A Report of The Open Science Initiative for Perfusion Imaging and The ISMRM Arterial Spin Labeling MRI Challenge. diff --git a/docs/tf/tf6-2.md b/docs/tf/tf6-2.md new file mode 100644 index 0000000..a856eb6 --- /dev/null +++ b/docs/tf/tf6-2.md @@ -0,0 +1,34 @@ +# TF6.2 — DCE/DSC Challenge + +Task Force 6.2 compares quantification pipelines for DSC/DCE-MRI in clinical applications and establishes benchmarks for perfusion imaging. + +The aim of this task force is to compare quantification pipelines for DSC/DCE-MRI in clinical applications. Through these challenges, the performance of DSC-/DCE-MRI perfusion analysis tools developed in-house by participating groups, or the available software packages, are tested and evaluated according to technical performance metrics (e.g. bias and precision on DROs, agreement with reference methods in-vivo, reproducibility on in-vivo data, processing time). The aim is to establish a set of benchmarks for perfusion imaging in different applications. + +The first challenge by this task force focused on benchmarking DCE software. As the use of artificial intelligence grows, the second challenge focuses on deep learning techniques. The goal is to encourage researchers to put their quantitative methods to the test, to stimulate collaboration, and to chart the heterogeneity of DCE analysis software. In this challenge, participants use deep learning techniques to estimate perfusion parameters in DCE-MRI of the uterus. The task force provides repeated in vivo data to assess the algorithm's precision, and simulated DCE-data to test the accuracy. + +!!! abstract "First DCE challenge" + This repository contains all the documentation and datasets provided for the first ISMRM-OSIPI DCE Challenge. + + [📘 Go to the first challenge](https://osf.io/u7a6f/) + +!!! abstract "Second DCE challenge" + Work-in-progress: topic will be deep learning for DCE analysis. Coming soon. + +## Leads + +- [Soudabeh Kargar](mailto:soudabeh.kargar@gmail.com) +- [Harrison Kim](mailto:hyunkikim@uabmc.edu) + +## Ongoing projects + +The clinical data for this challenge were previously used for studying endometrial hypoxia and kindly shared for this challenge. The dataset includes the MR images of the uterus of 12 healthy female volunteers with regular menstrual cycles. Each volunteer was scanned twice: during days 1–3 of menstruation and the early/mid-secretory phase of their cycle. The two relevant MRI sequences for this challenge are DCE-MRI and IR-TrueFISP. + +The task force is currently working on the design of the morphological phantom. This numeric phantom will be generated by assuming a series of perfusion parameters, T1 values, and a population-based Arterial Input Function (AIF). A two-compartment exchange model and the spoiled gradient-echo steady-state signal model will be used to create the voxel-wise signal. The assumed T1 values for blood and tissue will be provided to convert the signal to concentration. + +More details are available in the [two-year roadmap](https://docs.google.com/document/d/1FzOFMV420xew2oiSDq4Wi3tRZ45if73Rw-6at2hKNFw/edit#heading=h.m4pavixh6vsi). + +## Publications + +- ISMRM abstract 2021 — [cds.ismrm.org/protected/21MProceedings/PDFfiles/1094.html](https://cds.ismrm.org/protected/21MProceedings/PDFfiles/1094.html) +- ISMRM abstract 2022 — [cds.ismrm.org/protected/22MProceedings/PDFfiles/0047.html](https://cds.ismrm.org/protected/22MProceedings/PDFfiles/0047.html) +- Shalom ES, Kim H, van der Heijden RA, Ahmed Z, Patel R, Hormuth DA 2nd, DiCarlo JC, Yankeelov TE, Sisco NJ, Dortch RD, Stokes AM, Inglese M, Grech-Sollars M, Toschi N, Sahoo P, Singh A, Verma SK, Rathore DK, Kazerouni AS, Partridge SC, LoCastro E, Paudyal R, Wolansky IA, Shukla-Dave A, Schouten P, Gurney-Champion OJ, Jiřík R, Macíček O, Bartoš M, Vitouš J, Das AB, Kim SG, Bokacheva L, Mikheev A, Rusinek H, Berks M, Hubbard Cristinacce PL, Little RA, Cheung S, O'Connor JPB, Parker GJM, Moloney B, LaViolette PS, Bobholz S, Duenweg S, Virostko J, Laue HO, Sung K, Nabavizadeh A, Saligheh Rad H, Hu LS, Sourbron S, Bell LC, Fathi Kazerooni A. The ISMRM Open Science Initiative for Perfusion Imaging (OSIPI): Results from the OSIPI-Dynamic Contrast-Enhanced challenge. Magn Reson Med. 2023 Dec 19. doi: 10.1002/mrm.29909. diff --git a/mkdocs.yml b/mkdocs.yml index 2527b51..9ebdb4f 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -1,5 +1,5 @@ # Project information -site_name: OSIPI Documentation Hub +site_name: OSIPI site_url: https://github.com/OSIPI/osipi.github.io site_author: OSIPI site_description: >- @@ -73,6 +73,9 @@ extra: link: https://github.com/OSIPI - icon: fontawesome/brands/slack link: https://osipi.slack.com + - icon: simple/zenodo + link: https://zenodo.org/communities/ismrm-osipi/ + name: OSIPI on Zenodo extra_css: - assets/stylesheets/extra.css @@ -141,8 +144,33 @@ nav: - Getting started: - Overview: getting-started.md + - About: + - About OSIPI: about.md + - Executive & Management Board: emb.md + - Strategy Board: strategy-board.md + - Contributors: contributors.md + - Task Forces: - Overview: taskforces.md + - "Aim 1 – Software Inventories": + - "(TF1.1) ASL Software Inventory": tf/tf1-1.md + - "(TF1.2) DSC/DCE Software Inventory": tf/tf1-2.md + - "Aim 2 – Code Libraries": + - "(TF2.2) ASL Code": tf/tf2-2.md + - "(TF2.3) DSC/DCE Code": tf/tf2-3.md + - "(TF2.4) IVIM Code": tf/tf2-4.md + - "Aim 3 – Data": + - "(TF3.1) DROs & Phantoms": tf/tf3-1.md + - "(TF3.2) Clinical & Preclinical Data": tf/tf3-2.md + - "Aim 4 – Lexicons": + - "(TF4.1) ASL Lexicon": tf/tf4-1.md + - "(TF4.2) CAPLEX": tf/tf4-2.md + - "Aim 5 – Exchange & Education": + - "(TF5.1) Website & Technical Support": tf/tf5-1.md + - "(TF5.2) Education": tf/tf5-2.md + - "Aim 6 – Challenges": + - "(TF6.1) ASL Challenge": tf/tf6-1.md + - "(TF6.2) DSC/DCE Challenge": tf/tf6-2.md - "Roadmap 2026-2028": https://docs.google.com/document/d/1w2JlVK3hP5dgXMcrK8da5z94ivsK8Or__NU9qUR6WRk - Open Calls: @@ -185,4 +213,8 @@ nav: - Overview: publications.md - "OSIPI Papers": osipipapers.md - "ISMRM Abstracts": ismrmabstracts.md + + - News: + - Overview: news.md + - "Google Summer of Code": gsoc.md From f22872f56dd6be0959db0af9a403541244c90c77 Mon Sep 17 00:00:00 2001 From: Luis Torres Date: Sat, 6 Jun 2026 17:34:14 -0400 Subject: [PATCH 2/5] Reorganize navigation into six sections and rationalize icons - Consolidate 11 top-level nav tabs into 6: Home, About, Task Forces, Resources, Learning & Publications, News & Events - Add section landing pages: resources, learning-publications, news-events - Fold Getting started under About; rename "Python Code Repositories" to "Code Repositories" - Repoint TF5.1/5.2/6.1/6.2 overview links from the old external site to the local detail pages - Limit the book/test-tube icons to genuine Documentation/GitHub links and remove decorative emoji from landing and getting-started pages - Fix malformed Getting Started link in opencalls.md Co-Authored-By: Claude Opus 4.8 (1M context) --- docs/getting-started.md | 24 +++++----- docs/learning-publications.md | 13 +++++ docs/news-events.md | 18 +++++++ docs/opencalls.md | 2 +- docs/pyCode.md | 2 +- docs/resources.md | 18 +++++++ docs/taskforces.md | 26 +++++----- docs/tf/tf2-2.md | 2 +- docs/tf/tf2-3.md | 2 +- docs/tf/tf2-4.md | 2 +- mkdocs.yml | 89 +++++++++++++++++------------------ 11 files changed, 122 insertions(+), 76 deletions(-) create mode 100644 docs/learning-publications.md create mode 100644 docs/news-events.md create mode 100644 docs/resources.md diff --git a/docs/getting-started.md b/docs/getting-started.md index 97029da..1fa8429 100644 --- a/docs/getting-started.md +++ b/docs/getting-started.md @@ -8,27 +8,27 @@ Welcome to **OSIPI**, the Open Science Initiative for Perfusion Imaging. ## Who is this for? !!! note "" - This hub is designed for: + OSIPI is for: - - 🧠 **Researchers** analyzing perfusion MRI data - - 👩‍💻 **Developers** contributing tools or algorithms - - 🩺 **Clinicians** using MRI in practice - - 🌐 Anyone aiming to support reproducibility and interoperability + - **Researchers** analyzing perfusion MRI data + - **Developers** contributing tools or algorithms + - **Clinicians** using MRI in practice + - Anyone aiming to support reproducibility and interoperability ## Start here !!! tip "Explore the key sections" - - ℹ️ **[About OSIPI](about.md)** + - **[About OSIPI](about.md)** Mission, founding history, leadership, and how the initiative is governed - - 🧭 **[Task Forces](taskforces.md)** + - **[Task Forces](taskforces.md)** The working groups behind OSIPI's six aims, with leads and ongoing projects - - 📚 **[Lexicons](lexicons.md)** + - **[Lexicons](lexicons.md)** Standardized terminology for ASL and contrast-agent based perfusion MRI - - 🧪 **[Code Repositories](pyCode.md)** + - **[Code Repositories](pyCode.md)** Python and MATLAB tools for DCE, DSC, ASL, and IVIM analysis - - 🛠️ **[Tools](tools.md)** + - **[Tools](tools.md)** Web-based utilities for dataset validation and artifact reporting - - 📰 **[News](news.md)** + - **[News](news.md)** Announcements, challenges, events, and Google Summer of Code ## Get involved @@ -40,4 +40,4 @@ Welcome to **OSIPI**, the Open Science Initiative for Perfusion Imaging. --- -🧭 *Use the navbar to browse resources, or head directly to your topic of interest.* +*Use the navigation to browse resources, or head directly to your topic of interest.* diff --git a/docs/learning-publications.md b/docs/learning-publications.md new file mode 100644 index 0000000..f73b5b1 --- /dev/null +++ b/docs/learning-publications.md @@ -0,0 +1,13 @@ +# Learning & Publications + +Resources for learning perfusion MRI, together with the publications produced by OSIPI. + +!!! abstract "Learning" + Video tutorials and recommended literature for ASL, DSC, and DCE perfusion MRI. + + [Learning overview](learning.md) + +!!! abstract "Publications" + Peer-reviewed OSIPI papers and OSIPI-related ISMRM conference abstracts. + + [Publications overview](publications.md) diff --git a/docs/news-events.md b/docs/news-events.md new file mode 100644 index 0000000..64c07ce --- /dev/null +++ b/docs/news-events.md @@ -0,0 +1,18 @@ +# News & Events + +Announcements, community programs, and open opportunities to get involved with OSIPI. + +!!! abstract "News" + Announcements and updates from OSIPI. + + [News](news.md) + +!!! abstract "Google Summer of Code" + OSIPI's participation in Google Summer of Code, with project reports from 2024 and 2025. + + [Google Summer of Code](gsoc.md) + +!!! abstract "Open Calls" + Open challenges, data-collection initiatives, and calls for contribution. + + [Open Calls](opencalls.md) diff --git a/docs/opencalls.md b/docs/opencalls.md index bb74663..e137cb7 100644 --- a/docs/opencalls.md +++ b/docs/opencalls.md @@ -1,7 +1,7 @@ # Open Calls Announcements about open calls, upcoming challenges, workshops, and events are listed below. If you are interested in contributing to OSIPI -in any other way, please check the [Task Force list](taskforces.md) or the (Getting Started page)[getting-started.md]. +in any other way, please check the [Task Force list](taskforces.md) or the [Getting Started page](getting-started.md). !!! abstract "IVIM Data Collection Initiative" The IVIM community is looking for more sites to contribute data to the multi-site data collection study. diff --git a/docs/pyCode.md b/docs/pyCode.md index a1cc37b..3aef056 100644 --- a/docs/pyCode.md +++ b/docs/pyCode.md @@ -1,4 +1,4 @@ -# Python Code Repositories +# Code Repositories OSIPI supports a suite of open-source codebases