From luddy at indiana.edu Fri Feb 16 09:31:02 2024 From: luddy at indiana.edu (IU Garyfallidis Research Group) Date: Fri, 16 Feb 2024 08:31:02 -0600 Subject: [Neuroimaging] You're Invited: DIPY Online Workshop 2024 Message-ID: <3f609c40-8432-424f-a3e9-f8e382a036d3@atl1s07mta2173.xt.local> Garyfallidis Research Group https://click.e.iu.edu/?qs=3128619092b8fee1696daddc4382ef8bf830a7e767ab23a707e8da78dac777470cc8f9d8ae13f2c97a70bd5b34576c2112ccd8812eeccc7a7c6e0d8ba7b1d455 Luddy School of Informatics, Computing, and Engineering https://click.e.iu.edu/?qs=3128619092b8fee1245bedc916a3d60b4609206e6cbc442dd999d06f83653becd42ae6dac987617f891985b19f328f1d0cfd855fb1511c0daef255f4cdccaa81 Garyfallidis Research Group https://click.e.iu.edu/?qs=3128619092b8fee1245bedc916a3d60b4609206e6cbc442dd999d06f83653becd42ae6dac987617f891985b19f328f1d0cfd855fb1511c0daef255f4cdccaa81 https://click.e.iu.edu/?qs=3128619092b8fee1245bedc916a3d60b4609206e6cbc442dd999d06f83653becd42ae6dac987617f891985b19f328f1d0cfd855fb1511c0daef255f4cdccaa81 Garyfallidis Research Group You're Invited:DIPY Online Workshop 2024 Dear Colleague, You're invited to attend the 2024 DIPY Online Workshop, a 5-day seminar geared towards training the next generation of scientists, doctors, and engineers how to effectively use the DIPY software and shape the future of medical imaging. Dive into the world of advanced imaging technology and data analytics by getting hands-on experience, work directly with experts and leaders in the field, and receive a Certificate of Attendance at the end of the program. MARCH 11-15 DIPY Online Workshop 2024 Monday, March 11 through Friday, March 15 https://click.e.iu.edu/?qs=3128619092b8fee13649b36accc02b649957fbdc59b51a45daa06b6a32f8be918d16421355be069a9dbbac54c1d88ba9bcd280dd97398238 Learn more and register DIPY is a powerful software library for analyzing and processing medical imaging data. It is an open-source project with a large and active community of contributors who are dedicated to advancing the field of medical imaging and artificial intelligence. This year, our distinguished keynotes are Professor Paul Thomson (USC), Professor Gary Zhang (UCL), and Professor Markus Nilsson (Lund). In addition, Professors Garyfallidis, Rokem, Tax, Grusso, Harezlak, Esteban, and others will discuss a variety of techniques involved in the process of medical imaging including but not limited to: Preprocessing, Reconstruction, Denoising, Microstructure modeling, Knowledge Distillation, and Tractography Visualization. We look forward to seeing you online! DIPY Team @dipymri https://click.e.iu.edu/?qs=3128619092b8fee12d60cda238c0ea6b052cdc9468a5236b7862d01f888aef7f5936041085367cc45ca47c5ed979b61b00d8383d57de1c96 https://click.e.iu.edu/?qs=3128619092b8fee18a35d8781ad0e115228dbdb2f2f28c5ead1a94f995c8fefcce504785be94115354a838174bbe163a9b851432a59bd580 https://click.e.iu.edu/?qs=3128619092b8fee10fb21f75f7a89df49de28cb68e229a30ef125e8447c1bc57695cd05566e0eb250bc81a69930049c17c76c3607e84b21d