From alexandre.gramfort at inria.fr Fri Jan 6 12:12:07 2023 From: alexandre.gramfort at inria.fr (Alexandre Gramfort) Date: Fri, 6 Jan 2023 18:12:07 +0100 Subject: [Neuroimaging] [ANN] MNE 1.3 Release Message-ID: Hello everyone, Just before xmas we released MNE-Python 1.3! ? ? ? Please find a detailed list of changes and contributors below. All the best, Your MNE Team. A few highlights ============ - Mixed, cortical + discrete source spaces with fixed orientations are now allowed. (#11241 by Jevri Hanna ) - Add support for image_format='webp' to mne.Report when using Matplotlib 3.6+, which can reduce file sizes by up to 50% compared to 'png'. The new default image_format='auto' will automatically use this format if it?s available on the system (#11359 by Eric Larson ) - Add mne.beamformer.apply_dics_tfr_epochs() to apply a DICS beamformer to time-frequency resolved epochs (#11096 by Alex Rockhill ) - Check whether head radius (estimated from channel positions) is correct when reading EEGLAB data with read_raw_eeglab() and read_epochs_eeglab() . If head radius is not within likely values, warn informing about possible units mismatch and the new montage_units argument (#11283 by Miko?aj Magnuski ). - Add support for a callable passed in combine for mne.time_frequency.AverageTFR.plot and mne.time_frequency.AverageTFR.plot_joint (#11329 by Mathieu Scheltienne ) Notable API changes ================ We have changed a few things that will require you to adjust your code. - In mne.time_frequency.dpss_windows() , interpolating is deprecated (nowadays SciPy?s computations are fast enough for large N without interpolation). This affects parameters interp_from and interp_kind. Two new parameters of the underlying SciPy dpss() function are also exposed: sym (for choosing symmetric vs. periodic windows) and norm (window normalization method). (#11293 by Daniel McCloy ) - In mne.decoding.CSP.plot_patterns() , mne.decoding.CSP.plot_filters() , mne.preprocessing.ICA.plot_components() , and mne.viz.plot_ica_components() , the parameters vmin and vmax are deprecated in favor of vlim, for consistency with other topomap-plotting functions and methods (#11371 by Daniel McCloy ) - In mne.decoding.CSP.plot_patterns() and mne.decoding.CSP.plot_filters() the titleparameter is deprecated and will be removed in version 1.4 ( #11371 by Daniel McCloy ) - The APIs of mne.preprocessing.ICA.plot_components() and mne.viz.plot_ica_components() gained new parameters show_names, extrapolate, border, size, cnorm, cbar_fmt, axes, nrows, ncols, for consistency with other topomap-plotting functions and methods (#11371 by Daniel McCloy ) - The APIs of mne.decoding.CSP.plot_patterns() and mne.decoding.CSP.plot_filters() gained new parameters extrapolate, border, cnorm, axes, nrows, ncols, for consistency with other topomap-plotting functions and methods (#11371 by Daniel McCloy ) 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 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. Please follow the installation instructions on our website: https://mne.tools/stable/install/mne_python.html Feedback ======== As usual, we welcome your bug reports, feature requests, critiques, and 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 https://twitter.com/mne_news and on mastodon https://fosstodon.org/@mne We hope you will enjoy the new features and many, many small improvements we have added, and are looking forward to receiving your feedback. 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! 29 people contributed to this release ? and 13 were first-timers! Thank you all so very much for your time and effort, we truly appreciate it! Release contributors (+ are first time contributors): - Alex Rockhill - Alexandre Gramfort - Britta Westner - Carlos de la Torre+ - Daniel Hasegan+ - Daniel McCloy - Dinara Issagaliyeva+ - Enzo Altamiranda+ - Eric Brayet+ - Eric Larson - Erkka Heinila - Felix Klotzsche - Hakimeh Aslsardroud+ - Jennifer Behnke+ - Jevri Hanna - Lukas Hecker - Mark Alexander Henney+ - Mathieu Scheltienne - Mauricio Cespedes+ - Miko?aj Magnuski - Moritz Gerster - Omer Shubi+ - Pavel Navratil+ - Richard H?chenberger - Santeri Ruuskanen+ - Stefan Appelhoff - Timon Merk - Tom Ma+ - Toomas Erik Anij?rv+ -------------- next part -------------- An HTML attachment was scrubbed... URL: From jbpoline at gmail.com Fri Jan 6 12:13:21 2023 From: jbpoline at gmail.com (JB Poline) Date: Fri, 6 Jan 2023 12:13:21 -0500 Subject: [Neuroimaging] [ANN] MNE 1.3 Release In-Reply-To: References: Message-ID: A good start for 2023 :) ! JB On Fri, Jan 6, 2023 at 12:12 PM Alexandre Gramfort < alexandre.gramfort at inria.fr> wrote: > Hello everyone, > > Just before xmas we released MNE-Python 1.3! ? ? ? > > Please find a detailed list of changes and contributors below. > > All the best, > > Your MNE Team. > > > A few highlights > > ============ > > > - > > Mixed, cortical + discrete source spaces with fixed orientations are > now allowed. (#11241 > by Jevri Hanna > ) > - > > Add support for image_format='webp' to mne.Report > when > using Matplotlib 3.6+, which can reduce file sizes by up to 50% compared to > 'png'. The new default image_format='auto' will automatically use this > format if it?s available on the system (#11359 > by Eric Larson > ) > - > > Add mne.beamformer.apply_dics_tfr_epochs() > > to apply a DICS beamformer to time-frequency resolved epochs (#11096 > by Alex Rockhill > ) > - > > Check whether head radius (estimated from channel positions) is > correct when reading EEGLAB data with read_raw_eeglab() > > and read_epochs_eeglab() > . > If head radius is not within likely values, warn informing about possible > units mismatch and the new montage_units argument (#11283 > by Miko?aj > Magnuski ). > - > > Add support for a callable passed in combine for > mne.time_frequency.AverageTFR.plot > > and mne.time_frequency.AverageTFR.plot_joint > > (#11329 by Mathieu > Scheltienne ) > > > > Notable API changes > > ================ > > We have changed a few things that will require you to adjust your code. > > > - > > In mne.time_frequency.dpss_windows() > , > interpolating is deprecated (nowadays SciPy?s computations are fast enough > for large N without interpolation). This affects parameters interp_from > and interp_kind. Two new parameters of the underlying SciPy dpss() > > function are also exposed: sym (for choosing symmetric vs. periodic > windows) and norm (window normalization method). (#11293 > by Daniel McCloy > ) > - > > In mne.decoding.CSP.plot_patterns() > , > mne.decoding.CSP.plot_filters() > , > mne.preprocessing.ICA.plot_components() > , > and mne.viz.plot_ica_components() > , > the parameters vmin and vmax are deprecated in favor of vlim, for > consistency with other topomap-plotting functions and methods (#11371 > by Daniel McCloy > ) > - > > In mne.decoding.CSP.plot_patterns() > > and mne.decoding.CSP.plot_filters() > > the titleparameter is deprecated and will be removed in version 1.4 ( > #11371 by Daniel > McCloy ) > - > > The APIs of mne.preprocessing.ICA.plot_components() > > and mne.viz.plot_ica_components() > gained > new parameters show_names, extrapolate, border, size, cnorm, cbar_fmt, > axes, nrows, ncols, for consistency with other topomap-plotting > functions and methods (#11371 > by Daniel McCloy > ) > - > > The APIs of mne.decoding.CSP.plot_patterns() > > and mne.decoding.CSP.plot_filters() > gained > new parameters extrapolate, border, cnorm, axes, nrows, ncols, for > consistency with other topomap-plotting functions and methods (#11371 > by Daniel McCloy > ) > > > > 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 > > 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. Please > follow the installation instructions on our website: > > https://mne.tools/stable/install/mne_python.html > > Feedback > > ======== > > As usual, we welcome your bug reports, feature requests, critiques, and > 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 https://twitter.com/mne_news and on mastodon > https://fosstodon.org/@mne > > We hope you will enjoy the new features and many, many small improvements > we have added, and are looking forward to receiving your feedback. > > 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! 29 people contributed > to this release ? and 13 were first-timers! Thank you all so very much for > your time and effort, we truly appreciate it! > > Release contributors (+ are first time contributors): > > > - > > Alex Rockhill > - > > Alexandre Gramfort > - > > Britta Westner > - > > Carlos de la Torre+ > - > > Daniel Hasegan+ > - > > Daniel McCloy > - > > Dinara Issagaliyeva+ > - > > Enzo Altamiranda+ > - > > Eric Brayet+ > - > > Eric Larson > - > > Erkka Heinila > - > > Felix Klotzsche > - > > Hakimeh Aslsardroud+ > - > > Jennifer Behnke+ > - > > Jevri Hanna > - > > Lukas Hecker > - > > Mark Alexander Henney+ > - > > Mathieu Scheltienne > - > > Mauricio Cespedes+ > - > > Miko?aj Magnuski > - > > Moritz Gerster > - > > Omer Shubi+ > - > > Pavel Navratil+ > - > > Richard H?chenberger > - > > Santeri Ruuskanen+ > - > > Stefan Appelhoff > - > > Timon Merk > - > > Tom Ma+ > - > > Toomas Erik Anij?rv+ > > > > _______________________________________________ > Neuroimaging mailing list > Neuroimaging at python.org > https://mail.python.org/mailman/listinfo/neuroimaging > -------------- next part -------------- An HTML attachment was scrubbed... URL: From bertrand.thirion at inria.fr Fri Jan 6 12:14:53 2023 From: bertrand.thirion at inria.fr (Bertrand Thirion) Date: Fri, 6 Jan 2023 18:14:53 +0100 Subject: [Neuroimaging] [ANN] MNE 1.3 Release In-Reply-To: References: Message-ID: Congrats ! B Le 06/01/2023 ? 18:12, Alexandre Gramfort a ?crit?: > > Hello everyone, > > > Just before xmas we released MNE-Python 1.3! ? ? ? > > Please find a detailed list of changes and contributors below. > > Congrts > > All the best, > > > Your MNE Team. > > > > A few highlights > > ============ > > > * > > Mixed, cortical + discrete source spaces with fixed orientations > are now allowed. (#11241 > by Jevri > Hanna ) > > * > > Add support for image_format='webp'to mne.Report > when > using Matplotlib 3.6+, which can reduce file sizes by up to 50% > compared to 'png'. The new default image_format='auto'will > automatically use this format if it?s available on the system > (#11359 by > Eric Larson ) > > * > > Add mne.beamformer.apply_dics_tfr_epochs() > to > apply a DICS beamformer to time-frequency resolved epochs (#11096 > by Alex > Rockhill ) > > * > > Check whether head radius (estimated from channel positions) is > correct when reading EEGLAB data with read_raw_eeglab() > and > read_epochs_eeglab() > . > If head radius is not within likely values, warn informing about > possible units mismatch and the new montage_unitsargument (#11283 > by Miko?aj > Magnuski ). > > * > > Add support for a callable passed in combinefor > mne.time_frequency.AverageTFR.plot > and > mne.time_frequency.AverageTFR.plot_joint > (#11329 > by Mathieu > Scheltienne ) > > > > Notable API changes > > ================ > > > We have changed a few things that will require you to adjust your code. > > > * > > In mne.time_frequency.dpss_windows() > , > interpolating is deprecated (nowadays SciPy?s computations are > fast enough for large Nwithout interpolation). This affects > parameters interp_fromand interp_kind. Two new parameters of the > underlying SciPy dpss() > function > are also exposed: sym(for choosing symmetric vs. periodic windows) > and norm(window normalization method). (#11293 > by Daniel > McCloy ) > > * > > In mne.decoding.CSP.plot_patterns() > , > mne.decoding.CSP.plot_filters() > , > mne.preprocessing.ICA.plot_components() > , > and mne.viz.plot_ica_components() > , > the parameters vminand vmaxare deprecated in favor of vlim, for > consistency with other topomap-plotting functions and methods > (#11371 by > Daniel McCloy ) > > * > > In mne.decoding.CSP.plot_patterns() > and > mne.decoding.CSP.plot_filters() > the > titleparameter is deprecated and will be removed in version 1.4 > (#11371 by > Daniel McCloy ) > > * > > The APIs of mne.preprocessing.ICA.plot_components() > and > mne.viz.plot_ica_components() > gained > new parameters show_names, extrapolate, border, size, cnorm, > cbar_fmt, axes, nrows, ncols, for consistency with other > topomap-plotting functions and methods (#11371 > by Daniel > McCloy ) > > * > > The APIs of mne.decoding.CSP.plot_patterns() > and > mne.decoding.CSP.plot_filters() > gained > new parameters extrapolate, border, cnorm, axes, nrows, ncols, for > consistency with other topomap-plotting functions and methods > (#11371 by > Daniel McCloy ) > > > > 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 > > > > 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. > Please follow the installation instructions on our website: > > https://mne.tools/stable/install/mne_python.html > > > > Feedback > > ======== > > > As usual, we welcome your bug reports, feature requests, critiques, > and 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 Twitterhttps://twitter.com/mne_news > and on mastodon > https://fosstodon.org/@mne > > > We hope you will enjoy the new features and many, many small > improvements we have added, and are looking forward to receiving your > feedback. > > > 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! 29 people > contributed to this release ? and 13 were first-timers! Thank you all > so very much for your time and effort, we truly appreciate it! > > > Release contributors (+ are first time contributors): > > > * > > Alex Rockhill > > * > > Alexandre Gramfort > > * > > Britta Westner > > * > > Carlos de la Torre+ > > * > > Daniel Hasegan+ > > * > > Daniel McCloy > > * > > Dinara Issagaliyeva+ > > * > > Enzo Altamiranda+ > > * > > Eric Brayet+ > > * > > Eric Larson > > * > > Erkka Heinila > > * > > Felix Klotzsche > > * > > Hakimeh Aslsardroud+ > > * > > Jennifer Behnke+ > > * > > Jevri Hanna > > * > > Lukas Hecker > > * > > Mark Alexander Henney+ > > * > > Mathieu Scheltienne > > * > > Mauricio Cespedes+ > > * > > Miko?aj Magnuski > > * > > Moritz Gerster > > * > > Omer Shubi+ > > * > > Pavel Navratil+ > > * > > Richard H?chenberger > > * > > Santeri Ruuskanen+ > > * > > Stefan Appelhoff > > * > > Timon Merk > > * > > Tom Ma+ > > * > > Toomas Erik Anij?rv+ > > > > > _______________________________________________ > Neuroimaging mailing list > Neuroimaging at python.org > https://mail.python.org/mailman/listinfo/neuroimaging -------------- next part -------------- An HTML attachment was scrubbed... URL: From garyfallidis at gmail.com Fri Jan 6 17:32:36 2023 From: garyfallidis at gmail.com (Eleftherios Garyfallidis) Date: Fri, 6 Jan 2023 17:32:36 -0500 Subject: [Neuroimaging] DIPY - CZI EOSS Grant Award Announcement Message-ID: Dear DIPY and Neuroimaging communities, We are happy to announce that The Chan Zuckerberg Institute (CZI) has awarded an EOSS grant to the DIPY project. This grant will support Serge Koudoro (PI - Indiana university, USA), Dr. Girard (EPFL - Switzerland) and Dr. Rokem (UW - USA) to: - Extend DIPY to non-MRI data e.g. extending our registration framework - Add parallel computing capabilities - Improve our tractography framework - Expand documentation - Improve educational materials Community participation is highly encouraged in CZI grants and Serge who leads this project will follow up with more information about that during the following weeks and months. The official CZI EOSS announcement is here . Many Congratulations to Serge and team and Happy 2023 to you all! On behalf of the DIPY team, Eleftherios Garyfallidis, PhD Associate Professor Director of Graduate Studies Intelligent Systems Engineering Indiana University Luddy Hall 700 N Woodlawn Bloomington, IN 47408 GRG | DIPY | FURY -------------- next part -------------- An HTML attachment was scrubbed... URL: From jevillalonr at gmail.com Fri Jan 6 17:53:36 2023 From: jevillalonr at gmail.com (=?UTF-8?Q?Julio_Villal=C3=B3n?=) Date: Fri, 6 Jan 2023 14:53:36 -0800 Subject: [Neuroimaging] DIPY - CZI EOSS Grant Award Announcement In-Reply-To: References: Message-ID: Congrats! El vie, 6 ene 2023 a las 14:33, Eleftherios Garyfallidis (< garyfallidis at gmail.com>) escribi?: > Dear DIPY and Neuroimaging communities, > > We are happy to announce that The Chan Zuckerberg Institute (CZI) has > awarded an EOSS grant to the DIPY project. > > This grant will support Serge Koudoro (PI - Indiana university, USA), Dr. > Girard (EPFL - Switzerland) and Dr. Rokem (UW - USA) to: > > - Extend DIPY to non-MRI data e.g. extending our registration framework > - Add parallel computing capabilities > - Improve our tractography framework > - Expand documentation > - Improve educational materials > > Community participation is highly encouraged in CZI grants and Serge who > leads this project will follow up with more information about that during > the following weeks and months. > > The official CZI EOSS announcement is here > > . > > Many Congratulations to Serge and team and Happy 2023 to you all! > > On behalf of the DIPY team, > Eleftherios Garyfallidis, PhD > Associate Professor > Director of Graduate Studies > Intelligent Systems Engineering > Indiana University > Luddy Hall 700 N Woodlawn > Bloomington, IN 47408 > GRG | DIPY | FURY > > > > > _______________________________________________ > Neuroimaging mailing list > Neuroimaging at python.org > https://mail.python.org/mailman/listinfo/neuroimaging > -------------- next part -------------- An HTML attachment was scrubbed... URL: From satra at mit.edu Fri Jan 6 18:04:32 2023 From: satra at mit.edu (Satrajit Ghosh) Date: Fri, 6 Jan 2023 18:04:32 -0500 Subject: [Neuroimaging] DIPY - CZI EOSS Grant Award Announcement In-Reply-To: References: Message-ID: congrats! this will be very helpful to a large set of data coming online in the brain initiative consortia. cheers, satra On Fri, Jan 6, 2023 at 5:35 PM Eleftherios Garyfallidis < garyfallidis at gmail.com> wrote: > Dear DIPY and Neuroimaging communities, > > We are happy to announce that The Chan Zuckerberg Institute (CZI) has > awarded an EOSS grant to the DIPY project. > > This grant will support Serge Koudoro (PI - Indiana university, USA), Dr. > Girard (EPFL - Switzerland) and Dr. Rokem (UW - USA) to: > > - Extend DIPY to non-MRI data e.g. extending our registration framework > - Add parallel computing capabilities > - Improve our tractography framework > - Expand documentation > - Improve educational materials > > Community participation is highly encouraged in CZI grants and Serge who > leads this project will follow up with more information about that during > the following weeks and months. > > The official CZI EOSS announcement is here > > . > > Many Congratulations to Serge and team and Happy 2023 to you all! > > On behalf of the DIPY team, > Eleftherios Garyfallidis, PhD > Associate Professor > Director of Graduate Studies > Intelligent Systems Engineering > Indiana University > Luddy Hall 700 N Woodlawn > Bloomington, IN 47408 > GRG | DIPY | FURY > > > > > _______________________________________________ > Neuroimaging mailing list > Neuroimaging at python.org > https://mail.python.org/mailman/listinfo/neuroimaging > -------------- next part -------------- An HTML attachment was scrubbed... URL: From bertrand.thirion at inria.fr Sat Jan 7 02:33:42 2023 From: bertrand.thirion at inria.fr (Bertrand Thirion) Date: Sat, 7 Jan 2023 08:33:42 +0100 Subject: [Neuroimaging] DIPY - CZI EOSS Grant Award Announcement In-Reply-To: References: Message-ID: Congrats ! Bertrand Le 07/01/2023 ? 00:04, Satrajit Ghosh a ?crit?: > congrats! this will be very helpful to a large set of data coming > online in the brain initiative consortia. > > cheers, > > satra > > On Fri, Jan 6, 2023 at 5:35 PM Eleftherios Garyfallidis > wrote: > > Dear DIPY and Neuroimaging communities, > > We are happy to announce that The Chan Zuckerberg Institute (CZI) > has awarded an EOSS grant to the DIPY project. > > This grant will support Serge Koudoro (PI - Indiana university, > USA), ?Dr. Girard (EPFL - Switzerland) and Dr. Rokem (UW - USA) to: > > * Extend DIPY to non-MRI data e.g. extending our registration > framework > * Add parallel computing capabilities > * Improve our tractography framework > * Expand documentation > * Improve educational materials > > Community participation is highly encouraged in CZI grants and > Serge who leads this project will follow up with more information > about that during the following weeks and months. > > The official CZI EOSS announcement is here > . > > Many Congratulations to Serge and team and Happy 2023 to you all! > > On behalf of the DIPY team, > Eleftherios Garyfallidis, PhD > Associate Professor > Director of Graduate Studies > Intelligent Systems Engineering > Indiana University > Luddy Hall 700 N Woodlawn > Bloomington, IN 47408 > GRG | DIPY | > FURY > > > > _______________________________________________ > Neuroimaging mailing list > Neuroimaging at python.org > https://mail.python.org/mailman/listinfo/neuroimaging > > > _______________________________________________ > Neuroimaging mailing list > Neuroimaging at python.org > https://mail.python.org/mailman/listinfo/neuroimaging -------------- next part -------------- An HTML attachment was scrubbed... URL: From markiewicz at stanford.edu Fri Jan 6 12:17:45 2023 From: markiewicz at stanford.edu (Christopher Markiewicz) Date: Fri, 6 Jan 2023 17:17:45 +0000 Subject: [Neuroimaging] [ANN] MNE 1.3 Release In-Reply-To: References: Message-ID: Congrats, MNE team! Chris ________________________________ From: Neuroimaging on behalf of Bertrand Thirion Sent: Friday, January 6, 2023 12:14 To: neuroimaging at python.org Subject: Re: [Neuroimaging] [ANN] MNE 1.3 Release Congrats ! B Le 06/01/2023 ? 18:12, Alexandre Gramfort a ?crit : Hello everyone, Just before xmas we released MNE-Python 1.3! ? ? ? Please find a detailed list of changes and contributors below. Congrts All the best, Your MNE Team. A few highlights ============ * Mixed, cortical + discrete source spaces with fixed orientations are now allowed. (#11241 by Jevri Hanna) * Add support for image_format='webp' to mne.Report when using Matplotlib 3.6+, which can reduce file sizes by up to 50% compared to 'png'. The new default image_format='auto' will automatically use this format if it?s available on the system (#11359 by Eric Larson) * Add mne.beamformer.apply_dics_tfr_epochs() to apply a DICS beamformer to time-frequency resolved epochs (#11096 by Alex Rockhill) * Check whether head radius (estimated from channel positions) is correct when reading EEGLAB data with read_raw_eeglab() and read_epochs_eeglab(). If head radius is not within likely values, warn informing about possible units mismatch and the new montage_units argument (#11283 by Miko?aj Magnuski). * Add support for a callable passed in combine for mne.time_frequency.AverageTFR.plot and mne.time_frequency.AverageTFR.plot_joint (#11329 by Mathieu Scheltienne) Notable API changes ================ We have changed a few things that will require you to adjust your code. * In mne.time_frequency.dpss_windows(), interpolating is deprecated (nowadays SciPy?s computations are fast enough for large N without interpolation). This affects parameters interp_from and interp_kind. Two new parameters of the underlying SciPy dpss() function are also exposed: sym (for choosing symmetric vs. periodic windows) and norm (window normalization method). (#11293 by Daniel McCloy) * In mne.decoding.CSP.plot_patterns(), mne.decoding.CSP.plot_filters(), mne.preprocessing.ICA.plot_components(), and mne.viz.plot_ica_components(), the parameters vmin and vmax are deprecated in favor of vlim, for consistency with other topomap-plotting functions and methods (#11371 by Daniel McCloy) * In mne.decoding.CSP.plot_patterns() and mne.decoding.CSP.plot_filters() the titleparameter is deprecated and will be removed in version 1.4 (#11371 by Daniel McCloy) * The APIs of mne.preprocessing.ICA.plot_components() and mne.viz.plot_ica_components()gained new parameters show_names, extrapolate, border, size, cnorm, cbar_fmt, axes, nrows, ncols, for consistency with other topomap-plotting functions and methods (#11371 by Daniel McCloy) * The APIs of mne.decoding.CSP.plot_patterns() and mne.decoding.CSP.plot_filters()gained new parameters extrapolate, border, cnorm, axes, nrows, ncols, for consistency with other topomap-plotting functions and methods (#11371 by Daniel McCloy) 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 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. Please follow the installation instructions on our website: https://mne.tools/stable/install/mne_python.html Feedback ======== As usual, we welcome your bug reports, feature requests, critiques, and 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 https://twitter.com/mne_news and on mastodon https://fosstodon.org/@mne We hope you will enjoy the new features and many, many small improvements we have added, and are looking forward to receiving your feedback. 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! 29 people contributed to this release ? and 13 were first-timers! Thank you all so very much for your time and effort, we truly appreciate it! Release contributors (+ are first time contributors): * Alex Rockhill * Alexandre Gramfort * Britta Westner * Carlos de la Torre+ * Daniel Hasegan+ * Daniel McCloy * Dinara Issagaliyeva+ * Enzo Altamiranda+ * Eric Brayet+ * Eric Larson * Erkka Heinila * Felix Klotzsche * Hakimeh Aslsardroud+ * Jennifer Behnke+ * Jevri Hanna * Lukas Hecker * Mark Alexander Henney+ * Mathieu Scheltienne * Mauricio Cespedes+ * Miko?aj Magnuski * Moritz Gerster * Omer Shubi+ * Pavel Navratil+ * Richard H?chenberger * Santeri Ruuskanen+ * Stefan Appelhoff * Timon Merk * Tom Ma+ * Toomas Erik Anij?rv+ _______________________________________________ Neuroimaging mailing list Neuroimaging at python.org https://mail.python.org/mailman/listinfo/neuroimaging -------------- next part -------------- An HTML attachment was scrubbed... URL: From nayanw775 at gmail.com Fri Jan 6 18:28:26 2023 From: nayanw775 at gmail.com (Nayan Wadhwani) Date: Sat, 7 Jan 2023 04:58:26 +0530 Subject: [Neuroimaging] [DIPY] DIPY - CZI EOSS Grant Award Announcement In-Reply-To: References: Message-ID: Congrats to the whole DIPY team. Thank you for all the efforts you are making. Yours sincerely Nayan Wadhwani On Sat, Jan 7, 2023 at 4:06 AM Eleftherios Garyfallidis < garyfallidis at gmail.com> wrote: > Dear DIPY and Neuroimaging communities, > > We are happy to announce that The Chan Zuckerberg Institute (CZI) has > awarded an EOSS grant to the DIPY project. > > This grant will support Serge Koudoro (PI - Indiana university, USA), Dr. > Girard (EPFL - Switzerland) and Dr. Rokem (UW - USA) to: > > - Extend DIPY to non-MRI data e.g. extending our registration framework > - Add parallel computing capabilities > - Improve our tractography framework > - Expand documentation > - Improve educational materials > > Community participation is highly encouraged in CZI grants and Serge who > leads this project will follow up with more information about that during > the following weeks and months. > > The official CZI EOSS announcement is here > > . > > Many Congratulations to Serge and team and Happy 2023 to you all! > > On behalf of the DIPY team, > Eleftherios Garyfallidis, PhD > Associate Professor > Director of Graduate Studies > Intelligent Systems Engineering > Indiana University > Luddy Hall 700 N Woodlawn > Bloomington, IN 47408 > GRG | DIPY | FURY > > > > > _______________________________________________ > DIPY mailing list -- dipy at python.org > To unsubscribe send an email to dipy-leave at python.org > https://mail.python.org/mailman3/lists/dipy.python.org/ > Member address: nayanw775 at gmail.com > -------------- next part -------------- An HTML attachment was scrubbed... URL: From yuw154 at ucsd.edu Fri Jan 6 18:02:30 2023 From: yuw154 at ucsd.edu (Yusheng Wang) Date: Fri, 6 Jan 2023 15:02:30 -0800 Subject: [Neuroimaging] [DIPY] Re: DIPY - CZI EOSS Grant Award Announcement In-Reply-To: References: Message-ID: Congratulations! On Fri, Jan 6, 2023 at 2:57 PM Julio Villal?n wrote: > Congrats! > > El vie, 6 ene 2023 a las 14:33, Eleftherios Garyfallidis (< > garyfallidis at gmail.com>) escribi?: > >> Dear DIPY and Neuroimaging communities, >> >> We are happy to announce that The Chan Zuckerberg Institute (CZI) has >> awarded an EOSS grant to the DIPY project. >> >> This grant will support Serge Koudoro (PI - Indiana university, USA), >> Dr. Girard (EPFL - Switzerland) and Dr. Rokem (UW - USA) to: >> >> - Extend DIPY to non-MRI data e.g. extending our registration >> framework >> - Add parallel computing capabilities >> - Improve our tractography framework >> - Expand documentation >> - Improve educational materials >> >> Community participation is highly encouraged in CZI grants and Serge who >> leads this project will follow up with more information about that during >> the following weeks and months. >> >> The official CZI EOSS announcement is here >> >> . >> >> Many Congratulations to Serge and team and Happy 2023 to you all! >> >> On behalf of the DIPY team, >> Eleftherios Garyfallidis, PhD >> Associate Professor >> Director of Graduate Studies >> Intelligent Systems Engineering >> Indiana University >> Luddy Hall 700 N Woodlawn >> Bloomington, IN 47408 >> GRG >> >> | DIPY >> >> | FURY >> >> >> >> >> _______________________________________________ >> Neuroimaging mailing list >> Neuroimaging at python.org >> https://mail.python.org/mailman/listinfo/neuroimaging >> >> > _______________________________________________ > DIPY mailing list -- dipy at python.org > To unsubscribe send an email to dipy-leave at python.org > > https://urldefense.com/v3/__https://mail.python.org/mailman3/lists/dipy.python.org/__;!!Mih3wA!C1yr66c-ttd7T0kyRPV9eFsBDVKOB_r6TLT7Zm2gSyZ_w8hvI2mf7ADA0laIN3il0E7i-dRydQxcPPP4REr4GdA$ > Member address: yuw154 at ucsd.edu > -------------- next part -------------- An HTML attachment was scrubbed... URL: From vikaspareek at yahoo.com Fri Jan 6 21:23:54 2023 From: vikaspareek at yahoo.com (VIKAS PAREEK) Date: Sat, 7 Jan 2023 02:23:54 +0000 (UTC) Subject: [Neuroimaging] [DIPY] Re: DIPY - CZI EOSS Grant Award Announcement In-Reply-To: References: Message-ID: <1641210420.6725348.1673058234285@mail.yahoo.com> Congratulations!? ~Vikas On Fri, 6 Jan 2023 at 6:22 pm, Satrajit Ghosh wrote: _______________________________________________ DIPY mailing list -- dipy at python.org To unsubscribe send an email to dipy-leave at python.org https://mail.python.org/mailman3/lists/dipy.python.org/ Member address: vikaspareek at yahoo.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From hjara at bu.edu Fri Jan 6 21:40:16 2023 From: hjara at bu.edu (Jara, Hernan) Date: Sat, 7 Jan 2023 02:40:16 +0000 Subject: [Neuroimaging] [DIPY] Re: DIPY - CZI EOSS Grant Award Announcement In-Reply-To: References: Message-ID: My sincere congratulations! Get Outlook for Android ________________________________ From: Yusheng Wang via DIPY Sent: Friday, January 6, 2023 6:02:30 PM To: Julio Villal?n Cc: Neuroimaging analysis in Python ; dipy at python.org Subject: [DIPY] Re: [Neuroimaging] DIPY - CZI EOSS Grant Award Announcement Congratulations! On Fri, Jan 6, 2023 at 2:57 PM Julio Villal?n > wrote: Congrats! El vie, 6 ene 2023 a las 14:33, Eleftherios Garyfallidis (>) escribi?: Dear DIPY and Neuroimaging communities, We are happy to announce that The Chan Zuckerberg Institute (CZI) has awarded an EOSS grant to the DIPY project. This grant will support Serge Koudoro (PI - Indiana university, USA), Dr. Girard (EPFL - Switzerland) and Dr. Rokem (UW - USA) to: * Extend DIPY to non-MRI data e.g. extending our registration framework * Add parallel computing capabilities * Improve our tractography framework * Expand documentation * Improve educational materials Community participation is highly encouraged in CZI grants and Serge who leads this project will follow up with more information about that during the following weeks and months. The official CZI EOSS announcement is here. Many Congratulations to Serge and team and Happy 2023 to you all! On behalf of the DIPY team, Eleftherios Garyfallidis, PhD Associate Professor Director of Graduate Studies Intelligent Systems Engineering Indiana University Luddy Hall 700 N Woodlawn Bloomington, IN 47408 GRG | DIPY | FURY _______________________________________________ Neuroimaging mailing list Neuroimaging at python.org https://mail.python.org/mailman/listinfo/neuroimaging _______________________________________________ DIPY mailing list -- dipy at python.org To unsubscribe send an email to dipy-leave at python.org https://urldefense.com/v3/__https://mail.python.org/mailman3/lists/dipy.python.org/__;!!Mih3wA!C1yr66c-ttd7T0kyRPV9eFsBDVKOB_r6TLT7Zm2gSyZ_w8hvI2mf7ADA0laIN3il0E7i-dRydQxcPPP4REr4GdA$ Member address: yuw154 at ucsd.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From srisaikaew.p at gmail.com Fri Jan 6 22:33:41 2023 From: srisaikaew.p at gmail.com (Patcharaporn Srisaikaew) Date: Fri, 6 Jan 2023 22:33:41 -0500 Subject: [Neuroimaging] [DIPY] Re: DIPY - CZI EOSS Grant Award Announcement In-Reply-To: References: Message-ID: Congratulations to the DIPY team! :) Best, Patcharaporn S. --- *Patcharaporn Srisaikaew, PhD* Postdoctoral Research Fellow | Hodaie Surgical Imaging Laboratory, Division of Brain, Imaging and Behaviour at Krembil Brain Institute, Toronto Western Hospital, University Health Network 135 Nassau St, Toronto, ON, M5T 1M8 On Fri, 6 Jan 2023 at 21:31, Yusheng Wang via DIPY wrote: > Congratulations! > > > On Fri, Jan 6, 2023 at 2:57 PM Julio Villal?n > wrote: > >> Congrats! >> >> El vie, 6 ene 2023 a las 14:33, Eleftherios Garyfallidis (< >> garyfallidis at gmail.com>) escribi?: >> >>> Dear DIPY and Neuroimaging communities, >>> >>> We are happy to announce that The Chan Zuckerberg Institute (CZI) has >>> awarded an EOSS grant to the DIPY project. >>> >>> This grant will support Serge Koudoro (PI - Indiana university, USA), >>> Dr. Girard (EPFL - Switzerland) and Dr. Rokem (UW - USA) to: >>> >>> - Extend DIPY to non-MRI data e.g. extending our registration >>> framework >>> - Add parallel computing capabilities >>> - Improve our tractography framework >>> - Expand documentation >>> - Improve educational materials >>> >>> Community participation is highly encouraged in CZI grants and Serge who >>> leads this project will follow up with more information about that during >>> the following weeks and months. >>> >>> The official CZI EOSS announcement is here >>> >>> . >>> >>> Many Congratulations to Serge and team and Happy 2023 to you all! >>> >>> On behalf of the DIPY team, >>> Eleftherios Garyfallidis, PhD >>> Associate Professor >>> Director of Graduate Studies >>> Intelligent Systems Engineering >>> Indiana University >>> Luddy Hall 700 N Woodlawn >>> Bloomington, IN 47408 >>> GRG >>> >>> | DIPY >>> >>> | FURY >>> >>> >>> >>> >>> _______________________________________________ >>> Neuroimaging mailing list >>> Neuroimaging at python.org >>> https://mail.python.org/mailman/listinfo/neuroimaging >>> >>> >> _______________________________________________ >> DIPY mailing list -- dipy at python.org >> To unsubscribe send an email to dipy-leave at python.org >> >> https://urldefense.com/v3/__https://mail.python.org/mailman3/lists/dipy.python.org/__;!!Mih3wA!C1yr66c-ttd7T0kyRPV9eFsBDVKOB_r6TLT7Zm2gSyZ_w8hvI2mf7ADA0laIN3il0E7i-dRydQxcPPP4REr4GdA$ >> Member address: yuw154 at ucsd.edu >> > _______________________________________________ > DIPY mailing list -- dipy at python.org > To unsubscribe send an email to dipy-leave at python.org > https://mail.python.org/mailman3/lists/dipy.python.org/ > Member address: srisaikaew.p at gmail.com > -------------- next part -------------- An HTML attachment was scrubbed... URL: From redhatw at gmail.com Sat Jan 7 12:05:53 2023 From: redhatw at gmail.com (redhatw at gmail.com) Date: Sat, 7 Jan 2023 12:05:53 -0500 Subject: [Neuroimaging] DIPY - CZI EOSS Grant Award Announcement In-Reply-To: References: Message-ID: <096401d922ba$4d1f5220$e75df660$@gmail.com> Graduations! Ze From: Neuroimaging On Behalf Of Eleftherios Garyfallidis Sent: Friday, January 6, 2023 5:33 PM To: dipy at python.org; Neuroimaging analysis in Python Subject: [Neuroimaging] DIPY - CZI EOSS Grant Award Announcement Dear DIPY and Neuroimaging communities, We are happy to announce that The Chan Zuckerberg Institute (CZI) has awarded an EOSS grant to the DIPY project. This grant will support Serge Koudoro (PI - Indiana university, USA), Dr. Girard (EPFL - Switzerland) and Dr. Rokem (UW - USA) to: * Extend DIPY to non-MRI data e.g. extending our registration framework * Add parallel computing capabilities * Improve our tractography framework * Expand documentation * Improve educational materials Community participation is highly encouraged in CZI grants and Serge who leads this project will follow up with more information about that during the following weeks and months. The official CZI EOSS announcement is here . Many Congratulations to Serge and team and Happy 2023 to you all! On behalf of the DIPY team, Eleftherios Garyfallidis, PhD Associate Professor Director of Graduate Studies Intelligent Systems Engineering Indiana University Luddy Hall 700 N Woodlawn Bloomington, IN 47408 GRG | DIPY | FURY -------------- next part -------------- An HTML attachment was scrubbed... URL: From adluru at wisc.edu Sat Jan 7 11:26:32 2023 From: adluru at wisc.edu (Nagesh Adluru) Date: Sat, 7 Jan 2023 16:26:32 +0000 Subject: [Neuroimaging] [DIPY] Re: DIPY - CZI EOSS Grant Award Announcement In-Reply-To: References: Message-ID: Heartiest congratulations! Thank you. Nagesh ________________________________ From: Patcharaporn Srisaikaew Sent: Friday, January 6, 2023 9:33:41 PM To: Neuroimaging analysis in Python ; dipy at python.org Subject: [DIPY] Re: [Neuroimaging] DIPY - CZI EOSS Grant Award Announcement Congratulations to the DIPY team! :) Best, Patcharaporn S. --- Patcharaporn Srisaikaew, PhD Postdoctoral Research Fellow | Hodaie Surgical Imaging Laboratory, Division of Brain, Imaging and Behaviour at Krembil Brain Institute, Toronto Western Hospital, University Health Network 135 Nassau St, Toronto, ON, M5T 1M8 On Fri, 6 Jan 2023 at 21:31, Yusheng Wang via DIPY > wrote: Congratulations! On Fri, Jan 6, 2023 at 2:57 PM Julio Villal?n > wrote: Congrats! El vie, 6 ene 2023 a las 14:33, Eleftherios Garyfallidis (>) escribi?: Dear DIPY and Neuroimaging communities, We are happy to announce that The Chan Zuckerberg Institute (CZI) has awarded an EOSS grant to the DIPY project. This grant will support Serge Koudoro (PI - Indiana university, USA), Dr. Girard (EPFL - Switzerland) and Dr. Rokem (UW - USA) to: * Extend DIPY to non-MRI data e.g. extending our registration framework * Add parallel computing capabilities * Improve our tractography framework * Expand documentation * Improve educational materials Community participation is highly encouraged in CZI grants and Serge who leads this project will follow up with more information about that during the following weeks and months. The official CZI EOSS announcement is here. Many Congratulations to Serge and team and Happy 2023 to you all! On behalf of the DIPY team, Eleftherios Garyfallidis, PhD Associate Professor Director of Graduate Studies Intelligent Systems Engineering Indiana University Luddy Hall 700 N Woodlawn Bloomington, IN 47408 GRG | DIPY | FURY _______________________________________________ Neuroimaging mailing list Neuroimaging at python.org https://mail.python.org/mailman/listinfo/neuroimaging _______________________________________________ DIPY mailing list -- dipy at python.org To unsubscribe send an email to dipy-leave at python.org https://urldefense.com/v3/__https://mail.python.org/mailman3/lists/dipy.python.org/__;!!Mih3wA!C1yr66c-ttd7T0kyRPV9eFsBDVKOB_r6TLT7Zm2gSyZ_w8hvI2mf7ADA0laIN3il0E7i-dRydQxcPPP4REr4GdA$ Member address: yuw154 at ucsd.edu _______________________________________________ DIPY mailing list -- dipy at python.org To unsubscribe send an email to dipy-leave at python.org https://mail.python.org/mailman3/lists/dipy.python.org/ Member address: srisaikaew.p at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From frakkopesto at gmail.com Sat Jan 7 12:44:22 2023 From: frakkopesto at gmail.com (frakkopesto) Date: Sat, 7 Jan 2023 11:44:22 -0600 Subject: [Neuroimaging] DIPY - CZI EOSS Grant Award Announcement In-Reply-To: References: Message-ID: Congrats DIPy Team! Happy New Year. 