From garyfallidis at gmail.com Tue Jan 7 15:23:49 2025 From: garyfallidis at gmail.com (Eleftherios Garyfallidis) Date: Tue, 7 Jan 2025 15:23:49 -0500 Subject: [Neuroimaging] =?utf-8?q?ANN=3A_Happy_2025_with_DIPY_1=2E10=2E0_?= =?utf-8?b?8J+SpQ==?= Message-ID: Hello and Happy 2025 to all !, We are excited to announce a new release of DIPY: DIPY 1.10.0 ! DIPY 1.10.0 (Friday, 12 December 2024) The release 1.10.0 received contributions from 28 developers (the full release notes are at: https://docs.dipy.org/stable/release_notes/release1.10.html). Thank you all for your contributions and feedback! Please click here to check 1.10.0 API changes. Highlights of 1.10.0 release include: - NF: Patch2Self3 - Memory less denoising for dMRI is now available. - NF: Fiber density and spread from ODF using Bingham distributions method added. - NF: Iteratively reweighted least squares for robust fitting of diffusion models added. - NF: NDC - Neighboring DWI Correlation quality metric added. - NF: DAM - DWI-based tissue classification method added. - NF: New Parallel Backends (Ray, Joblib, Dask) for fitting reconstruction methods added. - RF: Deprecation of Tensorflow support. PyTorch support is now the default. - Transition to Keyword-only arguments (PEP 3102). - Zero-warnings policy (CIs, Compilation, doc generation) adopted. - Adoption of ruff for automatic style enforcement. - Transition to using f-strings. - Citation system updated. It is more uniform and robust. - Multiple Workflows updated. - Multiple DIPY Horizon features updated. - Large documentation update. - Closed 258 issues and merged 187 pull requests. To upgrade or install DIPY Run the following command in your terminal: pip install --upgrade dipy This version of DIPY depends on nibabel (3.0.0+). For visualization you need FURY (0.12.0+). Questions or suggestions? For any questions go to https://dipy.org, or send an e-mail to dipy at python.org We also have an instant messaging service and chat room available at https://gitter.im/dipy/dipy Finally, a new forum is available at https://github.com/dipy/dipy/discussions Have a wonderful time using the new version. In addition, registration for the online DIPY workshop 2025 (March 17-21) is open! The workshop will equip you with the skills and knowledge needed to master the latest techniques and tools in structural and diffusion imaging. See the exquisite program and keynote speakers here . Register today to save a spot! Please support us by citing DIPY in your papers using the following DOI: 10.3389/fninf.2014.00008 On behalf of the DIPY developers, Eleftherios Garyfallidis, Ariel Rokem, Serge Koudoro https://dipy.org/contributors -------------- next part -------------- An HTML attachment was scrubbed... URL: From brainandmorelab at gmail.com Tue Jan 28 10:25:14 2025 From: brainandmorelab at gmail.com (Brain and More Lab) Date: Tue, 28 Jan 2025 16:25:14 +0100 Subject: [Neuroimaging] Fwd: Effconnpy Python package for brain effective connectivity In-Reply-To: References: Message-ID: Dear all, I did a thing last week. Here is Python package for brain effective connectivity: https://pypi.org/project/effconnpy/ you can install it with "pip install effconnpy", or via git: https://github.com/alecrimi/effconnpy It assumes you have preprocessed the fMRI data with fMRIprep or somethingelse, and you have extracted the time series according to an atlas. The result is a brain effective connectivity matrix. The idea is to build something consistent more people as possible can agree. I tested it on fMRI series, I didn't have time to check for EEG or something else. The implemented methods includes: - Bivariate Granger Causality, Transfer Entropy, and Convergent Cross Mapping - Dynamic Bayesian Network, Structural Equation Modeling, DoWhy Causal Discovery, and Dynamic Causal Modeling (SPM free :-) ) - Multivariate Granger Causality as in Barnett & Seth 2014, Multivariate Convergent Cross-Mapping (CCM) as in Nithya & Tangirala 2019, multivariate transfer entropy as in Duan et al. 2022 Please send feedback, bugs, error and suggestions for improvements. Best, Alex -------------- next part -------------- An HTML attachment was scrubbed... URL: