From urs at kleinholdermann.de Mon Dec 4 23:51:35 2023 From: urs at kleinholdermann.de (Urs Kleinholdermann) Date: Tue, 5 Dec 2023 05:51:35 +0100 Subject: [Neuroimaging] [fmriprep] how to run ICA-AROMA after fmriprep Message-ID: <459b367e-a2b6-2c9f-df37-c825108abcb6@kleinholdermann.de> Dear all, I'm relatively new to fMRI analysis and totally new to this list so apologies if my question is off-topic to this list or has been answered before. I'd like to conduct ICA_AROMA on my fMRI data which has been preprocessed with fmriprep. Since the option to do this automagically has been removed from fmriprep and plans to conduct this in a separate workflow apparently are still waiting for implementation (https://github.com/nipreps/fmripost-aroma) I've tried to figure out how to do it manually but unfortunately have failed.? The files created by fmriprep do not seem to correspond to those expected as inputs by ICA_AROMA.py. Could someone perhaps tell me to how I can obtain the necessary files? Thanks for your help! Urs From markiewicz at stanford.edu Tue Dec 12 11:06:16 2023 From: markiewicz at stanford.edu (Christopher Markiewicz) Date: Tue, 12 Dec 2023 16:06:16 +0000 Subject: [Neuroimaging] [ANN] NiBabel 5.2.0 Message-ID: Hi all, We've released NiBabel 5.2.0. This release is largely a collection of small quality-of-life improvements. The main new feature is a pair of pointset data structures intended to unify representations needed for resampling data and representing surface meshes. These are experimental, and we may update the API on a faster time scale than usual. This release also has provisional support for the still-in-development NumPy 2.0, and we are testing their nightly builds. It's reasonable to expect them to continue breaking our assumptions, so please test off of our development branch if you're going to test with their nightly builds. Thanks to Mathieu Scheltienne and Eric Larson for their work in resolving the issues found so far. The next release series will be 6.0, which I anticipate in March 2024. As usual, major releases may see DeprecationWarnings turn into ExpiredDeprecationErrors. We maintain a removal schedule in https://github.com/nipy/nibabel/blob/master/nibabel/tests/test_removalschedule.py with all deprecations and when they will be entirely removed from the package. Where Python allows, we raise ExpiredDeprecationErrors for one major version before final removal, so look at both 6.0 and 7.0 removals if you want to get ahead of this. Many thanks to all contributors for using NiBabel, reporting bugs, updating documentation and contributing code. This release, we included commits from four new contributors: Blake Dewey, Peter Suter, Reinder Vos de Wael and Mathieu Scheltienne. If you use NiBabel, please cite the Zenodo archive: https://doi.org/10.5281/zenodo.10363247 The full changelog follows this message, and can also be found at the following links: * https://nipy.org/nibabel/changelog.html#monday-11-december-2023 * https://github.com/nipy/nibabel/releases/tag/5.2.0 Best, Chris ---- Most work on NiBabel so far has been by Matthew Brett (MB), Chris Markiewicz (CM), Michael Hanke (MH), Marc-Alexandre C?t? (MC), Ben Cipollini (BC), Paul McCarthy (PM), Chris Cheng (CC), Yaroslav Halchenko (YOH), Satra Ghosh (SG), Eric Larson (EL), Demian Wassermann, Stephan Gerhard and Ross Markello (RM). References like "pr/298" refer to github pull request numbers. 5.2.0 (Monday 11 December 2023) =============================== New feature release in the 5.2.x series. This release requires a minimum Python of 3.8 and NumPy 1.20, and has been tested up to Python 3.12 and NumPy 1.26. New features ------------ * Add generic :class:`~nibabel.pointset.Pointset` and regularly spaced :class:`~nibabel.pointset.Grid` data structures in preparation for coordinate transformation and resampling (pr/1251) (CM, reviewed by Oscar Esteban) Enhancements ------------ * Add :meth:`~nibabel.arrayproxy.ArrayProxy.copy` method to :class:`~nibabel.arrayproxy.ArrayProxy` (pr/1255) (CM, reviewed by Paul McCarthy) * Permit :meth:`~nibabel.xmlutils.XmlSerializable.to_xml` methods to pass keyword arguments to :func:`xml.etree.ElementTree.tostring` (pr/1258) (CM) * Allow user expansion (e.g., ``~/...