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 Fri, Jan 6, 2023 at 4:32 PM Eleftherios Garyfallidis < garyfallidis at gmail.com> wrote: > Dear DIPY and Neuroimaging communities, > > We are happy to announce that The Chan Zuckerberg Institute (CZI) has > awarded an EOSS grant to the DIPY project. > > This grant will support Serge Koudoro (PI - Indiana university, USA), Dr. > Girard (EPFL - Switzerland) and Dr. Rokem (UW - USA) to: > > - Extend DIPY to non-MRI data e.g. extending our registration framework > - Add parallel computing capabilities > - Improve our tractography framework > - Expand documentation > - Improve educational materials > > Community participation is highly encouraged in CZI grants and Serge who > leads this project will follow up with more information about that during > the following weeks and months. > > The official CZI EOSS announcement is here > > . > > Many Congratulations to Serge and team and Happy 2023 to you all! > > On behalf of the DIPY team, > Eleftherios Garyfallidis, PhD > Associate Professor > Director of Graduate Studies > Intelligent Systems Engineering > Indiana University > Luddy Hall 700 N Woodlawn > Bloomington, IN 47408 > GRG | DIPY | FURY > > > > > _______________________________________________ > Neuroimaging mailing list > Neuroimaging at python.org > https://mail.python.org/mailman/listinfo/neuroimaging > -------------- next part -------------- An HTML attachment was scrubbed... URL: From alexandre.gramfort at inria.fr Sun Jan 8 04:37:19 2023 From: alexandre.gramfort at inria.fr (Alexandre Gramfort) Date: Sun, 8 Jan 2023 10:37:19 +0100 Subject: [Neuroimaging] DIPY - CZI EOSS Grant Award Announcement In-Reply-To: References: Message-ID: hi congrats Dipy folks ! I can tell you that the MNE team is using dipy for coregistration eg between CT and MRI and we are super happy to see more efforts in this direction. ? Alex On Sat, Jan 7, 2023 at 6:45 PM frakkopesto wrote: > Congrats DIPy Team! > > Happy New Year. > > 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 Fri, Jan 6, 2023 at 4:32 PM Eleftherios Garyfallidis < > garyfallidis at gmail.com> wrote: > >> Dear DIPY and Neuroimaging communities, >> >> We are happy to announce that The Chan Zuckerberg Institute (CZI) has >> awarded an EOSS grant to the DIPY project. >> >> This grant will support Serge Koudoro (PI - Indiana university, USA), >> Dr. Girard (EPFL - Switzerland) and Dr. Rokem (UW - USA) to: >> >> - Extend DIPY to non-MRI data e.g. extending our registration >> framework >> - Add parallel computing capabilities >> - Improve our tractography framework >> - Expand documentation >> - Improve educational materials >> >> Community participation is highly encouraged in CZI grants and Serge who >> leads this project will follow up with more information about that during >> the following weeks and months. >> >> The official CZI EOSS announcement is here >> >> . >> >> Many Congratulations to Serge and team and Happy 2023 to you all! >> >> On behalf of the DIPY team, >> Eleftherios Garyfallidis, PhD >> Associate Professor >> Director of Graduate Studies >> Intelligent Systems Engineering >> Indiana University >> Luddy Hall 700 N Woodlawn >> Bloomington, IN 47408 >> GRG | DIPY | FURY >> >> >> >> >> _______________________________________________ >> Neuroimaging mailing list >> Neuroimaging at python.org >> https://mail.python.org/mailman/listinfo/neuroimaging >> > _______________________________________________ > Neuroimaging mailing list > Neuroimaging at python.org > https://mail.python.org/mailman/listinfo/neuroimaging > -------------- next part -------------- An HTML attachment was scrubbed... URL: From erick.canalesrodriguez at epfl.ch Sun Jan 8 08:45:55 2023 From: erick.canalesrodriguez at epfl.ch (Canales Rodriguez Erick Jorge) Date: Sun, 8 Jan 2023 13:45:55 +0000 Subject: [Neuroimaging] [DIPY] DIPY - CZI EOSS Grant Award Announcement In-Reply-To: References: Message-ID: Congratulations, DIPY! All the best, Erick ________________________________ From: Eleftherios Garyfallidis Sent: Friday, January 6, 2023 11:32 PM To: dipy at python.org; Neuroimaging analysis in Python Subject: [DIPY] DIPY - CZI EOSS Grant Award Announcement Dear DIPY and Neuroimaging communities, We are happy to announce that The Chan Zuckerberg Institute (CZI) has awarded an EOSS grant to the DIPY project. This grant will support Serge Koudoro (PI - Indiana university, USA), Dr. Girard (EPFL - Switzerland) and Dr. Rokem (UW - USA) to: * Extend DIPY to non-MRI data e.g. extending our registration framework * Add parallel computing capabilities * Improve our tractography framework * Expand documentation * Improve educational materials Community participation is highly encouraged in CZI grants and Serge who leads this project will follow up with more information about that during the following weeks and months. The official CZI EOSS announcement is here. Many Congratulations to Serge and team and Happy 2023 to you all! On behalf of the DIPY team, Eleftherios Garyfallidis, PhD Associate Professor Director of Graduate Studies Intelligent Systems Engineering Indiana University Luddy Hall 700 N Woodlawn Bloomington, IN 47408 GRG | DIPY | FURY -------------- next part -------------- An HTML attachment was scrubbed... URL: From yasmin.mzayek at inria.fr Mon Jan 9 04:36:45 2023 From: yasmin.mzayek at inria.fr (Yasmin Mzayek) Date: Mon, 9 Jan 2023 10:36:45 +0100 (CET) Subject: [Neuroimaging] Nilearn 0.10.0 Release Message-ID: <174559305.18715690.1673257005045.JavaMail.zimbra@inria.fr> Dear all, We have just released Nilearn 0.10.0! Importantly, we bumped up minimum version of the following: Python 3.7 is deprecated and will be removed in release 0.12. We recommend upgrading to Python 3.10. Minimum supported versions of packages have been bumped up: - Numpy ? v1.19.0 - SciPy ? v1.6.0 - Scikit-learn ? v1.0.0 - Nibabel ? v3.2.0 - Pandas ? v1.1.5 - Joblib ? v1.0.0 You can see the highlights of this release and a full list of changes here: [ https://nilearn.github.io/stable/changes/whats_new.html#id1 | https://nilearn.github.io/stable/changes/whats_new.html#id1 ] You can install nilearn with (recommended in a virtual environment): python -m pip install -U nilearn Thank you to all the contributors and we look forward to hearing your feedback! Best regards, Yasmin Mzayek On behalf of the Nilearn team -------------- next part -------------- An HTML attachment was scrubbed... URL: From jbpoline at gmail.com Mon Jan 9 08:59:55 2023 From: jbpoline at gmail.com (JB Poline) Date: Mon, 9 Jan 2023 08:59:55 -0500 Subject: [Neuroimaging] Nilearn 0.10.0 Release In-Reply-To: <174559305.18715690.1673257005045.JavaMail.zimbra@inria.fr> References: <174559305.18715690.1673257005045.JavaMail.zimbra@inria.fr> Message-ID: Congrats ! JB On Mon, Jan 9, 2023 at 4:52 AM Yasmin Mzayek wrote: > Dear all, > > We have just released Nilearn 0.10.0! > > Importantly, we bumped up minimum version of the following: > > *Python 3.7 is deprecated and will be removed in release 0.12.* > *We recommend upgrading to Python 3.10.* > > *Minimum supported versions of packages have been bumped up:* > - Numpy ? v1.19.0 > - SciPy ? v1.6.0 > - Scikit-learn ? v1.0.0 > - Nibabel ? v3.2.0 > - Pandas ? v1.1.5 > - Joblib ? v1.0.0 > > You can see the highlights of this release and a full list of changes > here: > > https://nilearn.github.io/stable/changes/whats_new.html#id1 > > > You can install nilearn with (recommended in a virtual environment): > > > python -m pip install -U nilearn > > > > Thank you to all the contributors and we look forward to hearing your > feedback! > > > > Best regards, > > Yasmin Mzayek > > On behalf of the Nilearn team > _______________________________________________ > Neuroimaging mailing list > Neuroimaging at python.org > https://mail.python.org/mailman/listinfo/neuroimaging > -------------- next part -------------- An HTML attachment was scrubbed... URL: From bertrand.thirion at inria.fr Mon Jan 9 10:02:36 2023 From: bertrand.thirion at inria.fr (Bertrand Thirion) Date: Mon, 9 Jan 2023 16:02:36 +0100 Subject: [Neuroimaging] Nilearn 0.10.0 Release In-Reply-To: <174559305.18715690.1673257005045.JavaMail.zimbra@inria.fr> References: <174559305.18715690.1673257005045.JavaMail.zimbra@inria.fr> Message-ID: Thx Yasmin and to all contributors ! Bertrand Le 09/01/2023 ? 10:36, Yasmin Mzayek a ?crit?: > > Dear all, > > > We have just released Nilearn 0.10.0! > > Importantly, we bumped up minimum version of the following: > > *Python 3.7 is deprecated and will be removed in release 0.12.* > *We recommend upgrading to Python 3.10.* > > *Minimum supported versions of packages have been bumped up:* > - Numpy ? v1.19.0 > - SciPy ? v1.6.0 > - Scikit-learn ? v1.0.0 > - Nibabel ? v3.2.0 > - Pandas ? v1.1.5 > - Joblib ? v1.0.0 > > You can see the highlights of this release and a full list of changes > here: > > https://nilearn.github.io/stable/changes/whats_new.html#id1 > > > You can install nilearn with (recommended in a virtual environment): > > > python -m pip install -U nilearn > > > > Thank you to all the contributors and we look forward to hearing your > feedback! > > > > Best regards, > > Yasmin Mzayek > > On behalf of the Nilearn team > > > _______________________________________________ > Neuroimaging mailing list > Neuroimaging at python.org > https://mail.python.org/mailman/listinfo/neuroimaging -------------- next part -------------- An HTML attachment was scrubbed... URL: From markiewicz at stanford.edu Mon Jan 9 10:35:58 2023 From: markiewicz at stanford.edu (Christopher Markiewicz) Date: Mon, 9 Jan 2023 15:35:58 +0000 Subject: [Neuroimaging] ANN: NiBabel 5.0 Message-ID: Hi all, I'm pleased to announce the release of NiBabel 5.0! This version requires Python 3.8 and numpy 1.19, in accordance with our version support schedule . As with other major version releases, there are DeprecationWarnings that will now become ExpiredDeprecationErrors, and ExpiredDeprecationErrors that will now become AttributeErrors, as the deprecated features are progressively removed. We had a shortened 4.x lifetime because it was discovered that a growing number of images were being created with int64 data types and causing problems with other neuroimaging tools. While the NIfTI standards permit int64 data, it is not widely adopted and there is no clear use case that is not better handled by float64. Therefore in 4.0, we introduced a warning if users generated int64 images (easy to do with `Nifti1Image(data.astype(int), affine)`) without providing an explicit dtype (or pre-generated header). With 5.0, this warning has become an error. Additional changes in 5.0 include an updated SerializableImage interface that allows you to serialize images to/from custom filehandles with to_stream()/from_stream(), as well as load images from URLs using, e.g., Nifti1Image.from_url(). With many thanks to everybody who reported issues, submitted patches, and especially reviewed PRs. Please test out the new version and report any issues you have to https://github.com/nipy/nibabel/issues. The full changelog can be found at https://github.com/nipy/nibabel/releases/tag/5.0.0. Best, --? Christopher J. Markiewicz, PhD Center for Reproducible Neuroscience Stanford University From z.baratz at gmail.com Mon Jan 9 10:41:17 2023 From: z.baratz at gmail.com (Zvi Baratz) Date: Mon, 9 Jan 2023 17:41:17 +0200 Subject: [Neuroimaging] ANN: NiBabel 5.0 In-Reply-To: References: Message-ID: ? ? Thank you for all your work on this release! On Mon, Jan 9, 2023 at 5:36 PM Christopher Markiewicz < markiewicz at stanford.edu> wrote: > Hi all, > > I'm pleased to announce the release of NiBabel 5.0! > > This version requires Python 3.8 and numpy 1.19, in accordance with our > version support schedule . > > As with other major version releases, there are DeprecationWarnings that > will now become ExpiredDeprecationErrors, and ExpiredDeprecationErrors that > will now become AttributeErrors, as the deprecated features are > progressively removed. > > We had a shortened 4.x lifetime because it was discovered that a growing > number of images were being created with int64 data types and causing > problems with other neuroimaging tools. While the NIfTI standards permit > int64 data, it is not widely adopted and there is no clear use case that is > not better handled by float64. Therefore in 4.0, we introduced a warning if > users generated int64 images (easy to do with > `Nifti1Image(data.astype(int), affine)`) without providing an explicit > dtype (or pre-generated header). With 5.0, this warning has become an error. > > Additional changes in 5.0 include an updated SerializableImage interface > that allows you to serialize images to/from custom filehandles with > to_stream()/from_stream(), as well as load images from URLs using, e.g., > Nifti1Image.from_url(). > > With many thanks to everybody who reported issues, submitted patches, and > especially reviewed PRs. > > Please test out the new version and report any issues you have to > https://github.com/nipy/nibabel/issues. > > The full changelog can be found at > https://github.com/nipy/nibabel/releases/tag/5.0.0. > > Best, > -- > Christopher J. Markiewicz, PhD > Center for Reproducible Neuroscience > Stanford University > _______________________________________________ > Neuroimaging mailing list > Neuroimaging at python.org > https://mail.python.org/mailman/listinfo/neuroimaging > -------------- next part -------------- An HTML attachment was scrubbed... URL: From bertrand.thirion at inria.fr Mon Jan 9 10:57:06 2023 From: bertrand.thirion at inria.fr (Bertrand Thirion) Date: Mon, 9 Jan 2023 16:57:06 +0100 (CET) Subject: [Neuroimaging] ANN: NiBabel 5.0 In-Reply-To: References: Message-ID: <445581802.19038902.1673279826668.JavaMail.zimbra@inria.fr> Congrats indeed ! 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 > From: "Zvi Baratz" > To: "Neuroimaging analysis in Python" > Sent: Monday, January 9, 2023 4:41:17 PM > Subject: Re: [Neuroimaging] ANN: NiBabel 5.0 > ? ? > Thank you for all your work on this release! > On Mon, Jan 9, 2023 at 5:36 PM Christopher Markiewicz < [ > mailto:markiewicz at stanford.edu | markiewicz at stanford.edu ] > wrote: >> Hi all, >> I'm pleased to announce the release of NiBabel 5.0! >> This version requires Python 3.8 and numpy 1.19, in accordance with our version >> support schedule < [ https://github.com/nipy/nibabel/issues/803 | >> https://github.com/nipy/nibabel/issues/803 ] >. >> As with other major version releases, there are DeprecationWarnings that will >> now become ExpiredDeprecationErrors, and ExpiredDeprecationErrors that will now >> become AttributeErrors, as the deprecated features are progressively removed. >> We had a shortened 4.x lifetime because it was discovered that a growing number >> of images were being created with int64 data types and causing problems with >> other neuroimaging tools. While the NIfTI standards permit int64 data, it is >> not widely adopted and there is no clear use case that is not better handled by >> float64. Therefore in 4.0, we introduced a warning if users generated int64 >> images (easy to do with `Nifti1Image(data.astype(int), affine)`) without >> providing an explicit dtype (or pre-generated header). With 5.0, this warning >> has become an error. >> Additional changes in 5.0 include an updated SerializableImage interface that >> allows you to serialize images to/from custom filehandles with >> to_stream()/from_stream(), as well as load images from URLs using, e.g., >> Nifti1Image.from_url(). >> With many thanks to everybody who reported issues, submitted patches, and >> especially reviewed PRs. >> Please test out the new version and report any issues you have to [ >> https://github.com/nipy/nibabel/issues | https://github.com/nipy/nibabel/issues >> ] . >> The full changelog can be found at [ >> https://github.com/nipy/nibabel/releases/tag/5.0.0 | >> https://github.com/nipy/nibabel/releases/tag/5.0.0 ] . >> Best, >> -- >> Christopher J. Markiewicz, PhD >> Center for Reproducible Neuroscience >> Stanford University >> _______________________________________________ >> Neuroimaging mailing list >> [ mailto:Neuroimaging at python.org | Neuroimaging at python.org ] >> [ https://mail.python.org/mailman/listinfo/neuroimaging | >> https://mail.python.org/mailman/listinfo/neuroimaging ] > _______________________________________________ > Neuroimaging mailing list > Neuroimaging at python.org > https://mail.python.org/mailman/listinfo/neuroimaging -------------- next part -------------- An HTML attachment was scrubbed... URL: From jbpoline at gmail.com Mon Jan 9 11:26:38 2023 From: jbpoline at gmail.com (JB Poline) Date: Mon, 9 Jan 2023 11:26:38 -0500 Subject: [Neuroimaging] ANN: NiBabel 5.0 In-Reply-To: <445581802.19038902.1673279826668.JavaMail.zimbra@inria.fr> References: <445581802.19038902.1673279826668.JavaMail.zimbra@inria.fr> Message-ID: Thanks a lot for that ! JB On Mon, Jan 9, 2023 at 10:57 AM Bertrand Thirion wrote: > Congrats indeed ! > > 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 > > ------------------------------ > > *From: *"Zvi Baratz" > *To: *"Neuroimaging analysis in Python" > *Sent: *Monday, January 9, 2023 4:41:17 PM > *Subject: *Re: [Neuroimaging] ANN: NiBabel 5.0 > > ? ? > > Thank you for all your work on this release! > > On Mon, Jan 9, 2023 at 5:36 PM Christopher Markiewicz < > markiewicz at stanford.edu> wrote: > >> Hi all, >> >> I'm pleased to announce the release of NiBabel 5.0! >> >> This version requires Python 3.8 and numpy 1.19, in accordance with our >> version support schedule . >> >> As with other major version releases, there are DeprecationWarnings that >> will now become ExpiredDeprecationErrors, and ExpiredDeprecationErrors that >> will now become AttributeErrors, as the deprecated features are >> progressively removed. >> >> We had a shortened 4.x lifetime because it was discovered that a growing >> number of images were being created with int64 data types and causing >> problems with other neuroimaging tools. While the NIfTI standards permit >> int64 data, it is not widely adopted and there is no clear use case that is >> not better handled by float64. Therefore in 4.0, we introduced a warning if >> users generated int64 images (easy to do with >> `Nifti1Image(data.astype(int), affine)`) without providing an explicit >> dtype (or pre-generated header). With 5.0, this warning has become an error. >> >> Additional changes in 5.0 include an updated SerializableImage interface >> that allows you to serialize images to/from custom filehandles with >> to_stream()/from_stream(), as well as load images from URLs using, e.g., >> Nifti1Image.from_url(). >> >> With many thanks to everybody who reported issues, submitted patches, and >> especially reviewed PRs. >> >> Please test out the new version and report any issues you have to >> https://github.com/nipy/nibabel/issues. >> >> The full changelog can be found at >> https://github.com/nipy/nibabel/releases/tag/5.0.0. >> >> Best, >> -- >> Christopher J. Markiewicz, PhD >> Center for Reproducible Neuroscience >> Stanford University >> _______________________________________________ >> Neuroimaging mailing list >> Neuroimaging at python.org >> https://mail.python.org/mailman/listinfo/neuroimaging >> > > _______________________________________________ > Neuroimaging mailing list > Neuroimaging at python.org > https://mail.python.org/mailman/listinfo/neuroimaging > > _______________________________________________ > Neuroimaging mailing list > Neuroimaging at python.org > https://mail.python.org/mailman/listinfo/neuroimaging > -------------- next part -------------- An HTML attachment was scrubbed... URL: From markiewicz at stanford.edu Mon Jan 9 11:51:50 2023 From: markiewicz at stanford.edu (Christopher Markiewicz) Date: Mon, 9 Jan 2023 16:51:50 +0000 Subject: [Neuroimaging] ANN: NiBabel 5.0 In-Reply-To: References: <445581802.19038902.1673279826668.JavaMail.zimbra@inria.fr> Message-ID: Quick update: Please cite the latest Zenodo archive, if you use NiBabel 5.0 in your analyses: https://doi.org/10.5281/zenodo.7516526 Best, Chris ________________________________________ From: Neuroimaging on behalf of JB Poline Sent: Monday, January 9, 2023 11:26 To: Neuroimaging analysis in Python Subject: Re: [Neuroimaging] ANN: NiBabel 5.0 Thanks a lot for that ! JB On Mon, Jan 9, 2023 at 10:57 AM Bertrand Thirion > wrote: Congrats indeed ! 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 ________________________________ From: "Zvi Baratz" > To: "Neuroimaging analysis in Python" > Sent: Monday, January 9, 2023 4:41:17 PM Subject: Re: [Neuroimaging] ANN: NiBabel 5.0 ? ? Thank you for all your work on this release! On Mon, Jan 9, 2023 at 5:36 PM Christopher Markiewicz > wrote: Hi all, I'm pleased to announce the release of NiBabel 5.0! This version requires Python 3.8 and numpy 1.19, in accordance with our version support schedule . As with other major version releases, there are DeprecationWarnings that will now become ExpiredDeprecationErrors, and ExpiredDeprecationErrors that will now become AttributeErrors, as the deprecated features are progressively removed. We had a shortened 4.x lifetime because it was discovered that a growing number of images were being created with int64 data types and causing problems with other neuroimaging tools. While the NIfTI standards permit int64 data, it is not widely adopted and there is no clear use case that is not better handled by float64. Therefore in 4.0, we introduced a warning if users generated int64 images (easy to do with `Nifti1Image(data.astype(int), affine)`) without providing an explicit dtype (or pre-generated header). With 5.0, this warning has become an error. Additional changes in 5.0 include an updated SerializableImage interface that allows you to serialize images to/from custom filehandles with to_stream()/from_stream(), as well as load images from URLs using, e.g., Nifti1Image.from_url(). With many thanks to everybody who reported issues, submitted patches, and especially reviewed PRs. Please test out the new version and report any issues you have to https://github.com/nipy/nibabel/issues. The full changelog can be found at https://github.com/nipy/nibabel/releases/tag/5.0.0. Best, -- Christopher J. Markiewicz, PhD Center for Reproducible Neuroscience Stanford University _______________________________________________ Neuroimaging mailing list Neuroimaging at python.org https://mail.python.org/mailman/listinfo/neuroimaging _______________________________________________ Neuroimaging mailing list Neuroimaging at python.org https://mail.python.org/mailman/listinfo/neuroimaging _______________________________________________ Neuroimaging mailing list Neuroimaging at python.org https://mail.python.org/mailman/listinfo/neuroimaging From markiewicz at stanford.edu Mon Jan 9 08:50:23 2023 From: markiewicz at stanford.edu (Christopher Markiewicz) Date: Mon, 9 Jan 2023 13:50:23 +0000 Subject: [Neuroimaging] Nilearn 0.10.0 Release In-Reply-To: <174559305.18715690.1673257005045.JavaMail.zimbra@inria.fr> References: <174559305.18715690.1673257005045.JavaMail.zimbra@inria.fr> Message-ID: Congrats, nilearn team! Best, Chris ________________________________ From: Neuroimaging on behalf of Yasmin Mzayek Sent: Monday, January 9, 2023 04:36 To: neuroimaging Subject: [Neuroimaging] Nilearn 0.10.0 Release Dear all, We have just released Nilearn 0.10.0! Importantly, we bumped up minimum version of the following: Python 3.7 is deprecated and will be removed in release 0.12. We recommend upgrading to Python 3.10. Minimum supported versions of packages have been bumped up: - Numpy ? v1.19.0 - SciPy ? v1.6.0 - Scikit-learn ? v1.0.0 - Nibabel ? v3.2.0 - Pandas ? v1.1.5 - Joblib ? v1.0.0 You can see the highlights of this release and a full list of changes here: https://nilearn.github.io/stable/changes/whats_new.html#id1 You can install nilearn with (recommended in a virtual environment): python -m pip install -U nilearn Thank you to all the contributors and we look forward to hearing your feedback! Best regards, Yasmin Mzayek On behalf of the Nilearn team -------------- next part -------------- An HTML attachment was scrubbed... URL: From gael.varoquaux at normalesup.org Mon Jan 9 15:51:42 2023 From: gael.varoquaux at normalesup.org (Gael Varoquaux) Date: Mon, 9 Jan 2023 21:51:42 +0100 Subject: [Neuroimaging] Nilearn 0.10.0 Release In-Reply-To: References: <174559305.18715690.1673257005045.JavaMail.zimbra@inria.fr> Message-ID: <20230109205142.amtzy4dnc4cc6cl3@gaellaptop> Hurray! Congratulations! And thanks to the team for the development and the release! Ga?l On Mon, Jan 09, 2023 at 08:59:55AM -0500, JB Poline wrote: > Congrats ! > JB > On Mon, Jan 9, 2023 at 4:52 AM Yasmin Mzayek wrote: > Dear all, > We have just released Nilearn 0.10.0! > Importantly, we bumped up minimum version of the following: > Python 3.7 is deprecated and will be removed in release 0.12. > We recommend upgrading to Python 3.10. > Minimum supported versions of packages have been bumped up: > - Numpy ? v1.19.0 > - SciPy ? v1.6.0 > - Scikit-learn ? v1.0.0 > - Nibabel ? v3.2.0 > - Pandas ? v1.1.5 > - Joblib ? v1.0.0 > You can see the highlights of this release and a full list of changes here: > https://nilearn.github.io/stable/changes/whats_new.html#id1 > You can install nilearn with (recommended in a virtual environment): > ??????? python -m pip install -U nilearn > Thank you to all the contributors and we look forward to hearing your > feedback! > Best regards, > Yasmin Mzayek > On behalf of the Nilearn team > _______________________________________________ > Neuroimaging mailing list > Neuroimaging at python.org > https://mail.python.org/mailman/listinfo/neuroimaging > _______________________________________________ > Neuroimaging mailing list > Neuroimaging at python.org > https://mail.python.org/mailman/listinfo/neuroimaging -- Gael Varoquaux Research Director, INRIA http://gael-varoquaux.info http://twitter.com/GaelVaroquaux From alex.crimi at yahoo.com Tue Jan 17 17:24:09 2023 From: alex.crimi at yahoo.com (Alex Crimi) Date: Tue, 17 Jan 2023 22:24:09 +0000 (UTC) Subject: [Neuroimaging] Using brain tractography with Nibabel or Dipy directly from Blender 3D References: <1219255406.1526592.1673994249189.ref@mail.yahoo.com> Message-ID: <1219255406.1526592.1673994249189@mail.yahoo.com> I know you are all interested in expanding Fury,?but ages ago I discussed with Eleftherios how to render streamlines (or use the entire Dipy) from Blender 3D.I made a video tutorial, the code is in the description of the videohttps://www.youtube.com/watch?v=ANkq9EAEEeI I hope I am not too late. Ale -------------- next part -------------- An HTML attachment was scrubbed... URL: From nsh531 at gmail.com Wed Jan 18 06:12:24 2023 From: nsh531 at gmail.com (=?UTF-8?B?16DXqteZINep15jXqNef?=) Date: Wed, 18 Jan 2023 13:12:24 +0200 Subject: [Neuroimaging] convolutional neural network for diagsois schizophrenia Message-ID: Greetings, I am developing a system for detecting schizophrenia through computerized decoding of FMRI scans using a convolutional neural network I would appreciate your cooperation on the above issue Best regards Netanel Stern XSCHIZO -- -------------- next part -------------- An HTML attachment was scrubbed... URL: From matthew.brett at lis.ac.uk Wed Jan 18 06:19:55 2023 From: matthew.brett at lis.ac.uk (Matthew Brett) Date: Wed, 18 Jan 2023 11:19:55 +0000 Subject: [Neuroimaging] convolutional neural network for diagsois schizophrenia In-Reply-To: References: Message-ID: Hi, ?On Wed, Jan 18, 2023 at 11:13 AM ???? ?????? wrote:? > > Greetings, > I am developing a system for detecting schizophrenia through computerized decoding of FMRI scans using a convolutional neural network > > I would appreciate your cooperation on the above issue Could you say more about what you're asking for, specifically? Cheers, Matthew From nsh531 at gmail.com Wed Jan 18 06:35:20 2023 From: nsh531 at gmail.com (=?UTF-8?B?16DXqteZINep15jXqNef?=) Date: Wed, 18 Jan 2023 13:35:20 +0200 Subject: [Neuroimaging] convolutional neural network for diagsois schizophrenia In-Reply-To: References: Message-ID: Greetings, I am an entrepreneur who is developing a system for detecting schizophrenia in FMRI scans using the NateNet convolutional neural network that I developed. The network I developed consists of several layers I would be happy to cooperate in the research field -- Best regards Netanel Stern XSCHIZO ??????? ??? ??, 18 ????? 2023 ?-13:21 ??? ?Matthew Brett?? :? > Hi, > > ?On Wed, Jan 18, 2023 at 11:13 AM ???? ?????? wrote:? > > > > Greetings, > > I am developing a system for detecting schizophrenia through > computerized decoding of FMRI scans using a convolutional neural network > > > > I would appreciate your cooperation on the above issue > > Could you say more about what you're asking for, specifically? > > Cheers, > > Matthew > _______________________________________________ > Neuroimaging mailing list > Neuroimaging at python.org > https://mail.python.org/mailman/listinfo/neuroimaging > -- -------------- next part -------------- An HTML attachment was scrubbed... URL: From elef at indiana.edu Wed Jan 18 14:24:25 2023 From: elef at indiana.edu (Eleftherios Garyfallidis) Date: Wed, 18 Jan 2023 14:24:25 -0500 Subject: [Neuroimaging] [DIPY] Using brain tractography with Nibabel or Dipy directly from Blender 3D In-Reply-To: <1219255406.1526592.1673994249189@mail.yahoo.com> References: <1219255406.1526592.1673994249189.ref@mail.yahoo.com> <1219255406.1526592.1673994249189@mail.yahoo.com> Message-ID: Very cool Alex! Wonderful job. Not late at all. Do we have your approval to highlight your video in our YouTube channel? Best, Elef On Tue, Jan 17, 2023 at 10:54 PM Alex Crimi via DIPY wrote: > I know you are all interested in expanding Fury, > but ages ago I discussed with Eleftherios how to render streamlines (or > use the entire Dipy) from Blender 3D. > I made a video tutorial, the code is in the description of the video > https://www.youtube.com/watch?v=ANkq9EAEEeI > > I hope I am not too late. > > Ale > > _______________________________________________ > DIPY mailing list -- dipy at python.org > To unsubscribe send an email to dipy-leave at python.org > https://mail.python.org/mailman3/lists/dipy.python.org/ > Member address: garyfallidis at gmail.com > -------------- next part -------------- An HTML attachment was scrubbed... URL: From alex.crimi at yahoo.com Thu Jan 19 05:18:23 2023 From: alex.crimi at yahoo.com (Alex Crimi) Date: Thu, 19 Jan 2023 10:18:23 +0000 (UTC) Subject: [Neuroimaging] [DIPY] Re: Using brain tractography with Nibabel or Dipy directly from Blender 3D In-Reply-To: References: <1219255406.1526592.1673994249189.ref@mail.yahoo.com> <1219255406.1526592.1673994249189@mail.yahoo.com> Message-ID: <1922849249.3539705.1674123503497@mail.yahoo.com> if you think it is useful.I added the code on github, as it is not so visible from the movie:alecrimi/python_blender (github.com) Best, Alex On Wednesday, January 18, 2023 at 08:29:25 PM GMT+1, Eleftherios Garyfallidis wrote: Very cool Alex! Wonderful job. Not late at all. Do we have your approval to highlight your video in our YouTube channel? Best,Elef On Tue, Jan 17, 2023 at 10:54 PM Alex Crimi via DIPY wrote: I know you are all interested in expanding Fury,?but ages ago I discussed with Eleftherios how to render streamlines (or use the entire Dipy) from Blender 3D.I made a video tutorial, the code is in the description of the videohttps://www.youtube.com/watch?v=ANkq9EAEEeI I hope I am not too late. Ale _______________________________________________ DIPY mailing list -- dipy at python.org To unsubscribe send an email to dipy-leave at python.org https://mail.python.org/mailman3/lists/dipy.python.org/ Member address: garyfallidis at gmail.com _______________________________________________ DIPY mailing list -- dipy at python.org To unsubscribe send an email to dipy-leave at python.org https://mail.python.org/mailman3/lists/dipy.python.org/ Member address: alex.crimi at yahoo.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From elef at indiana.edu Thu Jan 19 09:49:25 2023 From: elef at indiana.edu (Eleftherios Garyfallidis) Date: Thu, 19 Jan 2023 09:49:25 -0500 Subject: [Neuroimaging] [DIPY] Re: Using brain tractography with Nibabel or Dipy directly from Blender 3D In-Reply-To: <1922849249.3539705.1674123503497@mail.yahoo.com> References: <1219255406.1526592.1673994249189.ref@mail.yahoo.com> <1219255406.1526592.1673994249189@mail.yahoo.com> <1922849249.3539705.1674123503497@mail.yahoo.com> Message-ID: Great! Note also that the next version of FURY should be compatible with Blender. We are providing full GLTF support in Python. This is going to be fun for a lot of people! On Thu, Jan 19, 2023 at 6:05 AM Alex Crimi via DIPY wrote: > if you think it is useful. > I added the code on github, as it is not so visible from the movie: > alecrimi/python_blender (github.com) > > > Best, > Alex > > > > On Wednesday, January 18, 2023 at 08:29:25 PM GMT+1, Eleftherios > Garyfallidis wrote: > > > Very cool Alex! Wonderful job. Not late at all. > > Do we have your approval to highlight your video in our YouTube channel? > > Best, > Elef > > On Tue, Jan 17, 2023 at 10:54 PM Alex Crimi via DIPY > wrote: > > I know you are all interested in expanding Fury, > but ages ago I discussed with Eleftherios how to render streamlines (or > use the entire Dipy) from Blender 3D. > I made a video tutorial, the code is in the description of the video > https://www.youtube.com/watch?v=ANkq9EAEEeI > > I hope I am not too late. > > Ale > > _______________________________________________ > DIPY mailing list -- dipy at python.org > To unsubscribe send an email to dipy-leave at python.org > https://mail.python.org/mailman3/lists/dipy.python.org/ > Member address: garyfallidis at gmail.com > > _______________________________________________ > DIPY mailing list -- dipy at python.org > To unsubscribe send an email to dipy-leave at python.org > https://mail.python.org/mailman3/lists/dipy.python.org/ > Member address: alex.crimi at yahoo.com > _______________________________________________ > DIPY mailing list -- dipy at python.org > To unsubscribe send an email to dipy-leave at python.org > https://mail.python.org/mailman3/lists/dipy.python.org/ > Member address: garyfallidis at gmail.com > -------------- next part -------------- An HTML attachment was scrubbed... URL: From nsh531 at gmail.com Sun Jan 22 07:25:42 2023 From: nsh531 at gmail.com (=?UTF-8?B?16DXqteZINep15jXqNef?=) Date: Sun, 22 Jan 2023 14:25:42 +0200 Subject: [Neuroimaging] Fwd: Topic : : Opportunities in Mental Health Research for Studying Schizophrenia Using the DS000115 OpenNeuro Dataset. In-Reply-To: References: Message-ID: ---------- Forwarded message --------- ???: ??? ???? ?Date: ???, 21 ????? 2023 ?-22:00? Subject: Topic : : Opportunities in Mental Health Research for Studying Schizophrenia Using the DS000115 OpenNeuro Dataset. To: Dear Colleagues, I am writing to share with you an exciting opportunity for those in the field of mental health research. The DS000115 dataset, available on OpenNeuro, contains a wealth of data on individuals diagnosed with schizophrenia. This dataset includes both structural and functional MRI scans, as well as behavioral and cognitive data. This dataset represents a valuable resource for researchers interested in studying schizophrenia and developing new treatments. The data can be used to investigate the neural basis of the disorder, identify biomarkers for diagnosis, and evaluate the effectiveness of different treatment approaches. I encourage all researchers in the field of mental health to explore this dataset and consider the potential for making new discoveries and advancing our understanding of schizophrenia. The dataset can be accessed at https://openneuro.org/datasets/ds000115. Thank you for your consideration, and I look forward to seeing the innovative research that comes from this dataset. Sincerely, Netanel Stern +972559870641 nsh531 at gmail.com -- -------------- next part -------------- An HTML attachment was scrubbed... URL: From yann at cointepas.net Mon Jan 23 18:14:49 2023 From: yann at cointepas.net (Yann Cointepas) Date: Tue, 24 Jan 2023 00:14:49 +0100 Subject: [Neuroimaging] Using brain tractography with Nibabel or Dipy directly from Blender 3D In-Reply-To: <1219255406.1526592.1673994249189@mail.yahoo.com> References: <1219255406.1526592.1673994249189.ref@mail.yahoo.com> <1219255406.1526592.1673994249189@mail.yahoo.com> Message-ID: Hi, I'm trying to integrate brain volumes into Blender in my spare time. I thought you might be interested in my recent attempts to make dynamic slices of images read by Nibabel. I've detailed everything here: https://github.com/sapetnioc/brainblend Best, Yann -------------- next part -------------- An HTML attachment was scrubbed... URL: From elef at indiana.edu Mon Jan 23 19:52:50 2023 From: elef at indiana.edu (Eleftherios Garyfallidis) Date: Mon, 23 Jan 2023 19:52:50 -0500 Subject: [Neuroimaging] Using brain tractography with Nibabel or Dipy directly from Blender 3D In-Reply-To: <4dbff4858ed74a36a1023e4707982e23@CH0PR08MB8661.namprd08.prod.outlook.com> References: <1219255406.1526592.1673994249189.ref@mail.yahoo.com> <1219255406.1526592.1673994249189@mail.yahoo.com> <4dbff4858ed74a36a1023e4707982e23@CH0PR08MB8661.namprd08.prod.outlook.com> Message-ID: Great! Thank you for sharing Yann. On Mon, Jan 23, 2023 at 6:16 PM Yann Cointepas wrote: > Hi, > > I'm trying to integrate brain volumes into Blender in my spare time. I > thought you might be interested in my recent attempts to make dynamic > slices of images read by Nibabel. I've detailed everything here: > > https://github.com/sapetnioc/brainblend > > Best, > > Yann > -------------- next part -------------- An HTML attachment was scrubbed... URL: From arokem at gmail.com Mon Jan 30 14:38:40 2023 From: arokem at gmail.com (Ariel Rokem) Date: Mon, 30 Jan 2023 11:38:40 -0800 Subject: [Neuroimaging] NeuroHackademy 2023: Call for applications Message-ID: We are happy to announce a call for applications to participate in NeuroHackademy 2023! This two-week hands-on workshop will be held in a hybrid format, August 7th - 18th, 2022 at the University of Washington in Seattle, Washington, USA, and online. NeuroHackademy is an opportunity for participants to learn state-of-the-art methods for the analysis and management of large human neuroscience datasets while also networking and working with domain experts and each other on concrete neuroscience problems. The curriculum emphasizes large datasets of publicly available data (such as the Human Connectome Project, OpenNeuro, etc.), and on the value of making human neuroscience research open and reproducible. NeuroHackademy sessions in the first week will include lectures and tutorials on data science, machine learning, data visualization, and data resources, as well as extended Q&A sessions. The second week will be devoted primarily to participant-directed activities: guided work on team projects, hackathon sessions, and breakout sessions on topics of interest. This event will be held in a hybrid format, with options to attend in-person in Seattle, or online. Participants attending online will join the event through multiple online channels, including zoom-casts of lectures and breakout sessions, Slack conversations, and collaboration through GitHub and through the course?s online Juptyerhub. For more details and a preliminary list of instructors, see: https://neurohackademy.org/ We are now accepting applications to participate at: https://neurohackademy.org/apply/ Ideally, applicants should have some prior experience with programming and with neuroscience data analysis, but we welcome applications from participants with a variety of relevant backgrounds. For frequently asked questions, please refer to this page: https://neurohackademy.org/frequently-asked-questions/ Accepted applicants will be asked to pay a fee of $200 (in person) / $20 (online) upon final registration. Fees cover housing and two meals per day for in person participants. Support for participation through travel grants and fee waivers is also available. Important dates: April 17th, application deadline May 5th, notification of acceptance May 18th, final registration deadline August 7th - 18th: NeuroHackademy -------------- next part -------------- An HTML attachment was scrubbed... URL: