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DTSTART;TZID=Europe/Zurich:20240909T000000
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SUMMARY:fMRIPrep Bootcamp
DESCRIPTION:															\nThe CIBM Center for Biomedical Imaging is proud to announce its inaugural Bootcamp for fMRI researchers, focusing on the use of the fMRIPrep pipeline to prepare their fMRI data for analysis, including 7T fMRI. \nThis intensive 3-day bootcamp will cover all the steps of the preprocessing pipeline from BIDS and containers up to the interpretation of the analysis results. It will be led by two of the founders and principal developers of the fMRIPrep pipeline, Dr. Oscar Esteban and Dr. Chris Markiewicz. This is a unique opportunity to gain hands-on experience and deep insights directly from the experts who created the tool.\nThe fMRIPrep Bootcamp will be held from 9th to 11th September 2024 from 8:30am to 5:00pm at CMU, University of Geneva. The Bootcamp is designed for PhD students , post docs and research staff who are familiar with fMRI. \nRegistration is now closed\nLEARNING OUTCOMES\nAt the end of this course, we expect to have provided you with the following skills and abilities:\n\n Upload large neuroimaging datasets into HPC systems\nUnderstand BIDS, data organization, and the implications of these topics on reproducibility\nDeploy a data management strategy to future-proof your analyses\nProcess large datasets within HPC and desktop systems\nMaster the basics of containerization as a way to make analyses more reproducible\nExecute fMRIPrep on large datasets, understand and finally resolve issues that emerge down the line\nRecognize and operate on the fMRIPrep outputs to build your final fMRI analyses\nCritically evaluate the outputs of fMRIPrep to determine the quality of the processing\nAssess the quality of unprocessed images with MRIQC\n\nBOOTCAMP INSTRUCTORS\nThe Bootcamp will be taught by Dr Oscar Esteban (CHUV) and Dr Chris Markiewicz (Stanford University), two founders and main developers of the pipeline, so don’t miss out on this occasion!\n																														\nOscar Esteban\nLausanne University Hospital\nBIO\nOscar Esteban is a Research and Teaching Ambizione FNS Fellow at the Service of Radiology of the Lausanne University Hospital (CHUV) and the University of Lausanne. Oscar’s research aims at pushing the boundaries of human and nonhuman neuroimaging —magnetic resonance imaging (MRI) most often,— and by that, help other researchers advance our understanding of the brain. In more specific terms, Oscar is currently developing tools that cater to researchers with “analysis-grade” data (see www.nipreps.org for more on this concept,) so they can focus on statistical modeling and inference. Perhaps, the flagship of these tools is fMRIPrep. Oscar actively investigates the reliability and validity of diffusion and functional MRI measurements. As a fundamental step of the neuroimaging workflow, Oscar wants to improve the computational reproducibility of our results and minimize this methodological variability in the preprocessing step by standardizing workflows and reaching consensus implementations. In the longer term, Oscar’s vision is to contribute to uncovering the interplay of structure, function, and dynamics of brain connectivity using MRI.\n			\n											+BIO\n					\n																														\nChris Markiewicz\nStanford University\nBIO\nChristopher Markiewicz is a software developer for the Poldrack Lab at Stanford University and a research affiliate of the McGovern Institute for Brain Research. He has been a core developer of fMRIPrep and FitLins, and is a contributor to and maintainer of several open source, Python neuroimaging libraries, including Nipype and NiBabel.\n			\n											+BIO\n					\nPRELIMINARY PROGRAMME\nDAY 1 : September 9, 2024\n8h30: Welcome \n9h00: Opening of the Workshop\n9h30: Overview of the fMRI neuroimaging pipeline, fMRIPrep\n10h30: Coffee Break\n10h45: BIDS\n11h30: Overview of the 7T fMRI dataset\n12h00: Lunch Break\n13h30: Hands-on – Access to data on HPC\n14h30: Introduction to Containers\n15h00: Coffee Break\n15h15: Hands-on – first run of fMRIPrep on the 7T fMRI dataset\n17h00: End\n18h00: Welcome Dinner\n\nDAY 2 : September 10, 2024\n8h30: Arrival\n9h00: Fixing common fMRIPrep errors, Parallelisation and Resource planning\n10h30: Coffee Break\n10h45: Analysing data processed with fMRIPrep\n12h00: Lunch Break\n13h30: Quality control\n15h00: Coffee Break\n15h15: Hands-on advanced processing using fMRIPrep, run fMRIPrep on own data\n17h00: End\n\nDAY 3 : September 11, 2024\n8h30: Arrival \n9h00: Hackathon project pitches\n10h30: Coffee break\n10h45: Hacking!\n12h00: Lunch break\n13h00: Hacking\n15h00: Coffee break\n15h15: Round table – showcase results.\n16h30: End \n
URL:https://cibm.ch/event/fmriprep-bootcamp/
CATEGORIES:Public event
LOCATION:Centre Médical Universitaire, University of Geneva
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