https://click.e.iu.edu/?qs=3128619092b8fee106d27d022dd7e5726d4517c0a4dc14cb1c7550f64f3dbafbef7acdf2150f93d26150baf29ccd3c8e4ff0a317ecc12403ea85904c85a602c7 https://click.e.iu.edu/?qs=3128619092b8fee1ad59d182f95df7630dd8f4154924edd7aaee71d558944b5da542864f14772216b61ed1fd423564e233e58f056b1f37fc3c444cf9e056834e https://click.e.iu.edu/?qs=3128619092b8fee19a1783e26364dcd2b9238306932ffb750989ca5ccb6d44a887678f6693ecab57a68ff2fd04525e821877cb225e9effa9 https://click.e.iu.edu/?qs=3128619092b8fee17dc9deaa08d046a6c92ad6f785002d0e3f69a2a8c9567309eee004d574b0b52c0ee9b4ab6e06a025d3245ed2546034b2 https://click.e.iu.edu/?qs=3128619092b8fee1896b54f56c4e9ac05a052dfd2c38730e48b1ea39ab70f899e82f9d3ea2758379cf7352f5926dc14ebf0aa361fc4be25e https://click.e.iu.edu/?qs=3128619092b8fee184a688f902784c5cee475301be1a1bc244f9637068b5e5e58b77e7da80ff1844f6003045362bc8bd3d965d0d12f47204 https://click.e.iu.edu/?qs=3128619092b8fee1d0d4297700abaf043eb591bd8897e8292af1f7c2598fc9c708b1840ea42d3d11e63643eb920fb32251ee6efc5e8d8c7d https://click.e.iu.edu/?qs=3128619092b8fee11b67f5193732846c066ad3f011eacc6b203b44d8bb42af51e0fc23b92422b68c2fc1944b8e2b714624d6b9bc126ceb81 https://click.e.iu.edu/?qs=3128619092b8fee19ae50cf3b6c441aa7afa1e70af221519e0d1f435f8fe01e4591b7a2ab30acbe5b0dfde97441a68a22f79377e1426f3f5 https://click.e.iu.edu/?qs=3128619092b8fee15b6b93b0b8292e861d537ddd983ad5a3d502da8c5cbf970ceb4c5b879ea02feb02778152129962506da8576025dcd8c6 https://click.e.iu.edu/?qs=3128619092b8fee1512ad49c01cb90a3e20f14599be743459ec5668db2f675f620d4d1e583819fb625634800149870016b7139ebfcb5780c Indiana University 107 S. 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URL: From vsr2119 at columbia.edu Thu Feb 15 16:21:16 2024 From: vsr2119 at columbia.edu (Vinay S Raghavan) Date: Thu, 15 Feb 2024 16:21:16 -0500 Subject: [Neuroimaging] [PySurfer] Strange Render Message-ID: Hi there, I'm working with PySurfer on a Linux machine (see attached for environment.yml). Whenever I try out any of the examples or any of my own data, things generally work. However, the overlays seem to depend on the camera angle. When I use the mouse to move the camera, it changes what gets seen (see attached mp4). These incomplete plots also occur when using the PNG backend. Have you encountered this issue before? Or do you have any ideas where to start? Thank you! Vinay Raghavan Columbia University in the City of New York Neural Acoustic Processing Lab -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: environment.yml Type: application/x-yaml Size: 8628 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: brain.mp4 Type: video/mp4 Size: 837822 bytes Desc: not available URL: From news at dipy.org Tue Feb 20 19:44:35 2024 From: news at dipy.org (news at dipy.org) Date: Wed, 21 Feb 2024 00:44:35 -0000 Subject: [Neuroimaging] Join us online for the DIPY Workshop 2024! March 11-15! Message-ID: <22becb5e45bd945e054f3386f4eb1d7d@yagmail>



Dear Colleague,

The DIPY workshop starts Monday March 11 2024 at 9am ET!

Register at https://dipy.org/workshop/latest





DIPY is a powerful software library for analyzing and processing medical imaging data. It is an open-source project with a large and active
community of contributors who are dedicated to advancing the field of medical imaging and artifical intelligence. The DIPY workshop provides
an excellent opportunity for individuals to learn how to use this software effectively. The workshop covers a broad range of topics, from
basic concepts to advanced techniques, and provides hands-on experience with the software. By attending the DIPY workshop, you will not only
learn how to use this powerful tool, but also gain a deeper understanding of diffusion imaging and machine learning for imaging in general.
The workshop is led by expert instructors who have extensive experience in both diffusion imaging and DIPY, so attendees can be confident
that they are receiving accurate and up-to-date information.

In summary, the workshop offers:

1. Hands-on tutorials - Every single day of the 5 days !!!
2. Guided practice sessions - We provide data but we also encourage you to bring your own data!
3. Personalized certificates of attendance.
4. Effective networking opportunities with one-to-one follow ups.
5. Comprehensive explanation of theoretical foundations with practical examples.
6. Access to latest and established methods with code and interfaces.
7. Pointers to move beyond the current challenges and navigate hard to do analyses.
8. Multiple clinical use cases (AZ, Parkinson?s, MS, etc.)

Finally, many more crosscutting AI methods will be presented in 2024!!! Do not miss!

Register now at https://dipy.org/workshop/latest

See you online!,
DIPY Team!
@dipymri




-------------- next part -------------- An HTML attachment was scrubbed... URL: From etienne.roesch at gmail.com Wed Feb 21 05:26:49 2024 From: etienne.roesch at gmail.com (Etienne B. Roesch) Date: Wed, 21 Feb 2024 10:26:49 +0000 Subject: [Neuroimaging] Join the ReproPsy & e-ReproNim Fellowship Programmes! Message-ID: Application Form: https://bit.ly/repro-school-fellowships Deadline: 15/03/2024 midnight anywhere in the world. Join the ReproPsy & e-ReproNim Fellowship Programmes! Are you passionate about robust, rigorous, and transparent research practices in Psychology and/or Neuroscience? Do you want ?1,000 or (slightly) more to fund training to enhance your skills in software and data management? Do you want to join a vibrant community of practice ? Look no further! This is a second call for the first edition of two Fellowship programmes, ReproPsy and e-ReproNim. These are unique opportunities to become part of a vibrant community dedicated to advancing open and robust data practices in Psychological and Neuroscientific research. By becoming a ReproPsy Fellow, you will join a network of like-minded researchers dedicated to advancing data practices in Psychology and Neuroscience. Our programmes offer more than just financial support?it provides a platform for collaboration, knowledge sharing, and professional growth. The project is led by Dr Jim Grange (Keele University, UK) and Dr Etienne Roesch (University of Reading, UK). They are part of the repro.school collective, and funded by the Research Data Alliance (RDA), in collaboration with the European Open Science Cloud (EOSC Future), and the UK Reproducibility Network?s Open Research Programme . The RDA aims to develop and adopt infrastructure that promotes data-sharing and data-driven research, thereby grounding the fellowship programmes in networks of data specialists. - ReproPsy is part of the RDA Psychology Data Interest Group ; - e-ReproNim is part of the RDA Neuroimaging Data Working Group , and the European sister project to the North American repronim.org . The UK Reproducibility Network is a grassroot movement, created organically by researchers in the UK in 2019, in response to the so-called reproducibility crisis. It now gathers active representatives of 70 research-intensive Universities in the UK and lead major projects. Other national Reproducibility Networks exist; there might be one closer to you ? If not, contact us and we?ll help you set up. Open Data in Psychology & Neuroimaging In a context where results of research are questioned, open data is transforming the landscape of our practices, enabling collaboration, reproducibility, and innovation. As Psychology & Neuroscience embraces this paradigm shift, we aim to equip researchers like you with the necessary skills and resources to adopt and adapt your data practices, ensuring greater impact and scientific progress, and helping you help your community. Project overview The mission of the Fellowship programme is to empower communities to excel in open data practices. In each programme we are offering 15 fellowships, each worth up to ?1,000, to support early career researchers (ECRs) from both EU and UK institutions. ECRs typically donate their time to upskill and transmit this new knowledge to their local communities. We expect the funding awarded to be directed towards helping you create opportunities for learning and teaching, helping you fund your own software and data management training, and organise bespoke training sessions at your home institution. The funding could for instance be used to organise training from the Carpentries (http://carpentries.org) or similar venues; or, should your local policies on workload allocation permit, you could use the funding to offset time commitment towards such training, in agreement with your line manager. What we ask of you in return is a commitment to participate in the online events organised (at least once a month) and in the projects that may arise, such as scoping and designing training needs, contributing to writing training material, and other projects that you may bring to the table! More information about the programmes and to access the application form (including dropbox link to submit letters of support, evidence of claims and invoices), please visit https://repro.school/2023/05/31/join-the-repropsy-e-repronim-fellowship-programmes/ . Important: Because of constraints imposed on the funding, we must have received all claims and invoices for selected Fellows by the 31/3/2024. The deadline for application is 15/3, and applicants must include all claims and invoices in their application. Applications and documents sent after the deadline will not be processed. For enquiries about ReproPsy, contact j.a.grange at keele.ac.uk, and for e-ReproNim, contact e.b.roesch at reading.ac.uk . Application Process Applying for our Open Data Fellowship Program is simple! The link to the application form is at the bottom, but here's a brief outline of what you will need to consider before applying: - Field(s) of research (Up to 1000 char with spaces): What you do. - Training Needs (Up to 2000 char with spaces): In your application, highlight the training needs for yourself and your local research community. How can open data practices benefit your institution and Psychology as a whole? - Training Plan (Up to 2000 char with spaces): Describe the aim, motivation, and relevant prior experience related to the training you envision. How will this training empower your research and contribute to the open data movement? - Scope of Impact (Up to 2000 char with spaces): Outline the scope of your local community that would benefit from the training. Show us how this initiative can create a ripple effect, benefiting multiple researchers at your institution. - Special circumstances (Up to 2000 char with spaces): This is a gather-it-all section that allows you to bring anything you think might be relevant to the evaluators. Use this category to describe aspects related to equity, diversity and inclusion we ought to know about. - Justification of resources (Up to 5000 char with spaces): Provide itemised costs (including tax if applicable) describing how you plan to use the funding allocated in the Fellowship. Each Fellow can request funding for ?1,000 or (slightly) more AND upload all evidence of claims and scan of invoices in the dropbox link found at the bottom of the application form. - Host Institution Support (signed pdf with letterhead): Upload a letter of support from your host institution, as a PDF file, signed by your line manager, confirming their commitment to supporting your training and supporting you to organise training in your community. This could involve allocating time, which must be clearly stated (in number of hours estimated), or providing you with other necessary resources. Files must be uploaded onto the public dropbox link provided in the application form. You will be asked for your name, and your email address; we only need your name to link your file to your application, and the email address does not have to be real. Any issue with uploading a file, please email e.b.roesch at reading.ac.uk. Please also note: - The maximum number of characters allowed are not targets to be met. Be as concise as needed. - We are committed to supporting typically under-represented communities, and will apply a process of positive action towards supporting equity, diversity and inclusion. Specifically, after applications are graded by our evaluators and ranked, we will assert the landscape of the selection and adjust the selection if needed. Please use the Special Circumstances box to raise to the attention of the evaluators anything you think may deserve consideration. - The ReproPsy and e-ReproNim Fellowship programmes are separate projects, yet have lots in common?starting with the application form! We thus regret to say that we will not accept applications to both programmes, and you must specify one or the other on the application form. - Funding is only available to applicants from institutions hosted in the EU and the UK. Because of the structure of the funding allocation, we are reserving 5 fellowships to UK applicants in each of the fellowship programmes, 10 out of 30 in total. - Information related to the transfer of the award will be shared with successful applicants after selection. Fellows will be required to have identified who at their host institution will be managing this financial transaction: typically a post-award or a finance office. - Applications are managed using Google Forms, and PDF uploads with Dropbox. Neither of these platforms require you to create an account on Google or Dropbox. We collect your name and email addresses on the Google Form to identify your applications. This information is not shared with anyone, and only used for general statistics and logistics of the selection process. If you wish to be kept in the loop of what we do, please register to the Psychology Data Interest Group and Neuroimaging Data Working Group , with the Research Data Alliance. Alternatively, you can also visit our website . PS: I usually only manage to look at emails, Teams and the like after 2pm. For anything pressing, please call me or book yourself in my University Outlook calendar . ? *Prof. dr. Etienne B. Roesch* | *Professor of Applied Statistics & Cognitive Science* | *Univ. Reading* Institutional Lead for Open and Reproducible Research, UK Reproducibility Network Discipline Hopping Fellow, Natural Environment Research Council meetings: book yourself in my University Outlook calendar www: etienneroes.ch | osf.io/ede88 | github.com/eroesch | rdg.ac.uk/cinn | shop research: project-chai.org | rescience | ukrn -------------- next part -------------- An HTML attachment was scrubbed... URL: From vrajagopalan at chla.usc.edu Thu Feb 29 13:51:40 2024 From: vrajagopalan at chla.usc.edu (Rajagopalan, Vidya) Date: Thu, 29 Feb 2024 18:51:40 +0000 Subject: [Neuroimaging] FRIEND LAB at Children's Hospital of Los Angeles - Job Opening for Data Manager and Analyst Message-ID: FRIEND Lab (Fostering Resilience in Early Neurodevelopment) seeking a talented Data Manager and Analyst to contribute to our groundbreaking studies aimed at unraveling early neurodevelopment of the human brain. Our research focuses on advancing non-invasive methods imaging and computational modeling methods to understand healthy and pathological human brain development during the prenatal to pre-K period. As a Data Manager and Analyst, you will play a crucial role in managing and analyzing complex multimodal datasets (such as neuroimaging, histopathology, psychosocial data). You will work closely with our interdisciplinary team of researchers to ensure the efficient organization, storage, and analysis of data. Your expertise will be instrumental in extracting meaningful insights from large-scale datasets and contributing to groundbreaking discoveries in the field of early brain development. Key Responsibilities: * Develop and implement robust data management protocols to ensure the integrity, security, and accessibility of neuroimaging datasets. * Perform preprocessing, quality control, and statistical analysis of neuroimaging data using advanced software tools and techniques. * Collaborate with researchers to design and execute data analysis pipelines tailored to specific research questions and objectives. * Assist in the development of data visualization techniques to effectively communicate research findings. * Assist in the preparation of research communications such as manuscript, presentation, grant applications, and progress reports * Stay updated on the latest developments in neuroimaging methodologies and contribute to the integration of innovative techniques into research projects. Requirements: * Bachelor's or Master's degree biomedical engineering, computer science, statistics, or a related field. * Proven experience in managing and analyzing neuroimaging datasets, with proficiency in neuroimaging software packages (e.g., FSL, SPM, AFNI, FreeSurfer). * Strong programming skills in languages such as Python, R, or similar, with experience in scripting for data analysis and automation. * Familiarity with statistical methods and machine learning techniques applied to neuroimaging data analysis. * Excellent organizational skills and attention to detail, with the ability to handle multiple tasks and prioritize effectively. * Effective communication and interpersonal skills, with the ability to collaborate within a multidisciplinary team environment. Preferred Qualifications: * Experience working in a research or academic environment, particularly in the field of neuroscience or neuroimaging. * Knowledge of database management systems and data visualization tools. * Experience with version control systems (e.g., Git) and software development best practices. * Prior experience with advanced neuroimaging modalities and techniques (e.g., resting-state fMRI, diffusion MRI tractography). How to Apply: Interested candidates should submit a cover letter, resume/CV, and any relevant portfolio or project work demonstrating their expertise in data management and analysis. Please include contact information for references. Applications should be sent to vrajagopalan at chla.usc.edu with the subject line "Data Manager and Analyst Application - [Your Name]". Join us in unraveling the complexities of the human brain and making breakthrough discoveries that have the potential to transform our understanding of neurological disorders and cognitive function. We look forward to welcoming you to our team! CONFIDENTIALITY NOTICE: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential or legally 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 this original message. -------------- next part -------------- An HTML attachment was scrubbed... URL: