From matthew.m.mccormick at gmail.com Mon May 1 20:39:52 2023 From: matthew.m.mccormick at gmail.com (Matthew McCormick) Date: Mon, 1 May 2023 20:39:52 -0400 Subject: [Neuroimaging] 2nd Get Your Brain Together Hackathon Email Announcement Message-ID: 2nd Get Your Brain Together Hackathon ===================================== What? ----- The **Get Your Brain Together** hackathons **bring together neuroimage data generators, image registration researchers,** and **neurodata compute infrastructure providers** for a **hands-on, collaborative event**. This community collaboration aims to create reproducible, open source resources that enable discovery of the structure and function of brains. There are three components to the hackathon. First, the primary goal of each hackathon is the generation of a **Reproducible Resource** for registration and analysis of a specific brain imaging modality. **Tutorial** sessions share how to work with open source registration tools, open access datasets, or neurodata archives. **Birds-of-a-Feather (BOF) Breakout** sessions enable participants interested in collaborating to work on relevant topics. This hackathon will focus on registration of **mouse brain lightsheet volumes** to the Common Coordinate Framework version 3.1 (CCFv3.1). Example ways to participate: * [Contribute a registration pipeline resource](https://insightsoftwareconsortium.github.io/GetYourBrainTogether/HCK02_2023_Allen_Institute_Hybrid/#reproducible-resource-challenge) to register the challenge datasets. * [Give a tutorial](https://insightsoftwareconsortium.github.io/GetYourBrainTogether/HCK02_2023_Allen_Institute_Hybrid/#tutorials) about your registration tools. A pre-recorded or live presentation, along with example code and recipes, can teach a data analyst how to run your tool and use the output on the challenge dataset and/or another open dataset. * [Come and learn](https://insightsoftwareconsortium.github.io/GetYourBrainTogether/HCK02_2023_Allen_Institute_Hybrid/#birds-of-a-feather-breakouts) about registration from experts in the field. When, where? ------------ * Dates: Monday, May 22nd - Tuesday, May 23, 2023 * Location: The second hackathon will be a hybrid in-person and online event, held: * At the [Allen Institute in Seattle, WA, USA](https://alleninstitute.org/) * On Zoom videoconferencing * [Image.sc Island Gather.Town](https://j.mp/imagesc-island) virtual space, and * [Image.sc Zulip Chat](https://imagesc.zulipchat.com/). If traveling to attend in-person, * [Courtyard by Marriott Seattle Downtown/Lake Union](https://goo.gl/maps/mAgTi3ZHWvBCC5Fq8) * [EVEN Hotel Seattle - South Lake Union, an IHG Hotel](https://www.reservationdesk.com/hotel/6255f19/even-hotel-seattle-south-lake-union-seattle-wa/) * [Astra Hotel Seattle](https://astrahotelseattle.com/) * [Pan Pacific Seattle](https://www.panpacific.com/en/hotels-and-resorts/pp-seattle.html) are among nearby hotels. * Lead organizers / contacts: Matt McCormick (Kitware), Sharmishtaa Seshamani (Allen Institute for Neural Dynamics) * Registration: Limited seats will be available for in-person attendance. Registration details will be announced in the mailing list below. * Communication: to receive information about this and future events please join the [Hackathon Mailing List](https://groups.google.com/g/brain_straight_hackathon_announcements) How does it work? ----------------- Before the Hackathon * [Register](https://forms.gle/Z1Xzknz6Uxh5A7RZ7) for the event. * Sign up for the [mailing list](https://groups.google.com/g/brain_straight_hackathon_announcements). * Optionally prepare a tutorial or organize a Birds-of-a-Feather (BoF) Breakout. During the Hackathon -------------------- The week will start at 9 AM Pacific Time, 12 AM Eastern Time, Monday, May 22nd in an introductory all-hands videoconference. Following the introduction, participate in the Reproducible Resource Challenge, join the tutorials, and participate in BoF breakouts. Please bring a laptop. At the end of the day on Tuesday, participants will delegate one member to present their registration processing pipelines, results, and discuss lessons learned. For more information, visit: https://bit.ly/2nd-get-your-brain-together-hackathon From avesani at fbk.eu Mon May 8 09:48:29 2023 From: avesani at fbk.eu (Paolo Avesani) Date: Mon, 8 May 2023 15:48:29 +0200 Subject: [Neuroimaging] Open PhD Position on Machine Learning for Brain Connectivity in Clinical Neuroscience Message-ID: OPEN PHD POSITION ON MACHINE LEARNING FOR BRAIN CONNECTIVITY IN CLINICAL NEUROSCIENCE We are pleased to announce the opening of one PhD position in neuroinformatics at the International Doctoral School in Cognitive and Brain Sciences (CIMeC) of the University of Trento, Italy. The PhD Grant is funded by the Neuroinformatics Laboratory (NILab) of Fondazione Bruno Kessler (FBK). This project is in collaboration with the School of Medicine of the University of Trento and the Division of Neurosurgery, S. Chiara Hospital, Trento. Clinical neuroscience is playing a key role in the understanding of the brain with data of pathological alterations. The detection of anomalies in the brain structure and function is a crucial step not only for diagnosis and prognosis but also to decode the connectome of the human brain. Data driven approaches are providing promising results to characterize the patterns of the healthy brain. The challenge is to disentangle the intrinsic interindividual differences in the brain structure and function with respect to alterations related to cognitive impairment. The research objective is to investigate the most innovative techniques of Artificial Intelligence, such as geometric deep learning, to translate the knowledge of connectivity structures from a healthy population to the individual patients of a clinical study. The ultimate goal is the development of computational methods to support the detection of altered structures in the connectome affected by brain disorders. The successful candidate will have a MSc in computer science, biomedical engineering, physics, or any STEM discipline. Hands-on training in neuroimaging data analysis and/or software tools for brain connectivity will be highly valued. For reference to recent work of relevance to this project, please see Astolfi et al. MICCAI (2020), Legarreta et al., Medical Image Analysis (2021). The position is for a 4 year PhD program (Nov. 1, 2023- Oct. 31, 2027). Courses are in English. The salary is starting at approximately ?1.200/mo., net. An additional personal budget of around ?5.000 is provided for research and mobility. 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-excellence-in-three-areas ). Why choose Trento? ( http://www.unitn.it/en/ateneo/1629/why-choose-the-university-of-trento) Important dates: Deadline for application: 31 May 2023 Evaluation interview: 25 June 2023 Beginning of PhD program: 1 November 2023 Apply now: https://webapps.unitn.it/Apply/en/Web/GoHome/dott/cbs39 https://www.unitn.it/drcimec/105/2023-topic-specific-grants-and-descriptions You are kindly invited to contact in advance Paolo Avesani (paolo.avesani@ unitn.it). -- -- 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 finalit? 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. -------------- next part -------------- An HTML attachment was scrubbed... URL: From christine.r.farrugia at um.edu.mt Tue May 9 09:17:50 2023 From: christine.r.farrugia at um.edu.mt (Christine Farrugia) Date: Tue, 9 May 2023 15:17:50 +0200 Subject: [Neuroimaging] NiBabel on TestPyPI Message-ID: Hi, Would it be possible to make NiBabel available on TestPyPI please? Regards, Christine Farrugia -- Christine Farrugia | Scientific Officer B.Sc. (Hons.) M.Phil. Ph.D. MRI Lab (TRAKE) Faculty of Engineering Room 104, Biomedical Sciences Building +356 2340 3212 -------------- next part -------------- An HTML attachment was scrubbed... URL: From markiewicz at stanford.edu Fri May 12 08:48:51 2023 From: markiewicz at stanford.edu (Christopher Markiewicz) Date: Fri, 12 May 2023 12:48:51 +0000 Subject: [Neuroimaging] NiBabel on TestPyPI In-Reply-To: References: Message-ID: Hi Christine, That would require us to change our packaging setup. test.pypi.org does not accept packages with local version specifiers, and the utility we use for to generate versions based on the git history inserts local version specifiers. I'm curious: What is your use case for having packages on test.pypi.org? Best, Chris ________________________________________ From: Neuroimaging on behalf of Christine Farrugia Sent: Tuesday, May 9, 2023 09:17 To: neuroimaging at python.org Subject: [Neuroimaging] NiBabel on TestPyPI Hi, Would it be possible to make NiBabel available on TestPyPI please? Regards, Christine Farrugia -- [https://lh3.googleusercontent.com/C8WgS4LdUUvVfIn0LqF5Zfq7ZxeJuYueElb2wWMj9kaiZ-YE7g97vRDyFxO7uBWilMujyPWxOSjN4NEttHVvw3TbB83au-8LTWlfCEDu7_z64udwHnGGKtw96KvEMWNgSE4o-_SC] Christine Farrugia | Scientific Officer B.Sc. (Hons.) M.Phil. Ph.D. MRI Lab (TRAKE) Faculty of Engineering Room 104, Biomedical Sciences Building +356 2340 3212 From pestilli at utexas.edu Wed May 24 14:41:07 2023 From: pestilli at utexas.edu (Franco Pestilli) Date: Wed, 24 May 2023 13:41:07 -0500 Subject: [Neuroimaging] September 14-15 2023 Big Data Workshop Ohio State University Message-ID: Dear All We are pleased to announce the *Advanced Computational Neuroscience Network (ACNN) Big Data Workshop for 2023 will be taking place September 14 and 15* at the Ohio State University. This conference will feature national and international experts in neuroimaging, biomedical research, neuroscience, and data science, with a focus on highly dense behavioral and physiological data integration. The speakers will address challenges and successes in the integration of multimodal, multidimensional, multiscale data, regarding data standards, representation, and sharing. A workshop on the second day will focus on reproducible methods in neuroimaging. Students and trainees are encouraged to register and present a poster in the datablitz and poster sessions, and to interact with the speakers! Posters and presentations on neuroimaging, deep phenotyping analysis, heterogeneous dataset analyses with relevance to human neuroscience, and neuroinformatics, for example, are all welcome. The schedule of speakers and topics is in the attached flyer, and on our website!! When registration opens, current information will also be found here: https://neurosciencenetwork.org/ACNN_Workshop_2023.html We would greatly appreciate it, if you could share the announcement with your local mailing lists. Local organizers: Jessica Turner and Lei Wang *FRANCO PESTILLI*, *Ph.D.* | *Associate Professor* Department of Psychology | College of Liberal Arts | The University of Texas at Austin he/him | pestilli at utexas.edu | web | GitHub | Founder and Director brainlife.io Co-Chair Data Working Group internationalbraininitiative.org Director Wellcome-Kavli International Governance for Neurodata Director Brain Imaging Data Structure (BIDS) Connectivity Project Program Committee Association for Psychological Science CONFIDENTIALITY NOTICE: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message. -------------- next part -------------- An HTML attachment was scrubbed... URL: