Mailman 3 January 2022 - DIPY

Fwd: Shanahan Foundation Fellowship at the Interface of Data and Neuroscience - apply now!
by Ariel Rokem Jan. 20, 2022

Jan. 20, 2022

With apologies for cross-posting, this is a great opportunity at UW/Allen. Please forward to potential applicants and note upcoming deadline. Cheers, Ariel Overview The *Shanahan Foundation Fellowship at the Interface of Data and Neuroscience* is a three-year fellowship program that aims to: · Integrate data scientists in neuroscience research · Challenge traditional approaches to neuroscience · Provide multidisciplinary, multi-organizational co-mentorship · Provide a network and community · Support career development in data science The fellowship is co-hosted by the Allen Institute and the University of Washington (through the eScience Institute and the Computational Neuroscience Center) and is directed by Dr. Christof Koch at the Allen Institute. *Neuroscience needs data scientists.* The brain represents one of the most complex challenges facing science today. And now with advances in our methods to study the brain—Neuropixel probes that can record from 1000 neurons at once, growing consensus on data standards across laboratories—the field is flooded with data that needs interpretation. The skills of data scientists are essential to springboard the field to the next stage of discoveries. Towards that end, the Shanahan Foundation Fellowship was created to bring fresh perspectives into the field, encouraging data scientists from outside neuroscience to come and work with leading investigators at the Allen Institute and UW. The Allen Institute is unique in its infrastructure and pipeline that enables the production of standardized, reproducible data on the brain (as evidenced by our vast *data banks* <http://www.brain-map.org/>*)*. Together with our collaborators at the UW computational Neuroscience Center and eScience Institute, we provide data scientists with the ideal opportunity and resources to mine for novel insights and discoveries. Details *You do not need experience in neuroscience to apply. *The goal of the fellowship is to provide opportunities to non-traditional applicants who would not typically be funded by the typical postdoctoral fellowships in neuroscience. The fellowship has been purposefully designed to give fellows the time and mentorship to get up to speed in a new field and new data collection techniques and methods*.* Fellows will be employed by the Allen Institute as either a Scientist I or a Scientist II (with a matching salary) and will receive an affiliate postdoctoral appointment at UW. During the three-year fellowship, fellows will identify a mentor at the Allen Institute, where the fellows will be based. Fellows will select a co-mentor at the University of Washington who will provide additional guidance on a project designed by the fellow, focused on quantitative analysis of neuroscience data available through the Allen Institute’s vast data banks <http://www.brain-map.org/> – ranging from molecular, genomic, transcriptional, physiological, morphological, anatomical and functional whole-brain level in the brains of mice, non-human primates and humans – or through ongoing laboratory work. Each fellow will have the opportunity to mentor a fully-funded UW undergraduate or postbaccalaureate research assistant who helps with their research for 3-12 months. Fellows will participate in the postdoctoral career development program at the University’s *e-Science Institute* and the *UW Computational Neuroscience Center*. The eSciences Institute offers regular workshops on key topics including cloud computing, python and reproducibility. New fellows will attend the annual Summer Workshop on the Dynamic Brain <https://alleninstitute.org/what-we-do/brain-science/events-training/summer-…> where they will learn how to apply data science skills to neuroscience data and questions. Throughout the three years, fellows will be supported in developing a network in the neuroscience field and sharing their progress with peers at conferences. Up to three fellows will be selected to begin in Fall 2022. Eligibility Requirements Applicants must be data scientists in a broad sense, with a Ph.D. in a quantitative field such as computer science, statistics, electrical engineering, physics, mathematics or biology with a background in statistical, computational and machine learning methods. Ph.D.’s should have been awarded in the last 3 years. One goal of the fellowship is to build a network of collaborators, as such, priority will be given to applicants who are not currently postdoctoral fellows or scientists at the University of Washington or the Allen Institute. We believe high-quality science can only be produced when it includes different perspectives. We are building an environment of diversity and inclusion and encourage people from all backgrounds to apply for this fellowship. Application Instructions For full consideration, please submit your application by February 1, 2022. Applications may continue to be considered after this deadline on a rolling basis until positions are filled. Learn more and apply on the Shanahan Fellowship Website <https://alleninstitute.org/what-we-do/brain-science/careers/shanahan-founda…> . https://alleninstitute.org/what-we-do/brain-science/careers/shanahan-founda… Applications must include: · A curriculum vitae from the applicant · Two letters of support from advisors and other mentors · A one-page personal statement from the applicant describing their history, activities, and interests as an individual (especially those outside of science) which may give the committee a greater sense of you as a person and your ability to simultaneously interact with and challenge traditional scientific fields. · A two- to three-page research statement from the applicant describing their prior research, interests in applying data science to the field of neuroscience, potential research interests (including tools they are familiar with) and how this fellowship aligns with their career goals. · The choice of the final advisor/co-advisor will be accomplished during the first year of this fellowship. Questions? Email: shanahan.fellow(a)alleninstitute.org

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Streamline integration method
by Joan Falco Roget Jan. 19, 2022

Jan. 19, 2022

Dear all, I have a quick question regarding what numerical integration method does DIPY's "LocalTracking" use to generate the Streamlines. Does it use Runge-Kutta integration? If not, may I ask why? Thank you and cheers, Joan Joan Falco-Roget PhD Student [cid:534717a6-66b0-4efa-9c6b-faff78cf2ce6] Centre for Computational Personalised Medicine International Research Foundation Czarnowiejska 36, building C5 30-054 Kraków Poland Phone number: +34 610 068 599 j.roget(a)sano.science<mailto:n.surname@sano.science> https://sano.science<http://www.sano.science/>

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DMRIPREPS, FMRIPREP and DIPY
by Alex Crimi Jan. 12, 2022

Jan. 12, 2022

Hi, Happy new year! long story short, I am working on a followup of my implementation of effective connectivity: https://www.sciencedirect.com/science/article/pii/S1053811921005644 where I need both fMRI and diffusion data to build a structural connectome.Can we touch the topic of preprocessing pipelines jointly to structural connectome construction? In particular imagine I also have to do the preprocessing pipeline for fMRI (fMRIprep).I found this dmriprep https://github.com/nipreps/dmriprepis it something people here recommend? or simply given the BIDS format, I just do fMRIprep and then my own preprocessing and connectome construction (plus whatever I do with my effective connectivity)? I apologize if I am putting too many ideas at the same time.Best,Alex

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CNS 2022 - Important Update! - Poster Submissions EXTENDED to January 18, 2022 !
by CNS Meeting Jan. 10, 2022

Jan. 10, 2022

Poster Submissions Deadline EXTENDED Important Update! Due to overwhelming requests for a poster deadline extension, CNS will extend the poster deadline one week, to January 18th! In addition, we want to make it clear that POSTERS (only) can be presented virtually both by those attending the meeting in-person (offering additional exposure of your science) AND those who cannot attend in-person: This supports the society’s membership’s desire for increased access for those unable to attend. We look forward to seeing everyone is April! Poster Submissions IMPORTANT DATES & DEADLINES Young Investigator Award Nominations Close January 11, 2022 Symposium Submission Deadline January 11, 2022 Poster Submission Deadline January 18, 2022 Data Blitz Deadline January 18, 2022 GSA/PFA Deadline January 18, 2022 JoCN Travel Fellowship Submission Deadline January 31, 2022 Early Registration Rate Deadline February 25, 2022 Regular Registration Rate Deadline April 4, 2022 Onsite Registration Rates Begin April 5, 2022 Hotel Reservation Deadline April 6, 2022 CNS 2022 Annual Meeting April 23-26, 2022, San Francisco, CA IN THIS ISSUE: CNS 2022 Poster Submissions Deadline EXTENDED! Important Dates & Deadlines Cognitive Neuroscience Society https://www.cogneurosociety.org ‌ ‌ ‌ Cognitive Neuroscience Society | c/o Center for Mind and Brain , 267 Cousteau Place, Davis, CA 95618 Unsubscribe dipy(a)python.org Update Profile | Constant Contact Data Notice Sent by meeting(a)cogneurosociety.org powered by Try email marketing for free today!

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