From Peter.Thomas.While at stolav.no Tue Mar 1 04:58:47 2022 From: Peter.Thomas.While at stolav.no (While, Peter Thomas) Date: Tue, 1 Mar 2022 09:58:47 +0000 Subject: [Neuroimaging] [NIPY] Postdoctoral Fellowship in Deep Learning Applied to Magnetic Resonance Imaging/Physics Message-ID: <8455e6bb4eb3433ab6898db8ff8ad277@stolav.no> Dear colleagues, please let me draw your attention to a job posting for a postdoctoral fellowship at St. Olav's University Hospital in Trondheim, Norway. We seek a highly motivated researcher with a background in MRI physics, image processing and/or deep learning, to contribute to the project: "Deep learning cancer diagnostics from diffusion-weighted magnetic resonance imaging". The postdoc will have the opportunity to work on diverse topics according to their experience and interests. For example, they may contribute to work exploring the use of novel acquisition strategies for diffusion-weighted imaging, image reconstruction involving deep learning, pulse sequence development, advanced diffusion modelling and parameter estimation, and novel image processing techniques. The deadline for applications is the 20th of March. Further details can be found in the advert on the ISMRM Career Center: https://www.ismrm.org/jobs/j07827.pdf Best regards, Peter Peter T. While, Ph.D. Department of Radiology and Nuclear Medicine St. Olav's University Hospital Trondheim, Norway Email: Peter.Thomas.While at stolav.no Tlf: +47 728 36627 -------------- next part -------------- An HTML attachment was scrubbed... URL: From avesani at fbk.eu Mon Mar 7 13:17:20 2022 From: avesani at fbk.eu (Paolo Avesani) Date: Mon, 7 Mar 2022 19:17:20 +0100 Subject: [Neuroimaging] Postdoctoral Fellowship in Machine Learning for Brain Connectivity in Clinical Neuroscience Message-ID: A postdoctoral fellowship in Machine Learning for Brain Connectivity in Clinical Neuroscience We are pleased to announce the opening of one Postdoctoral Fellowship at the Neuroinformatics Lab, an interdisciplinary initiative between the Center for Mind/Brain Sciences (CIMeC) of the University of Trento, and the Center for Digital Health of Fondazione Bruno Kessler. The position is part of the ?Neusurplan? project, an integrated approach to neurosurgery planning based on multimodal and longitudinal data. The goal is to pursue an integrated approach to pre-operative neurosurgical planning, combining structural and functional characterization of brain connectivity. The data driven strategy will take advantage of a unique dataset of intra-operative points of directed electrical stimulation and the related functional responses. In this project, the candidate will pursue research on machine learning methods for neuroimaging data analysis to study and characterize brain connectivity, with applications to longitudinal studies and clinical practice. The ideal candidate should have a mixed background in neuroimaging techniques and numerate disciplines, like computer science, engineering, physics, or mathematics. This project is in collaboration with the Division of Neurosurgery, S. Chiara Hospital, Trento (IT). The position is for a 2 year Postdoc Fellowship (May, 2022 - April, 2024). To apply, follow the instructions at this link: https://bit.ly/nilab2022call Deadline for application: 21 March 2022. For questions about the position, please contact Paolo Avesani ( paolo.avesani at unitn.it) and/or Emanuele Olivetti (olivetti at fbk.eu). The University of Trento ranks among top Italian Universities ( https://www.unitn.it/en/ateneo/1636/rankings). Fondazione Bruno Kessler ranks first among the Italian research centers in Engineering and Computer Science ( https://magazine.fbk.eu/en/news/fbk-ranks-1st-in-italy-for-scientific-excellence-in-three-areas ). To also consider a work/life balance, there is more than our passion for translational research. You can check these pointers for a flavor of life quality in Trentino: https://www.visittrentino.info/en; https://www.discovertrento.it/en A few papers related to the project are below: Bert? G,et al., (2021) Classifyber, a robust streamline-based linear classifier for white matter bundle segmentation, Neuroimage, 224 https://doi.org/10.1016/j.neuroimage.2020.117402 Sarubbo S, et al., (2020) Mapping critical cortical hubs and white matter pathways by direct electrical stimulation: an original functional atlas of the human brain, Neuroimage, 205 https://doi.org/10.1016/j.neuroimage.2019.116237 Astolfi P, et al., (2020) Tractogram filtering of anatomically non-plausible fibers with geometric deep learning, International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI) LNCS, vol 12267. Springer https://doi.org/10.1007/978-3-030-59728-3_29 Sarubbo S, et al., (2021) Planning brain tumor resection using a probabilistic atlas of cortical and subcortical structures critical for functional processing: a proof of concept, Operative Neurosurgery, 20(3), 175-183 https://doi.org/10.1093/ons/opaa396 -- -- Le informazioni contenute nella presente comunicazione sono di natura? privata e come tali sono da considerarsi riservate ed indirizzate? esclusivamente ai destinatari indicati e per le finalit? strettamente? legate al relativo contenuto. Se avete ricevuto questo messaggio per? errore, vi preghiamo di eliminarlo e di inviare una comunicazione? all?indirizzo e-mail del mittente. -- The information transmitted is intended only for the person or entity to which it is addressed and may contain confidential and/or privileged material. If you received this in error, please contact the sender and delete the material. -------------- next part -------------- An HTML attachment was scrubbed... URL: From redhatw at gmail.com Thu Mar 10 16:47:58 2022 From: redhatw at gmail.com (Ze Wang) Date: Thu, 10 Mar 2022 21:47:58 +0000 Subject: [Neuroimaging] postdoc position in brain entropy mapping, clustering, and graph analysis Message-ID: A Neuroimaging postdoc position open in University of Maryland School of Medicine We are looking for a highly motivated postdoc research fellow in neuroimaging data processing. We are particularly interested in time series analysis, graph theory, gradient analysis, connectome analysis, and machine learning. The position is immediately available from now (Mar 10 2022) until filled. The candidate will be supported by a NIH R01 project. The ideal candidate should method development experience in fMRI or neuroimaging signal processing. Experience of clustering and graph analysis will be preferred. Python, Matlab programming skills are required. Experience on multi-band fMRI data processing is considered a plus. Candidates for these positions are expected to have good communication skills and have good writing skills. We are willing to provide competitive salary. Interested candidates should send CV and a brief introduction to Ze Wang: ze.wang at som.umaryland.edu. Information about Dr. Wang?s lab can be found in: https://www.medschool.umaryland.edu/pi/Ze-Wang-PhD/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From matthew.brett at gmail.com Fri Mar 11 12:08:36 2022 From: matthew.brett at gmail.com (Matthew Brett) Date: Fri, 11 Mar 2022 17:08:36 +0000 Subject: [Neuroimaging] Next data formats meeting - Monday 14th 15:00 EDT Message-ID: Hi, Our next data formats meeting is a discussion of the virtues and benefits of the current analysis / archive formats - on Monday 14th March, 15:00 EDT. More details at: https://nipy.discourse.group/t/data-format-pro-con-meeting-monday-14-march-15-00-edt Cheers, Matthew From elef at indiana.edu Fri Mar 11 17:55:57 2022 From: elef at indiana.edu (Eleftherios Garyfallidis) Date: Fri, 11 Mar 2022 17:55:57 -0500 Subject: [Neuroimaging] DIPY Workshop 2022 - Online Edition In-Reply-To: References: Message-ID: Dear Neuroimagers, Just in case you did not receive the schedule of the DIPY workshop in my previous email... This is available here . Registration information is available here Best regards, Eleftherios On Fri, Feb 25, 2022 at 5:24 PM Eleftherios Garyfallidis < garyfallidis at gmail.com> wrote: > Dear Neuroimaging Community, > > The Online DIPY Workshop is back with a great lineup of topics and > speakers! Please forward this email to any interested parties. > > [image: image.png] > > For registration and more information please visit > https://dipy.org/workshops/latest > > On behalf of the DIPY team, > Eleftherios Garyfallidis, PhD > Assistant Professor > Intelligent Systems Engineering > Indiana University > Luddy Hall 700 N Woodlawn > Bloomington, IN 47408 > GRG | DIPY | FURY > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 144580 bytes Desc: not available URL: From redhatw at gmail.com Mon Mar 14 21:12:11 2022 From: redhatw at gmail.com (Ze Wang) Date: Tue, 15 Mar 2022 01:12:11 +0000 Subject: [Neuroimaging] Fw: postdoc position for brain entropy mapping and clustering Message-ID: A Neuroimaging postdoc position open in University of Maryland School of Medicine We are looking for a highly motivated postdoc research fellow in neuroimaging data processing. We are particularly interested in time series analysis, graph theory, gradient analysis, connectome analysis, and machine learning. The position is immediately available from now (Mar 10 2022) until filled. The candidate will be supported by a NIH R01 project. The ideal candidate should method development experience in fMRI or neuroimaging signal processing. Experience of clustering and graph analysis will be preferred. Python, Matlab programming skills are required. Experience on multi-band fMRI data processing is considered a plus. Candidates for these positions are expected to have good communication skills and have good writing skills. We are willing to provide competitive salary. Interested candidates should send CV and a brief introduction to Ze Wang: ze.wang at som.umaryland.edu. Information about Dr. Wang?s lab can be found in: https://www.medschool.umaryland.edu/pi/Ze-Wang-PhD/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From elef at indiana.edu Thu Mar 17 16:58:54 2022 From: elef at indiana.edu (Eleftherios Garyfallidis) Date: Thu, 17 Mar 2022 16:58:54 -0400 Subject: [Neuroimaging] ANN: DIPY 1.5.0 Released! Message-ID: Dear all, We are excited to announce a new release of DIPY: version 1.5.0 is out of the oven! Just before the DIPY workshop ... continue reading ... DIPY 1.5.0 (Friday, 11 March 2022) The release 1.5.0 received contributions from 22 developers (the complete release notes are at: https://dipy.org/documentation/1.5.0/release_notes/release1.5/). Thank you all for your contributions and feedback! Please click here to check 1.5.0 API changes. Highlights of 1.5.0 release include: - New reconstruction model added: Q-space Trajectory Imaging (*QTI*). - New reconstruction model added: Robust and Unbiased Model-BAsed Spherical Deconvolution (*RUMBA-SD*). - New reconstruction model added: Residual block Deep Neural Network ( *ResDNN*). - Masking management in Affine Registration added. - Multiple *Workflows* updated (DTIFlow, DKIFlow, ImageRegistrationFlow) and added (MotionCorrectionFlow). - Compatibility with Python 3.10 added. - Migrations from Azure Pipeline to Github Actions. - Large codebase cleaning. - New parallelisation module added. - dipy.io.bvectxt module deprecated. - New DIPY *Horizon* features (ROI Visualizer, random colors flag). - Large documentation update. - Closed 129 issues and merged 72 pull requests. To upgrade or install DIPY Run the following command in your terminal: pip install --upgrade dipy or conda install -c conda-forge dipy This version of DIPY depends on nibabel (3.0.0+). For visualization you need FURY (0.8.0+). 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 This important release will be highlighted at the 5 day DIPY workshop starting this Monday, March 21st! Find the exquisite program here and register for the workshop here . *Have a wonderful research time using the new version *and 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 alexandre.gramfort at inria.fr Tue Mar 22 05:48:32 2022 From: alexandre.gramfort at inria.fr (Alexandre Gramfort) Date: Tue, 22 Mar 2022 10:48:32 +0100 Subject: [Neuroimaging] [ANN] MNE-Python 1.0 Message-ID: [Cross-posting with: https://mne.discourse.group/t/mne-python-is-turning-1-0/4595] ? MNE-Python is turning 1.0... In December 2010, freshly arrived in Boston to work as a postdoc at the Martinos Center with Matti Hamalainen, I started the MNE-Python project with NIH funding. Inspired by my early open-source development efforts on scikit-learn, I wanted to ?replicate the scikit-learn model? for the field of MEG/EEG data analysis. I wanted to create a Python project developed in the open ? on GitHub, with the support of a distributed community of contributors willing to give a bit of their time to share what works for them (and what doesn?t!). Very importantly, what I wanted was to encourage people outside of the Martinos Center at MGH to contribute to the MNE-Python code while getting public credit for their work. Before attracting users I needed to find contributors... and for this I needed to convince them that MNE-Python was not simply my own personal pet project, but rather something that belongs to its contributors. It has now been more than 11 years since MNE-Python was started, and as of now 285 contributors distributed all over the world have made MNE-Python a mature and successful project. This long effort has also been made possible by the sustained funding from NIH in the USA, as well as the ERC and ANR funding agencies in Europe and France. Now, we believe it?s finally time for MNE-Python to grow up and turn 1.0! ? I am particularly grateful first to Matti Hamalainen for teaching me so much about MEG and providing the groundwork with the MNE-C code he made public in 2006. MNE-C had already started the worldwide MNE project before MNE-Python was conceived. I am looking forward to seeing how MNE-Python will evolve in the future ? and let?s see if we?ll wait 11 more years for version 2.0? ? Alex --- Release notes --- A few highlights ============ - ? New standalone installers for macOS, Windows, and Linux should make onboarding of new users much easier and allow for offline installations! Download from https://mne.tools/stable/install/installers.html - ? A new viewer for Raw, Epoched, Evoked, and ICA data makes interactive data exploration much easier and smoother. See https://github.com/mne-tools/mne-qt-browser - ? We redesigned and decluttered large parts of the coregistration GUI to make it easier for you to find the functionality you?re looking for! - ? We also added numerous improvements to Reports, including a drastic speedup of Raw data plots. - ? Lastly, the iEEG contact localization GUI has seen a number of improvements, too. Notable API changes ================ We have changed a few things that will require you to adjust your code. - The verbose attribute of classes (e.g., mne.io.Raw, mne.Epochs, etc.) has been deprecated. Explicitly pass verbose to methods as necessary instead. - In mne.viz.set_browser_backend(), the mne-qt-browser-based backend is now called 'qt' rather than 'pyqtgraph' for simplicity. - mne.Info.pick_channels has been deprecated. Use inst.pick_channels to pick channels from Raw, Epochs, and Evoked. - All data_path functions now return modern pathlib.Path objects rather than strings. - The argument name event_list has been deprecated in favor of events in mne.write_events() - The max_ori_out parameter of mne.beamformer.apply_lcmv() and related functions is being removed as only signed estimates are supported. Full list of API changes: https://mne.tools/stable/whats_new.html#api-changes Full changelog =========== For a full list of improvements and API changes, see: https://mne.tools/stable/whats_new.html#version-1-0 Find the full documentation at https://mne.tools/ Installing the new release =================== Since quite a few things ? including dependencies ? have changed, we recommend creating a new environment with a ?fresh? installation. Or if you fancy, download one of our fresh and shiny new installers! Visit https://mne.tools/stable/install for instructions and download links. Feedback ======== If you have any questions or discovered a problem, please feel free to reach out to us on the MNE Forum: https://mne.discourse.group As usual, we welcome your bug reports, feature requests, critiques, and, of course, new contributions. ? Development takes place on GitHub. If you would like to contribute, star ? the project, or just take a peek at the code, visit https://github.com/mne-tools/mne-python. You may follow us on Twitter, too: https://twitter.com/mne_news We hope you will enjoy the new features and many, many small improvements we have added, and are looking forward to receiving your feedback. Stay safe and take care! The MNE-Python developers Contributors ========== MNE-Python is a community-driven project. We are always very happy to welcome new contributors of code and documentation! 33 people contributed to this release ? and 10 were first-timers! Thank you all so very much for your time and effort, we truly appreciate it! First-time contributors: - Adina Wagner - Etienne de Montalivet - Federico Zamberlan - Jan Zerfowski - John Veillette - Matthias Eberlein - Michiru Kaneda - Nikolai Chapochnikov - Scott Huberty - Senwen Deng Recurring contributors: - Adam Li - Alex Rockhill - Alexandre Gramfort - Britta Westner - Clemens Brunner - Daniel McCloy - Eduard Ort - Eric Larson - Guillaume Favelier - Jan Sosulski - Jeff Stout - Joshua Teves - Julia Guiomar Niso Gal?n - Luke Bloy - Marijn van Vliet - Martin Schulz - Mathieu Scheltienne - Miko?aj Magnuski - Richard H?chenberger - Robert Luke - Stefan Appelhoff - Steve Matindi - Thomas Hartmann -------------- next part -------------- An HTML attachment was scrubbed... URL: From bertrand.thirion at inria.fr Tue Mar 22 05:53:12 2022 From: bertrand.thirion at inria.fr (Bertrand Thirion) Date: Tue, 22 Mar 2022 10:53:12 +0100 (CET) Subject: [Neuroimaging] [ANN] MNE-Python 1.0 In-Reply-To: References: Message-ID: <812425213.6491456.1647942792293.JavaMail.zimbra@inria.fr> Congratulations ! Such a great milestone. Bertrand Thirion Head of science (d?l?gu? scientifique) Inria Saclay-?le-de-France Head of Parietal Team Neurospin, CEA Saclay, 91191 Gif sur Yvette +33 1 69 08 79 92 http://pages.saclay.inria.fr/bertrand.thirion > De: "Alexandre Gramfort" > ?: "Discussion and support forum for the users of MNE Software" > , "megcommunity" > , "megcommunity" , > "Neuroimaging analysis in Python" > Envoy?: Mardi 22 Mars 2022 10:48:32 > Objet: [Neuroimaging] [ANN] MNE-Python 1.0 > [Cross-posting with: [ > https://mne.discourse.group/t/mne-python-is-turning-1-0/4595 | > https://mne.discourse.group/t/mne-python-is-turning-1-0/4595 ] ] > ? MNE-Python is turning 1.0... > In December 2010, freshly arrived in Boston to work as a postdoc at the Martinos > Center with Matti Hamalainen, I started the MNE-Python project with NIH > funding. Inspired by my early open-source development efforts on scikit-learn, > I wanted to ?replicate the scikit-learn model? for the field of MEG/EEG data > analysis. I wanted to create a Python project developed in the open ? on > GitHub, with the support of a distributed community of contributors willing to > give a bit of their time to share what works for them (and what doesn?t!). Very > importantly, what I wanted was to encourage people outside of the Martinos > Center at MGH to contribute to the MNE-Python code while getting public credit > for their work. Before attracting users I needed to find contributors... and > for this I needed to convince them that MNE-Python was not simply my own > personal pet project, but rather something that belongs to its contributors. > It has now been more than 11 years since MNE-Python was started, and as of now > 285 contributors distributed all over the world have made MNE-Python a mature > and successful project. This long effort has also been made possible by the > sustained funding from NIH in the USA, as well as the ERC and ANR funding > agencies in Europe and France. Now, we believe it?s finally time for MNE-Python > to grow up and turn 1.0! ? > I am particularly grateful first to Matti Hamalainen for teaching me so much > about MEG and providing the groundwork with the MNE-C code he made public in > 2006. MNE-C had already started the worldwide MNE project before MNE-Python was > conceived. > I am looking forward to seeing how MNE-Python will evolve in the future ? and > let?s see if we?ll wait 11 more years for version 2.0? ? > Alex > --- Release notes --- > A few highlights > ============ > * > ? New standalone installers for macOS, Windows, and Linux should make > onboarding of new users much easier and allow for offline installations! > Download from [ https://mne.tools/stable/install/installers.html | > https://mne.tools/stable/install/installers.html ] > * > ? A new viewer for Raw, Epoched, Evoked, and ICA data makes interactive data > exploration much easier and smoother. See [ > https://github.com/mne-tools/mne-qt-browser | > https://github.com/mne-tools/mne-qt-browser ] > * > ? We redesigned and decluttered large parts of the coregistration GUI to make > it easier for you to find the functionality you?re looking for! > * > ? We also added numerous improvements to Reports, including a drastic speedup > of Raw data plots. > * > ? Lastly, the iEEG contact localization GUI has seen a number of improvements, > too. > Notable API changes > ================ > We have changed a few things that will require you to adjust your code. > * > The verbose attribute of classes (e.g., mne.io.Raw, mne.Epochs, etc.) has been > deprecated. Explicitly pass verbose to methods as necessary instead. > * > In mne.viz.set_browser_backend(), the mne-qt-browser-based backend is now called > 'qt' rather than 'pyqtgraph' for simplicity. > * > mne.Info.pick_channels has been deprecated. Use inst.pick_channels to pick > channels from Raw, Epochs, and Evoked. > * > All data_path functions now return modern pathlib.Path objects rather than > strings. > * > The argument name event_list has been deprecated in favor of events in > mne.write_events() > * > The max_ori_out parameter of mne.beamformer.apply_lcmv() and related functions > is being removed as only signed estimates are supported. > Full list of API changes: > [ https://mne.tools/stable/whats_new.html#api-changes | > https://mne.tools/stable/whats_new.html#api-changes ] > Full changelog > =========== > For a full list of improvements and API changes, see: > [ https://mne.tools/stable/whats_new.html#version-1-0 | > https://mne.tools/stable/whats_new.html#version-1-0 ] > Find the full documentation at [ https://mne.tools/stable/index.html | > https://mne.tools/ ] > Installing the new release > =================== > Since quite a few things ? including dependencies ? have changed, we recommend > creating a new environment with a ?fresh? installation. > Or if you fancy, download one of our fresh and shiny new installers! > Visit [ https://mne.tools/stable/install/index.html | > https://mne.tools/stable/install ] for instructions and download links. > Feedback > ======== > If you have any questions or discovered a problem, please feel free to reach out > to us on the MNE Forum: [ https://mne.discourse.group/ | > https://mne.discourse.group ] > As usual, we welcome your bug reports, feature requests, critiques, and, of > course, new contributions. ? Development takes place on GitHub. If you would > like to contribute, star ? the project, or just take a peek at the code, visit > [ https://github.com/mne-tools/mne-python | > https://github.com/mne-tools/mne-python ] . > You may follow us on Twitter, too: [ https://twitter.com/mne_news | > https://twitter.com/mne_news ] > We hope you will enjoy the new features and many, many small improvements we > have added, and are looking forward to receiving your feedback. > Stay safe and take care! > The MNE-Python developers > Contributors > ========== > MNE-Python is a community-driven project. We are always very happy to welcome > new contributors of code and documentation! 33 people contributed to this > release ? and 10 were first-timers! Thank you all so very much for your time > and effort, we truly appreciate it! > First-time contributors: > * > Adina Wagner > * > Etienne de Montalivet > * > Federico Zamberlan > * > Jan Zerfowski > * > John Veillette > * > Matthias Eberlein > * > Michiru Kaneda > * > Nikolai Chapochnikov > * > Scott Huberty > * > Senwen Deng > Recurring contributors: > * > Adam Li > * > Alex Rockhill > * > Alexandre Gramfort > * > Britta Westner > * > Clemens Brunner > * > Daniel McCloy > * > Eduard Ort > * > Eric Larson > * > Guillaume Favelier > * > Jan Sosulski > * > Jeff Stout > * > Joshua Teves > * > Julia Guiomar Niso Gal?n > * > Luke Bloy > * > Marijn van Vliet > * > Martin Schulz > * > Mathieu Scheltienne > * > Miko?aj Magnuski > * > Richard H?chenberger > * > Robert Luke > * > Stefan Appelhoff > * > Steve Matindi > * > Thomas Hartmann > _______________________________________________ > Neuroimaging mailing list > Neuroimaging at python.org > https://mail.python.org/mailman/listinfo/neuroimaging -------------- next part -------------- An HTML attachment was scrubbed... URL: From pestilli at utexas.edu Tue Mar 22 10:47:27 2022 From: pestilli at utexas.edu (Franco Pestilli) Date: Tue, 22 Mar 2022 09:47:27 -0500 Subject: [Neuroimaging] [ANN] MNE-Python 1.0 In-Reply-To: References: Message-ID: Congratulations Alex and team! Franco *FRANCO PESTILLI*, *Ph.D.* | *Associate Professor* Department of Psychology | College of Liberal Arts | The University of Texas at Austin he/him | pestilli at utexas.edu | web | GitHub | brainlife.io On Tue, Mar 22, 2022 at 4:49 AM Alexandre Gramfort < alexandre.gramfort at inria.fr> wrote: > [Cross-posting with: > https://mne.discourse.group/t/mne-python-is-turning-1-0/4595] > > ? MNE-Python is turning 1.0... > > In December 2010, freshly arrived in Boston to work as a postdoc at the > Martinos Center with Matti Hamalainen, I started the MNE-Python project > with NIH funding. Inspired by my early open-source development efforts on > scikit-learn, I wanted to ?replicate the scikit-learn model? for the field > of MEG/EEG data analysis. I wanted to create a Python project developed in > the open ? on GitHub, with the support of a distributed community of > contributors willing to give a bit of their time to share what works for > them (and what doesn?t!). Very importantly, what I wanted was to encourage > people outside of the Martinos Center at MGH to contribute to the > MNE-Python code while getting public credit for their work. Before > attracting users I needed to find contributors... and for this I needed to > convince them that MNE-Python was not simply my own personal pet project, > but rather something that belongs to its contributors. > > It has now been more than 11 years since MNE-Python was started, and as of > now 285 contributors distributed all over the world have made MNE-Python a > mature and successful project. This long effort has also been made possible > by the sustained funding from NIH in the USA, as well as the ERC and ANR > funding agencies in Europe and France. Now, we believe it?s finally time > for MNE-Python to grow up and turn 1.0! ? > > I am particularly grateful first to Matti Hamalainen for teaching me so > much about MEG and providing the groundwork with the MNE-C code he made > public in 2006. MNE-C had already started the worldwide MNE project before > MNE-Python was conceived. > > I am looking forward to seeing how MNE-Python will evolve in the future ? > and let?s see if we?ll wait 11 more years for version 2.0? ? > > Alex > > > --- Release notes --- > > A few highlights > > ============ > > > - > > ? New standalone installers for macOS, Windows, and Linux should make > onboarding of new users much easier and allow for offline installations! > Download from https://mne.tools/stable/install/installers.html > - > > ? A new viewer for Raw, Epoched, Evoked, and ICA data makes > interactive data exploration much easier and smoother. See > https://github.com/mne-tools/mne-qt-browser > - > > ? We redesigned and decluttered large parts of the coregistration GUI > to make it easier for you to find the functionality you?re looking for! > - > > ? We also added numerous improvements to Reports, including a drastic > speedup of Raw data plots. > - > > ? Lastly, the iEEG contact localization GUI has seen a number of > improvements, too. > > > > Notable API changes > > ================ > > We have changed a few things that will require you to adjust your code. > > > - > > The verbose attribute of classes (e.g., mne.io.Raw, mne.Epochs, etc.) > has been deprecated. Explicitly pass verbose to methods as necessary > instead. > - > > In mne.viz.set_browser_backend(), the mne-qt-browser-based backend is > now called 'qt' rather than 'pyqtgraph' for simplicity. > - > > mne.Info.pick_channels has been deprecated. Use inst.pick_channels to > pick channels from Raw, Epochs, and Evoked. > - > > All data_path functions now return modern pathlib.Path objects rather > than strings. > - > > The argument name event_list has been deprecated in favor of events in > mne.write_events() > - > > The max_ori_out parameter of mne.beamformer.apply_lcmv() and related > functions is being removed as only signed estimates are supported. > > > Full list of API changes: > > https://mne.tools/stable/whats_new.html#api-changes > > > Full changelog > > =========== > > For a full list of improvements and API changes, see: > > https://mne.tools/stable/whats_new.html#version-1-0 > > Find the full documentation at https://mne.tools/ > > > Installing the new release > > =================== > > Since quite a few things ? including dependencies ? have changed, we > recommend creating a new environment with a ?fresh? installation. > > Or if you fancy, download one of our fresh and shiny new installers! > > Visit https://mne.tools/stable/install > for instructions and > download links. > > Feedback > > ======== > > If you have any questions or discovered a problem, please feel free to > reach out to us on the MNE Forum: https://mne.discourse.group > > As usual, we welcome your bug reports, feature requests, critiques, and, > of course, new contributions. ? Development takes place on GitHub. If you > would like to contribute, star ? the project, or just take a peek at the > code, visit https://github.com/mne-tools/mne-python. > > You may follow us on Twitter, too: https://twitter.com/mne_news > > We hope you will enjoy the new features and many, many small improvements > we have added, and are looking forward to receiving your feedback. > > Stay safe and take care! > > The MNE-Python developers > > > Contributors > > ========== > > MNE-Python is a community-driven project. We are always very happy to > welcome new contributors of code and documentation! 33 people contributed > to this release ? and 10 were first-timers! Thank you all so very much for > your time and effort, we truly appreciate it! > > First-time contributors: > > > - > > Adina Wagner > - > > Etienne de Montalivet > - > > Federico Zamberlan > - > > Jan Zerfowski > - > > John Veillette > - > > Matthias Eberlein > - > > Michiru Kaneda > - > > Nikolai Chapochnikov > - > > Scott Huberty > - > > Senwen Deng > > > Recurring contributors: > > > - > > Adam Li > - > > Alex Rockhill > - > > Alexandre Gramfort > - > > Britta Westner > - > > Clemens Brunner > - > > Daniel McCloy > - > > Eduard Ort > - > > Eric Larson > - > > Guillaume Favelier > - > > Jan Sosulski > - > > Jeff Stout > - > > Joshua Teves > - > > Julia Guiomar Niso Gal?n > - > > Luke Bloy > - > > Marijn van Vliet > - > > Martin Schulz > - > > Mathieu Scheltienne > - > > Miko?aj Magnuski > - > > Richard H?chenberger > - > > Robert Luke > - > > Stefan Appelhoff > - > > Steve Matindi > - > > Thomas Hartmann > > > > _______________________________________________ > Neuroimaging mailing list > Neuroimaging at python.org > https://mail.python.org/mailman/listinfo/neuroimaging > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ainapuce at gmail.com Tue Mar 22 10:54:17 2022 From: ainapuce at gmail.com (Aina Puce) Date: Tue, 22 Mar 2022 10:54:17 -0400 Subject: [Neuroimaging] [ANN] MNE-Python 1.0 In-Reply-To: References: Message-ID: Alex, the MEG/EEG field owes you a great debt. Software that is well documented & that runs well is a rare gem... My congratulations to you!!! ??? Aina On Tue, Mar 22, 2022 at 10:47 AM Franco Pestilli wrote: > Congratulations Alex and team! > > Franco > > *FRANCO PESTILLI*, *Ph.D.* | *Associate Professor* > Department of Psychology > | College of > Liberal Arts | The University of Texas > at Austin > he/him | pestilli at utexas.edu | web > | GitHub > | brainlife.io > > On Tue, Mar 22, 2022 at 4:49 AM Alexandre Gramfort < > alexandre.gramfort at inria.fr> wrote: > >> [Cross-posting with: >> https://mne.discourse.group/t/mne-python-is-turning-1-0/4595] >> >> ? MNE-Python is turning 1.0... >> >> In December 2010, freshly arrived in Boston to work as a postdoc at the >> Martinos Center with Matti Hamalainen, I started the MNE-Python project >> with NIH funding. Inspired by my early open-source development efforts on >> scikit-learn, I wanted to ?replicate the scikit-learn model? for the field >> of MEG/EEG data analysis. I wanted to create a Python project developed in >> the open ? on GitHub, with the support of a distributed community of >> contributors willing to give a bit of their time to share what works for >> them (and what doesn?t!). Very importantly, what I wanted was to encourage >> people outside of the Martinos Center at MGH to contribute to the >> MNE-Python code while getting public credit for their work. Before >> attracting users I needed to find contributors... and for this I needed to >> convince them that MNE-Python was not simply my own personal pet project, >> but rather something that belongs to its contributors. >> >> It has now been more than 11 years since MNE-Python was started, and as >> of now 285 contributors distributed all over the world have made MNE-Python >> a mature and successful project. This long effort has also been made >> possible by the sustained funding from NIH in the USA, as well as the ERC >> and ANR funding agencies in Europe and France. Now, we believe it?s finally >> time for MNE-Python to grow up and turn 1.0! ? >> >> I am particularly grateful first to Matti Hamalainen for teaching me so >> much about MEG and providing the groundwork with the MNE-C code he made >> public in 2006. MNE-C had already started the worldwide MNE project before >> MNE-Python was conceived. >> >> I am looking forward to seeing how MNE-Python will evolve in the future ? >> and let?s see if we?ll wait 11 more years for version 2.0? ? >> >> Alex >> >> >> --- Release notes --- >> >> A few highlights >> >> ============ >> >> >> - >> >> ? New standalone installers for macOS, Windows, and Linux should >> make onboarding of new users much easier and allow for offline >> installations! Download from >> https://mne.tools/stable/install/installers.html >> - >> >> ? A new viewer for Raw, Epoched, Evoked, and ICA data makes >> interactive data exploration much easier and smoother. See >> https://github.com/mne-tools/mne-qt-browser >> - >> >> ? We redesigned and decluttered large parts of the coregistration >> GUI to make it easier for you to find the functionality you?re looking for! >> - >> >> ? We also added numerous improvements to Reports, including a >> drastic speedup of Raw data plots. >> - >> >> ? Lastly, the iEEG contact localization GUI has seen a number of >> improvements, too. >> >> >> >> Notable API changes >> >> ================ >> >> We have changed a few things that will require you to adjust your code. >> >> >> - >> >> The verbose attribute of classes (e.g., mne.io.Raw, mne.Epochs, etc.) >> has been deprecated. Explicitly pass verbose to methods as necessary >> instead. >> - >> >> In mne.viz.set_browser_backend(), the mne-qt-browser-based backend is >> now called 'qt' rather than 'pyqtgraph' for simplicity. >> - >> >> mne.Info.pick_channels has been deprecated. Use inst.pick_channels to >> pick channels from Raw, Epochs, and Evoked. >> - >> >> All data_path functions now return modern pathlib.Path objects rather >> than strings. >> - >> >> The argument name event_list has been deprecated in favor of events >> in mne.write_events() >> - >> >> The max_ori_out parameter of mne.beamformer.apply_lcmv() and related >> functions is being removed as only signed estimates are supported. >> >> >> Full list of API changes: >> >> https://mne.tools/stable/whats_new.html#api-changes >> >> >> Full changelog >> >> =========== >> >> For a full list of improvements and API changes, see: >> >> https://mne.tools/stable/whats_new.html#version-1-0 >> >> Find the full documentation at https://mne.tools/ >> >> >> Installing the new release >> >> =================== >> >> Since quite a few things ? including dependencies ? have changed, we >> recommend creating a new environment with a ?fresh? installation. >> >> Or if you fancy, download one of our fresh and shiny new installers! >> >> Visit https://mne.tools/stable/install >> for instructions and >> download links. >> >> Feedback >> >> ======== >> >> If you have any questions or discovered a problem, please feel free to >> reach out to us on the MNE Forum: https://mne.discourse.group >> >> As usual, we welcome your bug reports, feature requests, critiques, and, >> of course, new contributions. ? Development takes place on GitHub. If you >> would like to contribute, star ? the project, or just take a peek at the >> code, visit https://github.com/mne-tools/mne-python. >> >> You may follow us on Twitter, too: https://twitter.com/mne_news >> >> We hope you will enjoy the new features and many, many small improvements >> we have added, and are looking forward to receiving your feedback. >> >> Stay safe and take care! >> >> The MNE-Python developers >> >> >> Contributors >> >> ========== >> >> MNE-Python is a community-driven project. We are always very happy to >> welcome new contributors of code and documentation! 33 people contributed >> to this release ? and 10 were first-timers! Thank you all so very much for >> your time and effort, we truly appreciate it! >> >> First-time contributors: >> >> >> - >> >> Adina Wagner >> - >> >> Etienne de Montalivet >> - >> >> Federico Zamberlan >> - >> >> Jan Zerfowski >> - >> >> John Veillette >> - >> >> Matthias Eberlein >> - >> >> Michiru Kaneda >> - >> >> Nikolai Chapochnikov >> - >> >> Scott Huberty >> - >> >> Senwen Deng >> >> >> Recurring contributors: >> >> >> - >> >> Adam Li >> - >> >> Alex Rockhill >> - >> >> Alexandre Gramfort >> - >> >> Britta Westner >> - >> >> Clemens Brunner >> - >> >> Daniel McCloy >> - >> >> Eduard Ort >> - >> >> Eric Larson >> - >> >> Guillaume Favelier >> - >> >> Jan Sosulski >> - >> >> Jeff Stout >> - >> >> Joshua Teves >> - >> >> Julia Guiomar Niso Gal?n >> - >> >> Luke Bloy >> - >> >> Marijn van Vliet >> - >> >> Martin Schulz >> - >> >> Mathieu Scheltienne >> - >> >> Miko?aj Magnuski >> - >> >> Richard H?chenberger >> - >> >> Robert Luke >> - >> >> Stefan Appelhoff >> - >> >> Steve Matindi >> - >> >> Thomas Hartmann >> >> >> >> _______________________________________________ >> Neuroimaging mailing list >> Neuroimaging at python.org >> https://mail.python.org/mailman/listinfo/neuroimaging >> > -- Aina Puce, PhD (she/her) [image: A button with "Hear my name" text for name playback in email signature] Eleanor Cox Riggs Professor Psychological & Brain Sciences Programs in Neuroscience, Cognitive Science Affiliate, Indiana University Network Science Institute Indiana University, Bloomington IN 47405 USA -- Chair-Past, *Organization for Human Brain Mapping* Associate Editor, *Perspectives on Psychological Science* -- email: ainapuce at indiana.edu Twitter: @aina_puce Blog: https://neurowanderer.blog tel (cell): +1 812 650-2213 -------------- next part -------------- An HTML attachment was scrubbed... URL: From markiewicz at stanford.edu Mon Mar 28 11:42:21 2022 From: markiewicz at stanford.edu (Christopher Markiewicz) Date: Mon, 28 Mar 2022 15:42:21 +0000 Subject: [Neuroimaging] Data formats review - Surface and surface-sampled data Message-ID: Hi all, Continuing with our journal club on data formats, we're going to be talking about surface data. Full post is on the Discourse, including a link to find a good attendance time. https://nipy.discourse.group/t/data-formats-review-surface-and-surface-sampled-data/123 Best, -- Christopher J. Markiewicz, PhD Center for Reproducible Neuroscience Stanford University -------------- next part -------------- An HTML attachment was scrubbed... URL: