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
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Garyfallidis Research Group
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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
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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
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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
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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
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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.
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