``) in strings passed to functions that accept paths (pr/1260) (Reinder Vos de Wael, reviewed by CM) * Expand CIFTI-2 brain structures to permit synonyms (pr/1256) (CM, reviewed by Mathias Goncalves) * Annotate :class:`~nibabel.spatialimages.SpatialImage` as accepting ``affine=None`` argument (pr/1253) (Blake Dewey, reviewed by CM) * Warn on invalid MINC2 spacing declarations, treat as missing (pr/1237) (Peter Suter, reviewed by CM) * Refactor :func:`~nibabel.nicom.utils.find_private_section` for improved readability and maintainability (pr/1228) (MB, reviewed by CM) Bug fixes --------- * Resolve test failure related to randomly generated invalid case (pr/1221) (CM) Documentation ------------- * Remove references to NiPy data packages from documentation (pr/1275) (Dimitri Papadopoulos, reviewed by CM, MB) Maintenance ----------- * Quality of life improvements for CI, including color output and OIDC publishing (pr/1282) (CM) * Patch for NumPy 2.0 pre-release compatibility (pr/1250) (Mathieu Scheltienne and EL, reviewed by CM) * Add spellchecking to tox, CI and pre-commit (pr/1266) (CM) * Add py312-dev-x64 environment to Tox to test NumPy 2.0 pre-release compatibility (pr/1267) (CM, reviewed by EL) * Resurrect tox configuration to cover development workflows and CI checks (pr/1262) (CM) * Updates for Python 3.12 support (pr/1247, pr/1261, pr/1273) (CM) * Remove uses of deprecated ``numpy.compat.py3k`` module (pr/1243) (Eric Larson, reviewed by CM) * Various fixes for typos and style issues detected by Codespell, pyupgrade and refurb (pr/1263, pr/1269, pr/1270, pr/1271, pr/1276) (Dimitri Papadopoulos, reviewed by CM) * Use stable argsorts in PARREC tests to ensure consistent behavior on systems with AVX512 SIMD instructions and numpy 1.25 (pr/1234) (CM) * Resolve CodeCov submission failures (pr/1224) (CM) * Link to logo with full URL to avoid broken links in PyPI (pr/1218) (CM, reviewed by Zvi Baratz) API changes and deprecations ---------------------------- * The :mod:`nibabel.pydicom_compat` module is deprecated and will be removed in NiBabel 7.0. (pr/1280) * The :func:`~nibabel.casting.int_to_float` and :func:`~nibabel.casting.as_int` functions are no longer needed to work around NumPy deficiencies and have been deprecated (pr/1272) (CM, reviewed by EL) From bertrand.thirion at inria.fr Tue Dec 19 06:34:45 2023 From: bertrand.thirion at inria.fr (Bertrand Thirion) Date: Tue, 19 Dec 2023 12:34:45 +0100 (CET) Subject: [Neuroimaging] Hiring a developer for Nilearn Message-ID: <570906643.31101339.1702985685170.JavaMail.zimbra@inria.fr> Hi, We are hiring a developer to work on Nilearn. Specifically, we want to improve Nilearn's connectivity with other tools in the ecosystem, especially BIDS standards, to facilitate the analysis of BIDS-organised datasets. More generally, we would like to automate more of the key analytical steps in Nilearn to improve the user experience. We also want to improve the interactive visualisation tools with the integration of NiiVue, and aim to improve the performance of some Nilearn functionality based on profiling/memory management analysis, use of GPU computing, etc. A secondary task is to build robust neuroimaging data pre-processing pipelines for the MIND team, for data coming from our collaborating institutions. These pipelines will mainly deal with functional and diffusion MRI. The pipelines will be based on tools such as Fmriprep, Nilearn, Dipy, ANTs and FreeSurfer. Beyond the basic use of these powerful tools, we need to add steps for quality control of the output or special adaptations for the pathological cases in our collaboration, such as brain tumours. More information here: https://team.inria.fr/mind/files/2023/12/nistar.pdf Contact: bertrand.thirion at inria.fr Best, Bertrand Thirion Head of science (d?l?gu? scientifique) Inria Saclay Neurospin, CEA Saclay, 91191 Gif sur Yvette +33 1 69 08 79 92 