Migrate osipi content

.github/workflows/links.yml

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+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. 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:
+  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 200,206,403,429,503
+            --max-retries 2
+            "docs/**/*.md"
+            "mkdocs.yml"
+          fail: true
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.lycheeignore

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+cds\.ismrm\.org
+slack\.com
+docs\.google\.com
+linkedin\.com
+lnkd\.in
+eprints\.drcmr\.dk

docs/about.md

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+# 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)

docs/aslliterature.md

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+# 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)