From remi_gau at hotmail.com Mon Oct 2 14:05:15 2023 From: remi_gau at hotmail.com (Remi Gau) Date: Mon, 2 Oct 2023 20:05:15 +0200 Subject: [Neuroimaging] Nilearn 0.10.2 is out Message-ID: An HTML attachment was scrubbed... URL: From elef at indiana.edu Mon Oct 2 14:52:23 2023 From: elef at indiana.edu (Eleftherios Garyfallidis) Date: Mon, 2 Oct 2023 14:52:23 -0400 Subject: [Neuroimaging] Nilearn 0.10.2 is out In-Reply-To: <3253134cda96476f9280e768993309df@CH0PR08MB8661.namprd08.prod.outlook.com> References: <3253134cda96476f9280e768993309df@CH0PR08MB8661.namprd08.prod.outlook.com> Message-ID: Many congratulations Remi and all! Best regards, Elef On Mon, Oct 2, 2023 at 2:06?PM Remi Gau wrote: > Hello everyone! > > We have just released Nilearn 0.10.2! > > Update from PyPi: > > pip install --upgrade nilearn > > This is a minor release with some exciting new features: > > - > > Volume plotting functions like plot_img > > now have an optional radiological parameter, defaulting to False. If > True, this will invert the x-axis and L and R annotations to confirm > to radiological conventional view. > - > > The decoder class was updated: > - > > to use the more efficient LogisticRegressionCV > - > > to support LassoCV as a new estimator option > - > > Add vmin and symmetric_cbar arguments to plot_img_on_surf > > - > > Improved contrasts allowing fixed effects on F contrasts > - > > There is a new experimental surface API to facilitate working with > surface data in downstream surface-based analyses. We provide this API > as a nilearn.experimental.surface module as it is still incomplete and > subject to change without a deprecation cycle. > - > > We now have a DOI on Zenodo for all Nilearn versions: > https://doi.org/10.5281/zenodo.8397156 > > You can see the full changelog of this release here: > https://nilearn.github.io/stable/changes/whats_new.html#id1 > > 11 new contributors !!!! > > - > > Jonas Mago (https://github.com/jonasmago) made their first > contribution in https://github.com/nilearn/nilearn/pull/3738 > - > > Samante Tarum (https://github.com/tarunsamanta2k20) made their first > contribution in https://github.com/nilearn/nilearn/pull/3774 > - > > Czarina Sy (https://github.com/czarinasy) made their first > contribution in https://github.com/nilearn/nilearn/pull/3838 > - > > Alisha Kodibagkar (https://github.com/alishakodibagkar) made their > first contribution in https://github.com/nilearn/nilearn/pull/3855 > - > > Fran?ois Paugam (https://github.com/FrancoisPgm) made their first > contribution in https://github.com/nilearn/nilearn/pull/3854 > - > > Mathieu Dugr? (https://github.com/mathdugre) made their first > contribution in https://github.com/nilearn/nilearn/pull/3860 > - > > Rahul Brito (https://github.com/Rahul-Brito) made their first > contribution in https://github.com/nilearn/nilearn/pull/3847 > - > > Konarad Wagstyl (https://github.com/kwagstyl) made their first > contribution in https://github.com/nilearn/nilearn/pull/3172 > - > > Aswin Vijayan (https://github.com/vaswin0) made their first > contribution in https://github.com/nilearn/nilearn/pull/3597 > - > > Maximilian Cosmo Sitter (https://github.com/mcsitter) made their first > contribution in https://github.com/nilearn/nilearn/pull/3723 > - > > Alexandre Cionca (https://github.com/acionca) made their first > contribution in https://github.com/nilearn/nilearn/pull/3971 > > The full list of pull requests included in this version: > https://github.com/nilearn/nilearn/releases/tag/0.10.2 > The full ?diff? since last version: > https://github.com/nilearn/nilearn/compare/0.10.1...0.10.2 > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From markiewicz at stanford.edu Mon Oct 2 15:07:09 2023 From: markiewicz at stanford.edu (Christopher Markiewicz) Date: Mon, 2 Oct 2023 19:07:09 +0000 Subject: [Neuroimaging] Nilearn 0.10.2 is out In-Reply-To: References: Message-ID: Awesome! Congrats to the nilearn team! And it's great to see so many new contributors! Best, Chris ________________________________________ From: Neuroimaging on behalf of Remi Gau Sent: Monday, October 2, 2023 14:05 To: neuroimaging at python.org Subject: [Neuroimaging] Nilearn 0.10.2 is out Hello everyone! We have just released Nilearn 0.10.2! Update from PyPi: pip install --upgrade nilearn This is a minor release with some exciting new features: * Volume plotting functions like plot_img now have an optional radiological parameter, defaulting to False. If True, this will invert the x-axis and L and R annotations to confirm to radiological conventional view. * The decoder class was updated: * to use the more efficient LogisticRegressionCV * to support LassoCV as a new estimator option * Add vmin and symmetric_cbar arguments to plot_img_on_surf * Improved contrasts allowing fixed effects on F contrasts * There is a new experimental surface API to facilitate working with surface data in downstream surface-based analyses. We provide this API as a nilearn.experimental.surface module as it is still incomplete and subject to change without a deprecation cycle. * We now have a DOI on Zenodo for all Nilearn versions: https://doi.org/10.5281/zenodo.8397156 You can see the full changelog of this release here: https://nilearn.github.io/stable/changes/whats_new.html#id1 11 new contributors !!!! * Jonas Mago (https://github.com/jonasmago) made their first contribution in https://github.com/nilearn/nilearn/pull/3738 * Samante Tarum (https://github.com/tarunsamanta2k20) made their first contribution in https://github.com/nilearn/nilearn/pull/3774 * Czarina Sy (https://github.com/czarinasy) made their first contribution in https://github.com/nilearn/nilearn/pull/3838 * Alisha Kodibagkar (https://github.com/alishakodibagkar) made their first contribution in https://github.com/nilearn/nilearn/pull/3855 * Fran?ois Paugam (https://github.com/FrancoisPgm) made their first contribution in https://github.com/nilearn/nilearn/pull/3854 * Mathieu Dugr? (https://github.com/mathdugre) made their first contribution in https://github.com/nilearn/nilearn/pull/3860 * Rahul Brito (https://github.com/Rahul-Brito) made their first contribution in https://github.com/nilearn/nilearn/pull/3847 * Konarad Wagstyl (https://github.com/kwagstyl) made their first contribution in https://github.com/nilearn/nilearn/pull/3172 * Aswin Vijayan (https://github.com/vaswin0) made their first contribution in https://github.com/nilearn/nilearn/pull/3597 * Maximilian Cosmo Sitter (https://github.com/mcsitter) made their first contribution in https://github.com/nilearn/nilearn/pull/3723 * Alexandre Cionca (https://github.com/acionca) made their first contribution in https://github.com/nilearn/nilearn/pull/3971 The full list of pull requests included in this version: https://github.com/nilearn/nilearn/releases/tag/0.10.2 The full ?diff? since last version: https://github.com/nilearn/nilearn/compare/0.10.1...0.10.2 From satra at mit.edu Mon Oct 2 20:41:24 2023 From: satra at mit.edu (Satrajit Ghosh) Date: Mon, 2 Oct 2023 20:41:24 -0400 Subject: [Neuroimaging] Nilearn 0.10.2 is out In-Reply-To: References: Message-ID: congrats! wonderful to new contributors. cheers, satra On Mon, Oct 2, 2023 at 2:09?PM Remi Gau wrote: > Hello everyone! > > We have just released Nilearn 0.10.2! > > Update from PyPi: > > pip install --upgrade nilearn > > This is a minor release with some exciting new features: > > - > > Volume plotting functions like plot_img > > now have an optional radiological parameter, defaulting to False. If > True, this will invert the x-axis and L and R annotations to confirm > to radiological conventional view. > - > > The decoder class was updated: > - > > to use the more efficient LogisticRegressionCV > - > > to support LassoCV as a new estimator option > - > > Add vmin and symmetric_cbar arguments to plot_img_on_surf > > - > > Improved contrasts allowing fixed effects on F contrasts > - > > There is a new experimental surface API to facilitate working with > surface data in downstream surface-based analyses. We provide this API > as a nilearn.experimental.surface module as it is still incomplete and > subject to change without a deprecation cycle. > - > > We now have a DOI on Zenodo for all Nilearn versions: > https://doi.org/10.5281/zenodo.8397156 > > You can see the full changelog of this release here: > https://nilearn.github.io/stable/changes/whats_new.html#id1 > > 11 new contributors !!!! > > - > > Jonas Mago (https://github.com/jonasmago) made their first > contribution in https://github.com/nilearn/nilearn/pull/3738 > - > > Samante Tarum (https://github.com/tarunsamanta2k20) made their first > contribution in https://github.com/nilearn/nilearn/pull/3774 > - > > Czarina Sy (https://github.com/czarinasy) made their first > contribution in https://github.com/nilearn/nilearn/pull/3838 > - > > Alisha Kodibagkar (https://github.com/alishakodibagkar) made their > first contribution in https://github.com/nilearn/nilearn/pull/3855 > - > > Fran?ois Paugam (https://github.com/FrancoisPgm) made their first > contribution in https://github.com/nilearn/nilearn/pull/3854 > - > > Mathieu Dugr? (https://github.com/mathdugre) made their first > contribution in https://github.com/nilearn/nilearn/pull/3860 > - > > Rahul Brito (https://github.com/Rahul-Brito) made their first > contribution in https://github.com/nilearn/nilearn/pull/3847 > - > > Konarad Wagstyl (https://github.com/kwagstyl) made their first > contribution in https://github.com/nilearn/nilearn/pull/3172 > - > > Aswin Vijayan (https://github.com/vaswin0) made their first > contribution in https://github.com/nilearn/nilearn/pull/3597 > - > > Maximilian Cosmo Sitter (https://github.com/mcsitter) made their first > contribution in https://github.com/nilearn/nilearn/pull/3723 > - > > Alexandre Cionca (https://github.com/acionca) made their first > contribution in https://github.com/nilearn/nilearn/pull/3971 > > The full list of pull requests included in this version: > https://github.com/nilearn/nilearn/releases/tag/0.10.2 > The full ?diff? since last version: > https://github.com/nilearn/nilearn/compare/0.10.1...0.10.2 > > _______________________________________________ > 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 Tue Oct 3 08:16:52 2023 From: satra at mit.edu (Satrajit Ghosh) Date: Tue, 3 Oct 2023 08:16:52 -0400 Subject: [Neuroimaging] install Nipype In-Reply-To: <3c33132cb5d64d3ead76ddcdbf1a781e@inserm.fr> References: <3c33132cb5d64d3ead76ddcdbf1a781e@inserm.fr> Message-ID: hi jessica, arm versions are available here through conda forge: https://anaconda.org/conda-forge/nipype cheers, satra On Wed, Sep 20, 2023 at 11:43?AM JESSICA LEBENBERG < jessica.lebenberg at inserm.fr> wrote: > Hi, > > I'm installing my new laptop (Mac OS Ventura, M2 ship). > > but I cannot install Nipype with conda, nor pip. It seems I succeeded with > docker but I do not understand how use it within python (import Nipype did > not work). > > I have a look on https://repo.anaconda.com/pkgs/main/ and I cannot find > anymore Nipype. > > Nipype is not used anymore ? is there another package ? > > thanks in advance, > > jessica > > > Jessica LEBENBERG, PhD > Senior Research Engineer, > Centre NeuroVasculaire Translationnel (CNVT) > Direction de la Recherche Clinique et de l?Innovation (DRCI) de l?AP-HP > H?pital Lariboisi?re > 2 rue Ambroise Par?, 75010 PARIS > > INSERM U1141 NeuroDiderot > Bat. E. Bingen, H?pital Robert Debr? > 48, boulevard S?rurier, 75019 Paris > _______________________________________________ > 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 Tue Oct 3 08:24:13 2023 From: satra at mit.edu (Satrajit Ghosh) Date: Tue, 3 Oct 2023 08:24:13 -0400 Subject: [Neuroimaging] [nipype] SPM functions error In-Reply-To: References: Message-ID: dear elena, could you please post this as an issue in nipype? also helpful would be to post what happens when you launch matlab in the terminal inside jupyterlab. i suspect it could be because of something in the startup of matlab. cheers, satra On Fri, Sep 15, 2023 at 2:32?PM ????? ????? wrote: > Dear nipype community, > > > I have a problem with nipype and I'm unable to find a working solution. > Maybe you'll be able to help me? > > > I use Windows 10 Home 64-bit, Python 3.11, Matlab R2022a and SPM12 7771. I > run my scripts in Jupyter lab. It seems like I can't use any SPM functions > in nipype. When I type: > > > from nipype.interfaces import spm > > spm.SPMCommand().version > > > The matlab terminal window runs and closes quickly, and the output in > jupyter is "ValueError: substring not found". I attached the full text of > error in spm_version_error.txt. This happens with all SPM functions I try. > > > I've tried to used standalone version of SPM12 with MCR and executing the > following: > > > from nipype.interfaces import spm > > matlab_cmd = '/path/to/run_spm12.sh /path/to/Compiler_Runtime/v713/ script' > > spm.SPMCommand.set_mlab_paths(matlab_cmd=matlab_cmd, use_mcr=True) > > > This command causes the same error. I also tried to add > os.environ['FORCE_SPMMCR'] = "True" or os.environ['FORCE_SPMMCR'] = '1', > which also didn't have any effect. I've additionally tried to give up on > Windows and try this on Mac with Python 3.8, but the error is still there. > > > I hoped that you might help me with this. > > All the best, > -- > Elena Pitsik > researcher, Baltic Center for Artificial Intelligence and Neurotechnology, > Immanuel Kant Baltic Federal University. > _______________________________________________ > Neuroimaging mailing list > Neuroimaging at python.org > https://mail.python.org/mailman/listinfo/neuroimaging > -------------- next part -------------- An HTML attachment was scrubbed... URL: From arokem at uw.edu Sun Oct 22 12:57:29 2023 From: arokem at uw.edu (Ariel Rokem) Date: Sun, 22 Oct 2023 09:57:29 -0700 Subject: [Neuroimaging] Fwd: [Docker] Action Required - Credit Card Payment Failed In-Reply-To: <20231021164616.fa918645fecd1176@notify.docker.com> References: <20231021164616.fa918645fecd1176@notify.docker.com> Message-ID: Hello everyone, Does anyone need this subscription to dockerhub? I don't need it, and I am inclined to downgrade this organizational account, but if someone else needs it and needs me to provide access, let me know. Cheers, Ariel ---------- Forwarded message --------- From: Docker Date: Sat, Oct 21, 2023 at 9:46?AM Subject: [Docker] Action Required - Credit Card Payment Failed To: Hello nipy! We were unable to process a payment on your account for invoice # *INV-C17C0E* that was due on October 21, 2023 - the credit card was declined for an unknown reason. We appreciate you working with Docker on this and look forward to resolving the matter with you quickly. If you have already sent payment for this invoice, please contact Docker at billing at docker.com regarding invoice #*INV-C17C0E* to ensure your payment was received and applied to your account. Update billing information If the payment method associated with your account is not updated in *14* days, your subscription will be downgraded. Thank you, The Docker Team This email was sent to arokem at gmail.com to notify you of an update made to your Docker account. ? 2023 Docker Inc. 3790 El Camino Real #1052, Palo Alto, CA 94306 X Privacy Policy -------------- next part -------------- An HTML attachment was scrubbed... URL: From jbpoline at gmail.com Sun Oct 22 14:04:48 2023 From: jbpoline at gmail.com (JB Poline) Date: Sun, 22 Oct 2023 14:04:48 -0400 Subject: [Neuroimaging] Fwd: [Docker] Action Required - Credit Card Payment Failed In-Reply-To: References: <20231021164616.fa918645fecd1176@notify.docker.com> Message-ID: Not on my side cheers JB On Sun, Oct 22, 2023 at 2:01?PM Ariel Rokem wrote: > Hello everyone, > > Does anyone need this subscription to dockerhub? I don't need it, and I am > inclined to downgrade this organizational account, but if someone else > needs it and needs me to provide access, let me know. > > Cheers, > Ariel > > ---------- Forwarded message --------- > From: Docker > Date: Sat, Oct 21, 2023 at 9:46?AM > Subject: [Docker] Action Required - Credit Card Payment Failed > To: > > > > > > Hello nipy! > We were unable to process a payment on your account for invoice # > *INV-C17C0E* that was due on October 21, 2023 - the credit card was > declined for an unknown reason. > We appreciate you working with Docker on this and look forward to > resolving the matter with you quickly. > If you have already sent payment for this invoice, please contact Docker > at billing at docker.com regarding invoice #*INV-C17C0E* to ensure your > payment was received and applied to your account. > Update billing information > > If the payment method associated with your account is not updated in *14* > days, your subscription will be downgraded. > > Thank you, > The Docker Team > > > This email was sent to arokem at gmail.com to notify you of an update made > to your Docker account. > ? 2023 Docker Inc. > > 3790 El Camino Real #1052, Palo Alto, CA 94306 X > > Privacy Policy > > > > _______________________________________________ > 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 Mon Oct 23 08:00:00 2023 From: satra at mit.edu (Satrajit Ghosh) Date: Mon, 23 Oct 2023 08:00:00 -0400 Subject: [Neuroimaging] Fwd: [Docker] Action Required - Credit Card Payment Failed In-Reply-To: References: <20231021164616.fa918645fecd1176@notify.docker.com> Message-ID: hi ariel, i don't know what their opensource policy is now. i believe all of these did provide some of the benefits of teams (e.g. building images on repo commits) for free under the opensource plan. it may be they remove that from time to time and we need to request again. it's also possible i may have requested this in the past for all orgs i am part of. if there are auto builds on repos, we would have to change that to github action and push to dockerhub on releases or distribute through ghcr instead of docker. we can take a look at some of them and talk to the main maintainers of those repos. cheers, satra On Sun, Oct 22, 2023 at 2:00?PM Ariel Rokem wrote: > Hello everyone, > > Does anyone need this subscription to dockerhub? I don't need it, and I am > inclined to downgrade this organizational account, but if someone else > needs it and needs me to provide access, let me know. > > Cheers, > Ariel > > ---------- Forwarded message --------- > From: Docker > Date: Sat, Oct 21, 2023 at 9:46?AM > Subject: [Docker] Action Required - Credit Card Payment Failed > To: > > > > > > Hello nipy! > We were unable to process a payment on your account for invoice # > *INV-C17C0E* that was due on October 21, 2023 - the credit card was > declined for an unknown reason. > We appreciate you working with Docker on this and look forward to > resolving the matter with you quickly. > If you have already sent payment for this invoice, please contact Docker > at billing at docker.com regarding invoice #*INV-C17C0E* to ensure your > payment was received and applied to your account. > Update billing information > > If the payment method associated with your account is not updated in *14* > days, your subscription will be downgraded. > > Thank you, > The Docker Team > > > This email was sent to arokem at gmail.com to notify you of an update made > to your Docker account. > ? 2023 Docker Inc. > > 3790 El Camino Real #1052, Palo Alto, CA 94306 X > > Privacy Policy > > > > _______________________________________________ > Neuroimaging mailing list > Neuroimaging at python.org > https://mail.python.org/mailman/listinfo/neuroimaging > -------------- next part -------------- An HTML attachment was scrubbed... URL: From arokem at uw.edu Tue Oct 31 13:00:23 2023 From: arokem at uw.edu (Ariel Rokem) Date: Tue, 31 Oct 2023 10:00:23 -0700 Subject: [Neuroimaging] Fwd: [Docker] Action Required - Credit Card Payment Failed In-Reply-To: References: <20231021164616.fa918645fecd1176@notify.docker.com> Message-ID: Hello everyone, It looks like there are two (public) repositories managed through this organization: mindboggle and heudiconv. There are currently 7 members (see below). To downgrade to the free account we can have at most 3 members. I am happy to take myself off :-) Does someone here know whether the heudiconv or mindboggle repositories are stillI critical for anyone? As far as I can tell, maybe we can shut the whole thing down? I think that will happen anyway pretty soon if we don't do anything. Cheers, Ariel [image: Screenshot 2023-10-31 at 9.55.54 AM.png] On Mon, Oct 23, 2023 at 5:06?AM Satrajit Ghosh wrote: > hi ariel, > > i don't know what their opensource policy is now. i believe all of these > did provide some of the benefits of teams (e.g. building images on repo > commits) for free under the opensource plan. it may be they remove that > from time to time and we need to request again. it's also possible i may > have requested this in the past for all orgs i am part of. if there are > auto builds on repos, we would have to change that to github action and > push to dockerhub on releases or distribute through ghcr instead of docker. > > we can take a look at some of them and talk to the main maintainers of > those repos. > > cheers, > > satra > > On Sun, Oct 22, 2023 at 2:00?PM Ariel Rokem wrote: > >> Hello everyone, >> >> Does anyone need this subscription to dockerhub? I don't need it, and I >> am inclined to downgrade this organizational account, but if someone else >> needs it and needs me to provide access, let me know. >> >> Cheers, >> Ariel >> >> ---------- Forwarded message --------- >> From: Docker >> Date: Sat, Oct 21, 2023 at 9:46?AM >> Subject: [Docker] Action Required - Credit Card Payment Failed >> To: >> >> >> >> >> >> Hello nipy! >> We were unable to process a payment on your account for invoice # >> *INV-C17C0E* that was due on October 21, 2023 - the credit card was >> declined for an unknown reason. >> We appreciate you working with Docker on this and look forward to >> resolving the matter with you quickly. >> If you have already sent payment for this invoice, please contact Docker >> at billing at docker.com regarding invoice #*INV-C17C0E* to ensure your >> payment was received and applied to your account. >> Update billing information >> >> If the payment method associated with your account is not updated in *14* >> days, your subscription will be downgraded. >> >> Thank you, >> The Docker Team >> >> >> This email was sent to arokem at gmail.com to notify you of an update made >> to your Docker account. >> ? 2023 Docker Inc. >> >> 3790 El Camino Real #1052, Palo Alto, CA 94306 X >> >> Privacy Policy >> >> >> >> _______________________________________________ >> 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... 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