Mailman 3 February 2022 - DIPY

DIPY Workshop 2022 - Online Edition
by Eleftherios Garyfallidis March 11, 2022

March 11, 2022

Dear Neuroimaging Community, The Online DIPY Workshop is back with a great lineup of topics and speakers! Please forward this email to any interested parties. [image: image.png] For registration and more information please visit https://dipy.org/workshops/latest On behalf of the DIPY team, Eleftherios Garyfallidis, PhD Assistant Professor Intelligent Systems Engineering Indiana University Luddy Hall 700 N Woodlawn Bloomington, IN 47408 GRG <https://grg.luddy.indiana.edu/> | DIPY <http://dipy.org/> | FURY <https://fury.gl/>

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Postdoctoral position: neuroinformatics and neuroscience of aging
by Ariel Rokem Feb. 28, 2022

Feb. 28, 2022

The Neuroinformatics Research & Development Group at the University of Washington Department of Psychology and eScience Institute <https://neuroinformatics.uw.edu/> conducts research on the biological basis of brain function using computational tools that we develop and maintain. We are seeking to fill an open position for a postdoctoral researcher. The successful candidate will have the opportunity to work together with a wide network of collaborators on data from the Adult Changes in Thought Study <https://www.kpwashingtonresearch.org/our-research/research-areas/aging-geri…>. The position is funded through a new 5-year NIH grant <https://www.kpwashingtonresearch.org/news-and-events/recent-news/news-2021/…> . The researcher will have an opportunity to ask a range of questions and study unique datasets of multi-modal imaging data that include longitudinal measurements of functional MRI, diffusion MRI, ante- and post-mortem measurements of structural MRI, as well as histological measurements conducted in the same individuals. These measurements are done in the context of a wealth of measurements of cognition, health, lifestyle, and environment. The position provides an opportunity to develop novel analysis pipelines and statistical methods to process, merge, and interpret these datasets in light of scientific questions about the brain basis of cognitive aging, with a particular focus on Alzheimer’s disease. *Required qualifications:*- PhD in Psychology, Neuroscience, or related fields. - Strong programming skills (preferably in the Python programming language) - (Experience analyzing large, complex, and heterogeneous datasets is preferred) Interested applicants should send a cover letter detailing their research interests, CV and the names of three references to arokem(a)uw.edu or apply through: https://apply.interfolio.com/94186

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Postdoctoral Fellowship in Deep Learning Applied to Magnetic Resonance Imaging/Physics
by While, Peter Thomas Feb. 28, 2022

Feb. 28, 2022

Dear colleagues, please let me draw your attention to a job posting for a postdoctoral fellowship at St. Olav's University Hospital in Trondheim, Norway. We seek a highly motivated researcher with a background in MRI physics, image processing and/or deep learning, to contribute to the project: "Deep learning cancer diagnostics from diffusion-weighted magnetic resonance imaging". The postdoc will have the opportunity to work on diverse topics according to their experience and interests. For example, they may contribute to work exploring the use of novel acquisition strategies for diffusion-weighted imaging, image reconstruction involving deep learning, pulse sequence development, advanced diffusion modelling and parameter estimation, and novel image processing techniques. The deadline for applications is the 20th of March. Further details can be found in the advert on the ISMRM Career Center: https://www.ismrm.org/jobs/j07827.pdf Best regards, Peter Peter T. While, Ph.D. Department of Radiology and Nuclear Medicine St. Olav's University Hospital Trondheim, Norway Email: Peter.Thomas.While(a)stolav.no<mailto:Peter.Thomas.While@stolav.no> Tlf: +47 728 36627

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Open Meeting - Coding Sprint - Starts in 15 min
by Koudoro, Serge Feb. 24, 2022

Feb. 24, 2022

Hello all, Just a friendly reminder concerning the DIPY Open Meeting - Coding Sprint it starts in 15 minutes! (1 pm Eastern Time (7pm CET / 10am PT)). During this meeting, we will create a breakout room to focus on different topics: * Your question/problem. an open breakout room will be available to help you with and specific subject. * QTI Model * Streamlines Linear Registration * DIPY Horizon (#2429) * Multithreading (#2519) Duration: 45min 1h15min Connect here: https://iu.zoom.us/j/84926066336 Schedule: https://github.com/dipy/dipy/discussions/2398 See you soon, On Behalf of the DIPY Team Serge Koudoro Software Developer Intelligent Systems Engineering Garyfallidis Research Group<https://grg.luddy.indiana.edu/> School of Informatics, Computing, and Engineering Luddy Hall 700 N Woodlawn Ave, 4056 Bloomington, IN 47408 skoudoro(a)iu.edu<mailto:skoudoro@indiana.edu>

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Open Meeting - Coding Sprint
by Koudoro, Serge Feb. 23, 2022

Feb. 23, 2022

Hello all, This week (Thursday, February 24th), at 1 pm Eastern Time (7pm CET / 10am PT), the theme of the Open Meeting is Code Sprint. During this meeting, we will create a breakout room to focus on different topics: * Your question/problem. an open breakout room will be available to help you with and specific subject. * QTI Model * Patch2Self * Streamlines Linear Registration * DIPY Horizon (#2429) * Multithreading (#2519) Duration: 45min 1h15min Connect here: https://iu.zoom.us/j/84926066336 Schedule: https://github.com/dipy/dipy/discussions/2398 See you Tomorrow, On Behalf of the DIPY Team Serge Koudoro Software Developer Intelligent Systems Engineering Garyfallidis Research Group<https://grg.luddy.indiana.edu/> School of Informatics, Computing, and Engineering Luddy Hall 700 N Woodlawn Ave, 4056 Bloomington, IN 47408 skoudoro(a)iu.edu<mailto:skoudoro@indiana.edu>

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International Neuro Summer School 2022 Lipari (Italy)
by Alex Crimi Feb. 14, 2022

Feb. 14, 2022

Dear Colleagues, I would like to invite you to | | | | | | | | | | | | | | A first edition of the Neuro Summer School dedicated to bridging global neuroscience world International Neuro Imaging Summer School 4th-9th July 2022 | | | | | | | | | | It’s time to put our brains together! After the pandemic of the last 2 years, we want to restart connecting people working on neuro-imaging, neuro-oncology, and neuroscience. N3S2 is calling! 4th-9th July 2022, the Lipari Island, the best opportunity to meet world-class scientists and discover neuro-imaging, neuro-oncology, neuro-science. Meet great brains and participate in fruitful discussions, share the scientific passion in the idyllic background of the Aeolian Islands. Join N3S2 Summer School. The event will be held at the Aktea hotel of Lipari (ME) in Italy. | | | | | Apply now | | | | | | | | | Meet our speakers! | | | | | | | | | | | | | | The N3S2 idea and what to expect | | | | | | - Theoretical lectures by well-known experts - Practical workshops - Networking (event around the Stromboli Volcano) - Poster session - Culinary experience guaranteed by the Mediterranean flavors - … even dolphins’ watching is possible! Sounds like a perfect beginning of summer? Si! Absolutely yes! Join us!!! | | | | | Apply | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Sano – Centre for Computational Personalised Medicine - International Research Foundation sano.science | info(a)sano.science Czarnowiejska 36 building C5 30-054 Kraków, Poland | | | | | | | | | | This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 857533 and from the International Research Agendas Programme of the Foundatin for Polish Science No MAB PLUS/2019/13. | | | | | | | | | | | | | |

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Open Meeting - Future Plan, Talks, and Coding Sprint
by Koudoro, Serge Feb. 10, 2022

Feb. 10, 2022

Hello all, A new exciting year has started! It is time to start the first DIPY Open Meeting! During this meeting, we will: * Talk of the future plans of DIPY including preparation for the workshop * Coding Sprint: We recommend to all DIPY Core maintainers to be present (everyone is welcome) The meeting will be held on Thursday, February 10th, at 1 pm Eastern Time (7pm CET / 10am PT). The zoom link for this meeting is https://iu.zoom.us/j/84926066336 More information about the open meetings is available here: https://github.com/dipy/dipy/discussions/2398 See you tomorrow, On Behalf of the DIPY Team, Serge Koudoro Software Developer Intelligent Systems Engineering Garyfallidis Research Group<https://grg.luddy.indiana.edu/> School of Informatics, Computing, and Engineering Luddy Hall 700 N Woodlawn Ave, 4056 Bloomington, IN 47408 skoudoro(a)iu.edu<mailto:skoudoro@indiana.edu>

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Postdoctoral Fellowship in Machine Learning for Brain Connectivity in Clinical Neuroscience
by Paolo Avesani Feb. 9, 2022

Feb. 9, 2022

A postdoctoral fellowship in Machine Learning for Brain Connectivity in Clinical Neuroscience We are pleased to announce the opening of one Postdoctoral Fellowship at the Neuroinformatics Lab, an interdisciplinary initiative between the Center for Mind/Brain Sciences (CIMeC) of the University of Trento, and the Center for Digital Health of Fondazione Bruno Kessler. The position is part of the “Neusurplan” project, an integrated approach to neurosurgery planning based on multimodal and longitudinal data. The goal is to pursue an integrated approach to pre-operative neurosurgical planning, combining structural and functional characterization of brain connectivity. The data driven strategy will take advantage of a unique dataset of intra-operative points of directed electrical stimulation and the related functional responses. In this project, the candidate will pursue research on machine learning methods for neuroimaging data analysis to study and characterize brain connectivity, with applications to longitudinal studies and clinical practice. The ideal candidate should have a mixed background in neuroimaging techniques and numerate disciplines, like computer science, engineering, physics, or mathematics. This project is in collaboration with the Division of Neurosurgery, S. Chiara Hospital, Trento (IT). The position is for a 2 year Postdoc Fellowship (May, 2022 - April, 2024). We welcome expressions of interest for this position, please contact Paolo Avesani (paolo.avesani(a)unitn.it) and/or Emanuele Olivetti (olivetti(a)fbk.eu) with your CV and a statement of intent. The University of Trento ranks among top Italian Universities ( https://www.unitn.it/en/ateneo/1636/rankings). Fondazione Bruno Kessler ranks first among the Italian research centers in Engineering and Computer Science ( https://magazine.fbk.eu/en/news/fbk-ranks-1st-in-italy-for-scientific-excel… ). To also consider a work/life balance, there is more than our passion for translational research. You can check these pointers for a flavor of life quality in Trentino: https://www.visittrentino.info/en; https://www.discovertrento.it/en A few papers related to the project are below: Bertò G,et al., (2021) Classifyber, a robust streamline-based linear classifier for white matter bundle segmentation, Neuroimage, 224 https://doi.org/10.1016/j.neuroimage.2020.117402 Sarubbo S, et al., (2020) Mapping critical cortical hubs and white matter pathways by direct electrical stimulation: an original functional atlas of the human brain, Neuroimage, 205 https://doi.org/10.1016/j.neuroimage.2019.116237 Astolfi P, et al., (2020) Tractogram filtering of anatomically non-plausible fibers with geometric deep learning, International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI) LNCS, vol 12267. Springer https://doi.org/10.1007/978-3-030-59728-3_29 Sarubbo S, et al., (2021) Planning brain tumor resection using a probabilistic atlas of cortical and subcortical structures critical for functional processing: a proof of concept, Operative Neurosurgery, 20(3), 175-183 https://doi.org/10.1093/ons/opaa396 -- -- Le informazioni contenute nella presente comunicazione sono di natura privata e come tali sono da considerarsi riservate ed indirizzate esclusivamente ai destinatari indicati e per le finalità strettamente legate al relativo contenuto. Se avete ricevuto questo messaggio per errore, vi preghiamo di eliminarlo e di inviare una comunicazione all’indirizzo e-mail del mittente. -- The information transmitted is intended only for the person or entity to which it is addressed and may contain confidential and/or privileged material. If you received this in error, please contact the sender and delete the material.

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NeuroHackademy 2022: Call for applications
by Ariel Rokem Feb. 8, 2022

Feb. 8, 2022

We are happy to announce a call for applications to participate in NeuroHackademy 2022! This two-week hands-on workshop will be held in a hybrid format, July 25th - August 5th, 2022 at the University of Washington in Seattle, Washington, USA and online. NeuroHackademy is an opportunity for participants to learn state-of-the-art methods for the analysis and management of large human neuroscience datasets while also networking and working with domain experts and each other on concrete neuroscience problems. The curriculum emphasizes large datasets of publicly available data (such as the Human Connectome Project, OpenNeuro, etc.), and on the value of making human neuroscience research open and reproducible. NeuroHackademy sessions in the first week will include lectures and tutorials on data science, machine learning, data visualization, and data resources, as well as extended Q&A sessions. The second week will be devoted primarily to participant-directed activities: guided work on team projects, hackathon sessions, and breakout sessions on topics of interest. If public health constraints related to COVID allow it, we will hold an in-person event in Seattle. Regardless, we will allow participants who are interested in this option to join the event through multiple online channels, including zoom-casts of lectures and breakout sessions, Slack conversations, and collaboration through GitHub and through the course’s online Juptyerhub. For more details and a preliminary list of instructors, see: https://neurohackademy.org/ We are now accepting applications to participate at: https://neurohackademy.org/apply/ Ideally, applicants should have some prior experience with programming and with neuroscience data analysis, but we welcome applications from participants with a variety of relevant backgrounds. Accepted applicants will be asked to pay a fee of $200 (in person) / $20 (online) upon final registration. Fees cover housing and two meals per day for in person participants. A limited number of fee waivers / travel grants will be available. Important dates: April 4th: application deadline May 2nd: Notification of acceptance May 23rd: Final registration deadline

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