for reproducible and standardized perfusion MRI analysis: diff --git a/docs/resources.md b/docs/resources.md new file mode 100644 index 0000000..e43345f --- /dev/null +++ b/docs/resources.md @@ -0,0 +1,18 @@ +# Resources + +OSIPI develops and maintains open resources for perfusion MRI analysis. + +!!! abstract "Lexicons" + Standardized terminology for ASL and contrast-agent based perfusion MRI. + + [Lexicons overview](lexicons.md) + +!!! abstract "Code Repositories" + Open-source code libraries for DCE, DSC, ASL, and IVIM analysis. + + [Code Repositories overview](pyCode.md) + +!!! abstract "Tools" + Web-based utilities for dataset validation and artifact reporting. + + [Tools overview](tools.md) diff --git a/docs/taskforces.md b/docs/taskforces.md index 1c7c2bc..dec616d 100644 --- a/docs/taskforces.md +++ b/docs/taskforces.md @@ -11,12 +11,12 @@ Inventories and evaluation of available complete perfusion image analysis tools !!! abstract "TF1.1 — ASL software inventory" Inventory of publicly available ASL pipelines along with their features, compatibility, and links to manuals and source code. - [📘 Task Force 1.1 details](tf/tf1-1.md) + [Task Force 1.1 details](tf/tf1-1.md) !!! abstract "TF1.2 — DCE/DSC inventory (inactive)" Inventory of software packages for DCE/DSC image analysis. This task force is currently inactive due to insufficient members. - [📘 Task Force 1.2 details](tf/tf1-2.md) + [Task Force 1.2 details](tf/tf1-2.md) ## Aim 2 — Code Libraries @@ -25,17 +25,17 @@ Develops community-driven open-source code libraries for perfusion imaging analy !!! abstract "TF2.2 — ASL code contributions" Code collection of open-source functions, scripts, and in-house pipelines for ASL perfusion imaging analysis. - [📘 Task Force 2.2 details](tf/tf2-2.md) + [Task Force 2.2 details](tf/tf2-2.md) !!! abstract "TF2.3 — DSC/DCE code contributions" Tested code collection of open-source Python functions for DCE/DSC perfusion imaging analysis. - [📘 Task Force 2.3 details](tf/tf2-3.md) + [Task Force 2.3 details](tf/tf2-3.md) !!! abstract "TF2.4 — IVIM code contributions" Gathered and tested code for intravoxel incoherent motion (IVIM) analysis, with model fitting code in Python and Matlab. - [📘 Task Force 2.4 details](tf/tf2-4.md) + [Task Force 2.4 details](tf/tf2-4.md) ## Aim 3 — Data Inventory @@ -44,12 +44,12 @@ Inventories with open-access (pre-)clinical or phantom data and digital referenc !!! abstract "TF3.1 — Digital Reference Objects and Phantoms" Inventory of digital reference objects and phantom data for perfusion MRI. - [📘 Task Force 3.1 details](tf/tf3-1.md) + [Task Force 3.1 details](tf/tf3-1.md) !!! abstract "TF3.2 — Clinical and preclinical data (inactive)" Inventory of freely available clinical and preclinical perfusion MRI data. This task force is currently inactive due to insufficient members. - [📘 Task Force 3.2 details](tf/tf3-2.md) + [Task Force 3.2 details](tf/tf3-2.md) ## Aim 4 — Lexicons @@ -58,13 +58,13 @@ Develop terminology and reporting guidelines for image acquisition and perfusion !!! abstract "TF4.1 — ASL Lexicon" Standardized terminology and reporting recommendations for arterial spin labeling imaging. - [📘 Lexicons overview](lexicons.md)
+ [Lexicons overview](lexicons.md)
[📘 ASL Lexicon documentation](https://osipi.github.io/ASL-Lexicon/) !!! abstract "TF4.2 — DSC/DCE Lexicon (CAPLEX)" Lexicon of definitions for quantities, models, and analysis methods used in contrast-agent-based perfusion MRI. - [📘 Lexicons overview](lexicons.md)
+ [Lexicons overview](lexicons.md)
[📘 CAPLEX documentation](https://osipi.github.io/OSIPI_CAPLEX/) ## Aim 5 — Exchange and Education platform @@ -74,12 +74,12 @@ Dissemination of resources through website and educational activities. !!! abstract "TF5.1 — Website" Develops and maintains the OSIPI website for sharing resources with the community. - [📘 Task Force 5.1](https://osipi.ismrm.org/task-forces/task-force-5-1/) + [Task Force 5.1 details](tf/tf5-1.md) !!! abstract "TF5.2 — Education" Develops educational activities and materials for perfusion imaging. - [📘 Task Force 5.2](https://osipi.ismrm.org/task-forces/task-force-5-2/) + [Task Force 5.2 details](tf/tf5-2.md) ## Aim 6 — Challenges @@ -88,9 +88,9 @@ Develop challenges that compare the performance of perfusion image analysis soft !!! abstract "TF6.1 — ASL challenges" Develops challenges comparing ASL perfusion image analysis software. - [📘 Task Force 6.1](https://osipi.ismrm.org/task-forces/task-force-6-1/) + [Task Force 6.1 details](tf/tf6-1.md) !!! abstract "TF6.2 — DSC/DCE challenges" Develops challenges comparing DSC/DCE perfusion image analysis software. - [📘 Task Force 6.2](https://osipi.ismrm.org/task-forces/task-force-6-2/) + [Task Force 6.2 details](tf/tf6-2.md) diff --git a/docs/tf/tf2-2.md b/docs/tf/tf2-2.md index e198bdf..bbaf1c9 100644 --- a/docs/tf/tf2-2.md +++ b/docs/tf/tf2-2.md @@ -2,7 +2,7 @@ The aim of TF2.2 is to develop a code collection of open-source functions, scripts, and in-house pipelines for ASL perfusion imaging analysis. This is aimed at developers of ASL perfusion methods looking for specific functionality or development templates, or who want to share their own in-house code with others. Contributions will be sourced from the community and may include individual functions and more complete pipelines in various programming languages. TF2.2 will organize these in a coherent and well documented structure. -The code repository details are listed on the [Python Code Repositories page](../pyCode.md). +The code repository details are listed on the [Code Repositories page](../pyCode.md). ## Leads diff --git a/docs/tf/tf2-3.md b/docs/tf/tf2-3.md index 41a2b86..0407a78 100644 --- a/docs/tf/tf2-3.md +++ b/docs/tf/tf2-3.md @@ -4,7 +4,7 @@ TF2.3 has built a code collection consisting of open-source python functions for The main aim of the current OSIPI roadmap is to make this code user-friendly, providing users with the building blocks for DCE analysis (e.g. different kinetic models) in standard nomenclature, and the ability to link them together. We will use the lexicon notation for quantities, models and analysis developed by TF4.2 and rework the existing code to develop a new python package. -The code repository details are listed on the [Python Code Repositories page](../pyCode.md). +The code repository details are listed on the [Code Repositories page](../pyCode.md). ## Leads diff --git a/docs/tf/tf2-4.md b/docs/tf/tf2-4.md index fe3ee62..00e2508 100644 --- a/docs/tf/tf2-4.md +++ b/docs/tf/tf2-4.md @@ -2,7 +2,7 @@ As of the start of the second OSIPI roadmap, a task force dedicated towards code contributions for intravoxel incoherent motion (IVIM) analysis was founded (TF2.4). The aim of the task force is to gather and test code relevant for IVIM analysis. In particular, model fitting code in Python and Matlab will be gathered. A test bed including automated tests as well as both simulated and in vivo data of the brain and upper abdomen will be used to evaluate the gathered code. The phantoms and tests can also serve as a benchmark for future developments. Building upon the code and resources generated in its roadmap, a long-term goal of the task force is to form a harmonized code library for IVIM-related code. -The code repository details are listed on the [Python Code Repositories page](../pyCode.md). +The code repository details are listed on the [Code Repositories page](../pyCode.md). ## Leads diff --git a/mkdocs.yml b/mkdocs.yml index 9ebdb4f..99f8524 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -141,10 +141,8 @@ not_in_nav: | nav: - Home: index.md - - Getting started: - - Overview: getting-started.md - - About: + - Getting started: getting-started.md - About OSIPI: about.md - Executive & Management Board: emb.md - Strategy Board: strategy-board.md @@ -173,48 +171,47 @@ nav: - "(TF6.2) DSC/DCE Challenge": tf/tf6-2.md - "Roadmap 2026-2028": https://docs.google.com/document/d/1w2JlVK3hP5dgXMcrK8da5z94ivsK8Or__NU9qUR6WRk - - Open Calls: - - Overview: opencalls.md - - "IVIM Data Collection Initiative": https://docs.google.com/forms/d/1WHHWj5jNg5NSdvVH-E1QQzF5pQMnN9cWeDvaVPdVwO8/edit - - - Lexicons: - - Overview: lexicons.md - - "(TF4.1) ASL Lexicon": https://osipi.github.io/ASL-Lexicon/ - - "(TF4.2) Caplex – Contrast-agent based perfusion MRI": "!import https://github.com/OSIPI/OSIPI_CAPLEX?branch=main&docs_dir=docs&multi_docs=True&config=mkdocs.yml&keep_docs_dir=true" - - - Python Code Repositories: - - Overview: pyCode.md - - - "OSIPI Python package": - - Documentation: https://osipi.github.io/osipy - - - "(TF2.2) ASL repository": - - Documentation: https://osipi.github.io/TF2.2_OSIPI-ASL-toolbox/ - - "(TF2.3) DCE/DSC repository": - - Documentation: https://osipi.github.io/DCE-DSC-MRI_CodeCollection/ - - "(TF2.4) IVIM repository": - - Documentation: https://osipi.github.io/TF2.4_IVIM-MRI_CodeCollection/ - - - Tools: - - Overview: tools.md - - "ASL parameter generator": https://github.com/OSIPI/asl-parameter-reporter - - "Artefact database": https://github.com/OSIPI/perfusion-artifacts - - - Learning: - - Overview: learning.md - - "ASL Tutorials": https://youtube.com/playlist?list=PLTIlnXdb9rwhoO8afyba3GQSh8ueShJ03&si=rTJUBVXftFicno3j - - "Recommended Literature": - - "ASL Literature": aslliterature.md - - "DSC Literature": dscliterature.md - - "DCE Literature": dceliterature.md - - "TACTIX MRI Tutorials": https://www.youtube.com/@TACTIXTwinningProject/playlists - - - Publications: - - Overview: publications.md - - "OSIPI Papers": osipipapers.md - - "ISMRM Abstracts": ismrmabstracts.md - - - News: - - Overview: news.md + - Resources: + - resources.md + - Lexicons: + - Overview: lexicons.md + - "(TF4.1) ASL Lexicon": https://osipi.github.io/ASL-Lexicon/ + - "(TF4.2) Caplex – Contrast-agent based perfusion MRI": "!import https://github.com/OSIPI/OSIPI_CAPLEX?branch=main&docs_dir=docs&multi_docs=True&config=mkdocs.yml&keep_docs_dir=true" + - Code Repositories: + - Overview: pyCode.md + - "OSIPI Python package": + - Documentation: https://osipi.github.io/osipy + - "(TF2.2) ASL repository": + - Documentation: https://osipi.github.io/TF2.2_OSIPI-ASL-toolbox/ + - "(TF2.3) DCE/DSC repository": + - Documentation: https://osipi.github.io/DCE-DSC-MRI_CodeCollection/ + - "(TF2.4) IVIM repository": + - Documentation: https://osipi.github.io/TF2.4_IVIM-MRI_CodeCollection/ + - Tools: + - Overview: tools.md + - "ASL parameter generator": https://github.com/OSIPI/asl-parameter-reporter + - "Artefact database": https://github.com/OSIPI/perfusion-artifacts + + - Learning & Publications: + - learning-publications.md + - Learning: + - Overview: learning.md + - "ASL Tutorials": https://youtube.com/playlist?list=PLTIlnXdb9rwhoO8afyba3GQSh8ueShJ03&si=rTJUBVXftFicno3j + - "Recommended Literature": + - "ASL Literature": aslliterature.md + - "DSC Literature": dscliterature.md + - "DCE Literature": dceliterature.md + - "TACTIX MRI Tutorials": https://www.youtube.com/@TACTIXTwinningProject/playlists + - Publications: + - Overview: publications.md + - "OSIPI Papers": osipipapers.md + - "ISMRM Abstracts": ismrmabstracts.md + + - News & Events: + - news-events.md + - News: news.md - "Google Summer of Code": gsoc.md + - Open Calls: + - Overview: opencalls.md + - "IVIM Data Collection Initiative": https://docs.google.com/forms/d/1WHHWj5jNg5NSdvVH-E1QQzF5pQMnN9cWeDvaVPdVwO8/edit From e2c1de0954afb4904f61beb18f615720a6d062cd Mon Sep 17 00:00:00 2001 From: Luis Torres Date: Sat, 6 Jun 2026 17:37:44 -0400 Subject: [PATCH 3/5] Add link-check GitHub Action Runs on push and pull_request to catch broken links before merge: - `mkdocs build --strict` fails on broken internal links and missing nav targets - lychee checks external http/https links in docs and mkdocs.yml Auth-gated / bot-blocking hosts (ISMRM proceedings, Slack, Google Docs, LinkedIn) are listed in .lycheeignore so they don't cause unreliable failures. Co-Authored-By: Claude Opus 4.8 (1M context) --- .github/workflows/links.yml | 54 +++++++++++++++++++++++++++++++++++++ .lycheeignore | 5 ++++ 2 files changed, 59 insertions(+) create mode 100644 .github/workflows/links.yml create mode 100644 .lycheeignore diff --git a/.github/workflows/links.yml b/.github/workflows/links.yml new file mode 100644 index 0000000..e59df61 --- /dev/null +++ b/.github/workflows/links.yml @@ -0,0 +1,54 @@ +name: Check links + +# Catches broken links before they reach master. Two layers: +# 1. `mkdocs build --strict` fails on broken internal links and missing +# navigation targets. +# 2. lychee checks external (http/https) links in the docs and mkdocs.yml. +# Hosts that require a login or block automated requests are listed in +# .lycheeignore so they don't produce unreliable failures. + +on: + push: + pull_request: + workflow_dispatch: + +permissions: + contents: read + +jobs: + links: + runs-on: ubuntu-latest + steps: + - name: Checkout repository + uses: actions/checkout@v4 + with: + fetch-depth: 0 + + - name: Set up Python + uses: actions/setup-python@v5 + with: + python-version: '3.x' + + - name: Install dependencies + run: | + python -m pip install --upgrade pip + pip install -r requirements.txt + + - name: Build site (fails on broken internal links and nav) + run: mkdocs build --strict + + - name: Check external links + uses: lycheeverse/lychee-action@v2 + with: + args: >- + --no-progress + --scheme http + --scheme https + --accept 200,206,429 + --max-retries 2 + "docs/**/*.md" + "mkdocs.yml" + "Readme.md" + fail: true + env: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} diff --git a/.lycheeignore b/.lycheeignore new file mode 100644 index 0000000..907957c --- /dev/null +++ b/.lycheeignore @@ -0,0 +1,5 @@ +cds\.ismrm\.org +slack\.com +docs\.google\.com +linkedin\.com +lnkd\.in From 884d94cad1cd3dc7f83e8acb8f28bb980840e49c Mon Sep 17 00:00:00 2001 From: Luis Torres Date: Sat, 6 Jun 2026 17:42:31 -0400 Subject: [PATCH 4/5] Tune link checker and fix broken GSoC report link MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit - Accept 403/429/503 (publisher and doi.org bot-blocks / transient) so valid citation links don't fail; 404s and connection errors still fail - Drop Readme.md from the scan (its localhost example is not a real link) and ignore the SSL-broken eprints.drcmr.dk host - gsoc.md: the linked README no longer exists (404) — point to the project repository instead Co-Authored-By: Claude Opus 4.8 (1M context) --- .github/workflows/links.yml | 7 ++++--- .lycheeignore | 1 + docs/gsoc.md | 2 +- 3 files changed, 6 insertions(+), 4 deletions(-) diff --git a/.github/workflows/links.yml b/.github/workflows/links.yml index e59df61..a6aa4b3 100644 --- a/.github/workflows/links.yml +++ b/.github/workflows/links.yml @@ -5,7 +5,9 @@ name: Check links # navigation targets. # 2. lychee checks external (http/https) links in the docs and mkdocs.yml. # Hosts that require a login or block automated requests are listed in -# .lycheeignore so they don't produce unreliable failures. +# .lycheeignore. Publishers and doi.org commonly return 403/429 to bots even +# for valid links, so those codes (plus transient 503) are accepted; genuine +# 404s, dead domains, and connection errors still fail the build. on: push: @@ -44,11 +46,10 @@ jobs: --no-progress --scheme http --scheme https - --accept 200,206,429 + --accept 200,206,403,429,503 --max-retries 2 "docs/**/*.md" "mkdocs.yml" - "Readme.md" fail: true env: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} diff --git a/.lycheeignore b/.lycheeignore index 907957c..f2e0bfe 100644 --- a/.lycheeignore +++ b/.lycheeignore @@ -3,3 +3,4 @@ slack\.com docs\.google\.com linkedin\.com lnkd\.in +eprints\.drcmr\.dk diff --git a/docs/gsoc.md b/docs/gsoc.md index 2956b6c..de8fe9f 100644 --- a/docs/gsoc.md +++ b/docs/gsoc.md @@ -15,7 +15,7 @@ OSIPI participates in the Google Summer of Code (GSoC) program to expand its con **Hanliang Xu** created a tool that automatically extracts and generates "ASL parameters" from DICOM and BIDS images. This tool is designed to assist researchers in easily describing standardized imaging parameters in their scientific publications. This work is related to TF4.1. -See the [tool here](https://osipi.ismrm.org/task-forces/tf4-1/asl-methods-generator/). [Read the full report](https://github.com/Hanliang-Xu/Hanliang-Xu.github.io/blob/main/README.md). +See the [tool here](https://osipi.ismrm.org/task-forces/tf4-1/asl-methods-generator/). [View the project repository](https://github.com/Hanliang-Xu/Hanliang-Xu.github.io). ### Setting up a framework for large-scale development From 42349fe31584dca5b8be19c7102f1a049326ff63 Mon Sep 17 00:00:00 2001 From: Luis Torres Date: Sat, 6 Jun 2026 17:44:45 -0400 Subject: [PATCH 5/5] Fix two ASL literature DOI links with trailing period The migrated markdown captured the sentence-ending period into the URL, producing 404s. Caught by the new link checker. Co-Authored-By: Claude Opus 4.8 (1M context) --- docs/aslliterature.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/aslliterature.md b/docs/aslliterature.md index 6034fde..188bb66 100644 --- a/docs/aslliterature.md +++ b/docs/aslliterature.md @@ -50,9 +50,9 @@ Key manuscripts in perfusion MRI, curated by OSIPI Task Force 5.2 for those gett - Wong EC. An introduction to ASL labeling techniques. J Magn Reson Imaging. 2014 Jul;40(1):1-10. Revised: - Michael Chappell, Bradley MacIntosh, and Thomas Okell. [​​Introduction to Perfusion Quantification using Arterial Spin Labelling Oxford Neuroimaging Primers](https://doi.org/10.1093/oso/9780198793816.003.0001) - Grade M et al. [A neuroradiologist’s guide to arterial spin labeling MRI in clinical practice. Neuroradiology. 2015 57:1181–202.](https://doi.org/10.1007/s00234-015-1571-z) -- Clement P et al. [Variability of physiological brain perfusion in healthy subjects - A systematic review of modifiers. Considerations for multi-center ASL studies. J Cereb Blood Flow Metab. 2018 Sep;38(9):1418-1437](https://doi.org/10.1177/0271678X17702156.) +- Clement P et al. [Variability of physiological brain perfusion in healthy subjects - A systematic review of modifiers. Considerations for multi-center ASL studies. J Cereb Blood Flow Metab. 2018 Sep;38(9):1418-1437](https://doi.org/10.1177/0271678X17702156) - Aguirre GK, Detre J a., Wang J. [Perfusion fMRI for Functional Neuroimaging. Int Rev Neurobiol 2005; 66:213–236](https://doi.org/10.1016/S0074-7742(05)66007-2) -- Haller S, Zaharchuk G, Thomas DL, Lovblad KO, Barkhof F, Golay X. [Arterial Spin Labeling Perfusion of the Brain: Emerging Clinical Applications. Radiology. 2016 Nov;281(2):337-356.](https://doi.org/10.1148/radiol.2016150789.) +- Haller S, Zaharchuk G, Thomas DL, Lovblad KO, Barkhof F, Golay X. [Arterial Spin Labeling Perfusion of the Brain: Emerging Clinical Applications. Radiology. 2016 Nov;281(2):337-356.](https://doi.org/10.1148/radiol.2016150789) - Odudu A et al. [Arterial spin labelling MRI to measure renal perfusion: a systematic review and statement paper. Nephrol Dial Transplant. 2018 Sep 1;33(suppl_2):ii15-ii21](https://doi.org/10.1093/ndt/gfy180) - Nery F et al. [Consensus-based technical recommendations for clinical translation of renal ASL MRI. MAGMA. 2020 Feb;33(1):141-161](https://doi.org/10.1007/s10334-019-00800-z)