http://pages.saclay.inria.fr/bertrand.thirion -------------- next part -------------- An HTML attachment was scrubbed... URL: From matthew.brett at gmail.com Thu Dec 21 11:55:23 2023 From: matthew.brett at gmail.com (Matthew Brett) Date: Thu, 21 Dec 2023 16:55:23 +0000 Subject: [Neuroimaging] Nipy 0.6.0 Message-ID: Dear all, We (see below) took it upon ourselves to update Nipy for Python 3.12, including porting the build process from Numpy distutils to Meson. There was a lot of hard and largely thankless work on the way, to keep Nipy working, with special thanks to Chris Markiewicz and Ben Beasley, who did nearly all of the work. The last push to Python 3.12 was possible because of a big and successful rush at the problem with Jarrod Millman and Stefan van der Walt, to whom special thanks for his Meson wizardry. https://pypi.org/project/nipy/0.6.0/ There are wheels for all common platforms from Pythons 3.8 through 3.12. This will probably be the last release of Nipy, as we think hard about what to do next. Cheers, Matthew (for the Nipythoneers). From garyfallidis at gmail.com Fri Dec 22 14:45:36 2023 From: garyfallidis at gmail.com (Eleftherios Garyfallidis) Date: Fri, 22 Dec 2023 14:45:36 -0500 Subject: [Neuroimaging] ANN: DIPY 1.8.0 Message-ID: Hello all, We are excited to announce a new release of DIPY: DIPY 1.8.0 ! This release includes many new features and updates to support the latest Python, Numpy, Scipy and Cython versions. The Pythonic ecosystem is growing fast. Which is great. But please report any issues you may find. DIPY 1.8.0 (Friday, 13 December 2023) The release 1.8.0 received contributions from 28 developers (the full release notes are at: https://docs.dipy.org/stable/release_notes/release1.8.html). Thank you all for your contributions and feedback! Please click here to check 1.8.0 API changes. Highlights of 1.8.0 release include: - Python 3.12.0 support. - Cython 3.0.0 compatibility. - Migrated to Meson build system. Setuptools is no more. - EVAC+ novel DL-based brain extraction method added. - Parallel Transport Tractography (PTT) 10X faster. - Many Horizon updates. Fast overlays of many images. - New Correlation Tensor Imaging (CTI) method added. - Improved warnings for optional dependencies. - Large documentation update. New theme/design integration. - Closed 197 issues and merged 130 pull requests. Here is also a reminder of the previous highlights (which was not announced - due to the large changes in the Pythonic ecosystem). Highlights of 1.7.0 release include: - NF: BundleWarp - Streamline-based nonlinear registration method for bundles added. - NF: DKI+ - Diffusion Kurtosis modeling with advanced constraints added. - NF: Synb0 - Synthetic b0 creation added using deep learning added. - NF: New Parallel Transport Tractography (PTT) added. - NF: Fast Streamline Search algorithm added. - NF: New denoising methods based on 1D CNN added. - Handle Asymmetric Spherical Functions. - Large update of DIPY Horizon features. - Multiple Workflows updated - Large codebase cleaning. - Large documentation update. Integration of Sphinx-Gallery. - Closed 53 issues and merged 34 pull requests. To upgrade or install DIPY Run the following command in your terminal (works across Mac, Linux, Win): pip install --upgrade dipy This version of DIPY depends on nibabel (3.0.0+). For visualization you need FURY (0.9.0+). Questions or suggestions? For any questions go to our new website at 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 discussion forum is available at https://github.com/dipy/dipy/discussions Have a wonderful time using this new version and please support us by citing DIPY in your papers using the following DOI: 10.3389/fninf.2014.00008 In addition, registration for the online DIPY workshop 2024 (March 11-15) is open! The workshop will continue equipping 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 now ! On behalf of the DIPY developers, Eleftherios Garyfallidis, Ariel Rokem, Serge Koudoro https://dipy.org/contributors -------------- next part -------------- An HTML attachment was scrubbed... URL: