From AiWern.Chung at childrens.harvard.edu Mon Jun 11 11:37:13 2018 From: AiWern.Chung at childrens.harvard.edu (Chung, Ai Wern) Date: Mon, 11 Jun 2018 15:37:13 +0000 Subject: [Neuroimaging] Deadline extended: Call for Papers MICCAI 2018 Connectomics in NeuroImaging Workshop In-Reply-To: <1525184505400.41354@childrens.harvard.edu> References: <1525146658594.86048@childrens.harvard.edu>, <1525184505400.41354@childrens.harvard.edu> Message-ID: <1528731433339.33564@childrens.harvard.edu> Submission deadline has been extended to June 25th, 2018! This is a Call for Papers for the 2nd International Workshop on Connectomics in NeuroImaging (CNI 2018), which will be held in parallel with the 21st International Conference on Medical Image Computing and Computer-assisted Intervention (MICCAI 2018) in Granada Spain. CNI 2018 is a full day workshop that will take place September 20th, 2018. Our topics of interest cover (but are not limited to): (1) New developments in connectome construction from different imaging modalities; (2) Development of data driven techniques to identify biomarkers in connectome data; (3) Brain network modeling and formal conceptual models of connectome data; (4) Machine learning algorithms and connectome data analysis; (5) Evaluation and validation of connectome models. If you have research that fits into the scope of our workshop detailed on our website (http://munsellb.people.cofc.edu/cni.html), we encourage you to submit a paper or an abstract! ** Why submit to the CNI workshop? ** - Three great keynote speakers, presentations and poster sessions with accompanying power pitches will provide you with ample opportunity for exchanges and discussions with international computational neuroscientists and clinicians; - Accepted papers will be published in an LNCS proceedings and will be invited to submit to a special issue in Brain Connectivity; - There will be an INCF sponsored Best Paper Award. ** Full length paper submission ** Paper submission deadline, June 25th via https://cmt3.research.microsoft.com/CNI2018 For more information visit http://munsellb.people.cofc.edu/cni.html ** Full length important dates ** Submission deadline: 11:59 PM PST, June 25th, 2018 Notification of acceptance: July 2nd, 2018 Camera-ready deadline: 11:59 PST, July 16th, 2018 Workshop date: Sept. 20th, 2018 We look forward to your participation! If you have any additional questions, please contact Brent Munsell (munsellb at cofc.edu) or Ai Chung (aiwern.chung at childrens.harvard.edu) ========================= CNI 2018 Chairs ----------------------------------------- Islem Rekik, University of Dundee Ai Wern Chung, Boston Children's Hospital, Harvard Medical School Markus Schirmer, Massachusetts General Hospital, Harvard Medical School Guorong Wu, University of North Carolina, Chapel Hill Brent Munsell, College of Charleston -------------- next part -------------- An HTML attachment was scrubbed... URL: From docpatient at gmail.com Mon Jun 11 16:19:14 2018 From: docpatient at gmail.com (Francesco Sammartino) Date: Mon, 11 Jun 2018 16:19:14 -0400 Subject: [Neuroimaging] Faculty position open at the Division of Stereotactic and Functional Neurosurgery - The Ohio State University Message-ID: The Division of Stereotactic and Functional Neurosurgery in the Department of Neurological Surgery at the Ohio State University College of Medicine (OSUWMC) is initiating a search for outstanding scientists for tenure track faculty position at all ranks. This position will join a collaborative research and educational environment with strengths in multiple aspects of neuroanatomy, neurophysiology, functional neuroimaging, and data analytics. Individuals with strengths in structural and functional connectivity analysis, diffusion weighted imaging, neurophysiology, local field potential analysis will be strongly considered. Candidates should have a Ph.D. and/or M.D. degree, a commitment to basic and/or translational research and a history of strong research productivity. Individuals will be evaluated on their ability to establish innovative independent research programs as well as develop collaborative areas of focus with existing programs. Individuals must have strong communication and interpersonal skills. Applicants are expected to have a Ph.D. and/or M.D. or equivalent degree, at least 3 years of post-doctoral training, a commitment to basic and/or translational research, and a strong record of research productivity. Applications should include a detailed curriculum vitae and a description of independent research plans (2 pages) to: Stereotactic & Functional Neurosurgery Division Search Committee, c/o melinda.hollingshead at osumc.edu by July 1, 2018. *The Ohio State University is an equal opportunity employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation or identity, national origin, disability status, or protected veteran status.* -------------- next part -------------- An HTML attachment was scrubbed... URL: From markiewicz at stanford.edu Tue Jun 12 14:06:01 2018 From: markiewicz at stanford.edu (Christopher Markiewicz) Date: Tue, 12 Jun 2018 18:06:01 +0000 Subject: [Neuroimaging] ANN: Nibabel release 2.3 Message-ID: Hi all, Nibabel 2.3 has been released just in time for OHBM. It's been published to PyPI and should be available on conda-forge within the next day. Features to look out for in this release are a new image slicing interface and TRK/TCK conversion tools. There have also been a number of first-time contributors, which is always good to see. As always, thanks to all contributors, reviewers and users. Please cite using the Zenodo DOI: https://doi.org/10.5281/zenodo.1287921 The full changelog follows: New feature release for the 2.3 series. Most work on NiBabel so far has been by Matthew Brett (MB), Michael Hanke (MH) Ben Cipollini (BC), Marc-Alexandre C?t? (MC), Chris Markiewicz (CM), Stephan Gerhard (SG) and Eric Larson (EL). References like "pr/298" refer to github pull request numbers. New features ------------ * TRK <=> TCK streamlines conversion CLI tools (pr/606) (MC, reviewed by CM) * Image slicing for SpatialImages (pr/550) (CM) Enhancements ------------ * Simplify MGHImage and add footer fields (pr/569) (CM, reviewed by MB) * Force sform/qform codes to be ints, rather than numpy types (pr/575) (Paul McCarthy, reviewed by MB, CM) * Auto-fill color table in FreeSurfer annotation file (pr/592) (Paul McCarthy, reviewed by CM, MB) * Set default intent code for CIFTI2 images (pr/604) (Mathias Goncalves, reviewed by CM, Satra Ghosh, MB, Tim Coalson) * Raise informative error on empty files (pr/611) (Pradeep Raamana, reviewed by CM, MB) * Accept degenerate filenames such as ``.nii`` (pr/621) (Dimitri Papadopoulos-Orfanos, reviewed by Yaroslav Halchenko) * Take advantage of ``IndexedGzipFile`` ``drop_handles`` flag to release filehandles by default (pr/614) (Paul McCarthy, reviewed by CM, MB) Bug fixes --------- * Preserve first point of `LazyTractogram` (pr/588) (MC, reviewed by Nil Goyette, CM, MB) * Stop adding extraneous metadata padding (pr/593) (Jon Stutters, reviewed by CM, MB) * Accept lower-case orientation codes in TRK files (pr/600) (Kesshi Jordan, MB, reviewed by MB, MC, CM) * Annotation file reading (pr/592) (Paul McCarthy, reviewed by CM, MB) * Fix buffer size calculation in ArraySequence (pr/597) (Serge Koudoro, reviewed by MC, MB, Eleftherios Garyfallidis, CM) * Resolve ``UnboundLocalError`` in Python 3 (pr/607) (Jakub Kaczmarzyk, reviewed by MB, CM) * Do not crash on non-``ImportError`` failures in optional imports (pr/618) (Yaroslav Halchenko, reviewed by CM) * Return original array from ``get_fdata`` for array image, if no cast required (pr/638, MB, reviewed by CM) Maintenance ----------- * Use SSH address to use key-based auth (pr/587) (CM, reviewed by MB) * Fix doctests for numpy 1.14 array printing (pr/591) (MB, reviewed by CM) * Refactor for pydicom 1.0 API changes (pr/599) (MB, reviewed by CM) * Increase test coverage, remove unreachable code (pr/602) (CM, reviewed by Yaroslav Halchenko, MB) * Move ``nib-ls`` and other programs to a new cmdline module (pr/601, pr/615) (Chris Cheng, reviewed by MB, Yaroslav Halchenko) * Remove deprecated numpy indexing (EL, reviewed by CM) * Update documentation to encourage ``get_fdata`` over ``get_data`` (pr/637, MB, reviewed by CM) API changes and deprecations ---------------------------- * Support for ``keep_file_open = 'auto'`` as a parameter to ``Opener()`` will be deprecated in 2.4, for removal in 3.0. Accordingly, support for ``openers.KEEP_FILE_OPEN_DEFAULT = 'auto'`` will be dropped on the same schedule. * Drop-in support for ``indexed_gzip < 0.7`` has been removed. Enjoy, -- Chris Markiewicz Center for Reproducible Neuroscience Stanford University -------------- next part -------------- An HTML attachment was scrubbed... URL: From elef at indiana.edu Tue Jun 12 15:13:17 2018 From: elef at indiana.edu (Eleftherios Garyfallidis) Date: Tue, 12 Jun 2018 15:13:17 -0400 Subject: [Neuroimaging] ANN: Nibabel release 2.3 In-Reply-To: References: Message-ID: Thank you Nibabel devs! We will need to change our minimum requirements for Nibabel in DIPY! Yeah! Fix bugs and move on! :) On Tue, Jun 12, 2018 at 2:36 PM Christopher Markiewicz < markiewicz at stanford.edu> wrote: > Hi all, > > Nibabel 2.3 has been released just in time for OHBM. It's been published > to PyPI and should be available on conda-forge within the next day. > > Features to look out for in this release are a new image slicing interface > and TRK/TCK conversion tools. There have also been a number of first-time > contributors, which is always good to see. > > As always, thanks to all contributors, reviewers and users. > > Please cite using the Zenodo DOI: > > https://doi.org/10.5281/zenodo.1287921 > > The full changelog follows: > > > New feature release for the 2.3 series. > > Most work on NiBabel so far has been by Matthew Brett (MB), Michael Hanke > (MH) > Ben Cipollini (BC), Marc-Alexandre C?t? (MC), Chris Markiewicz (CM), > Stephan > Gerhard (SG) and Eric Larson (EL). > > References like "pr/298" refer to github pull request numbers. > > New features > ------------ > * TRK <=> TCK streamlines conversion CLI tools (pr/606) (MC, reviewed by > CM) > * Image slicing for SpatialImages (pr/550) (CM) > > Enhancements > ------------ > * Simplify MGHImage and add footer fields (pr/569) (CM, reviewed by MB) > * Force sform/qform codes to be ints, rather than numpy types (pr/575) > (Paul > McCarthy, reviewed by MB, CM) > * Auto-fill color table in FreeSurfer annotation file (pr/592) (Paul > McCarthy, > reviewed by CM, MB) > * Set default intent code for CIFTI2 images (pr/604) (Mathias Goncalves, > reviewed by CM, Satra Ghosh, MB, Tim Coalson) > * Raise informative error on empty files (pr/611) (Pradeep Raamana, > reviewed > by CM, MB) > * Accept degenerate filenames such as ``.nii`` (pr/621) (Dimitri > Papadopoulos-Orfanos, reviewed by Yaroslav Halchenko) > * Take advantage of ``IndexedGzipFile`` ``drop_handles`` flag to release > filehandles by default (pr/614) (Paul McCarthy, reviewed by CM, MB) > > Bug fixes > --------- > * Preserve first point of `LazyTractogram` (pr/588) (MC, reviewed by Nil > Goyette, CM, MB) > * Stop adding extraneous metadata padding (pr/593) (Jon Stutters, reviewed > by > CM, MB) > * Accept lower-case orientation codes in TRK files (pr/600) (Kesshi Jordan, > MB, reviewed by MB, MC, CM) > * Annotation file reading (pr/592) (Paul McCarthy, reviewed by CM, MB) > * Fix buffer size calculation in ArraySequence (pr/597) (Serge Koudoro, > reviewed by MC, MB, Eleftherios Garyfallidis, CM) > * Resolve ``UnboundLocalError`` in Python 3 (pr/607) (Jakub Kaczmarzyk, > reviewed by MB, CM) > * Do not crash on non-``ImportError`` failures in optional imports (pr/618) > (Yaroslav Halchenko, reviewed by CM) > * Return original array from ``get_fdata`` for array image, if no cast > required (pr/638, MB, reviewed by CM) > > Maintenance > ----------- > * Use SSH address to use key-based auth (pr/587) (CM, reviewed by MB) > * Fix doctests for numpy 1.14 array printing (pr/591) (MB, reviewed by CM) > * Refactor for pydicom 1.0 API changes (pr/599) (MB, reviewed by CM) > * Increase test coverage, remove unreachable code (pr/602) (CM, reviewed > by > Yaroslav Halchenko, MB) > * Move ``nib-ls`` and other programs to a new cmdline module (pr/601, > pr/615) > (Chris Cheng, reviewed by MB, Yaroslav Halchenko) > * Remove deprecated numpy indexing (EL, reviewed by CM) > * Update documentation to encourage ``get_fdata`` over ``get_data`` > (pr/637, > MB, reviewed by CM) > > API changes and deprecations > ---------------------------- > * Support for ``keep_file_open = 'auto'`` as a parameter to ``Opener()`` > will > be deprecated in 2.4, for removal in 3.0. Accordingly, support for > ``openers.KEEP_FILE_OPEN_DEFAULT = 'auto'`` will be dropped on the same > schedule. > * Drop-in support for ``indexed_gzip < 0.7`` has been removed. > > > Enjoy, > > -- > > Chris Markiewicz > > 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 matthew.brett at gmail.com Tue Jun 12 16:00:22 2018 From: matthew.brett at gmail.com (Matthew Brett) Date: Tue, 12 Jun 2018 21:00:22 +0100 Subject: [Neuroimaging] ANN: Nibabel release 2.3 In-Reply-To: References: Message-ID: Hi Chris, On Tue, Jun 12, 2018 at 7:06 PM, Christopher Markiewicz wrote: > Hi all, > > Nibabel 2.3 has been released just in time for OHBM. It's been published to > PyPI and should be available on conda-forge within the next day. > > Features to look out for in this release are a new image slicing interface > and TRK/TCK conversion tools. There have also been a number of first-time > contributors, which is always good to see. > > As always, thanks to all contributors, reviewers and users. > > Please cite using the Zenodo DOI: https://doi.org/10.5281/zenodo.1287921 > > The full changelog follows: Thanks very much for taking on all this work, and well done for getting out the release so fast. Cheers, Matthew From bertrand.thirion at inria.fr Tue Jun 12 16:20:14 2018 From: bertrand.thirion at inria.fr (bthirion) Date: Tue, 12 Jun 2018 22:20:14 +0200 Subject: [Neuroimaging] ANN: Nibabel release 2.3 In-Reply-To: References: Message-ID: Congratulations for the release ! Bertrand On 12/06/2018 20:06, Christopher Markiewicz wrote: > Hi all, > > Nibabel 2.3 has been released just in time for OHBM. It's been > published to PyPI and should be available on conda-forge within the > next day. > > Features to look out for in this release are a new image slicing > interface and TRK/TCK conversion tools. There have also been a number > of first-time contributors, which is always good to see. > > As always, thanks to all contributors, reviewers and users. > > Please cite using the Zenodo DOI: https://doi.org/10.5281/zenodo.1287921 > > The full changelog follows: > > > New feature release for the 2.3 series. > > Most work on NiBabel so far has been by Matthew Brett (MB), Michael > Hanke (MH) > Ben Cipollini (BC), Marc-Alexandre C?t? (MC), Chris Markiewicz (CM), > Stephan > Gerhard (SG) and Eric Larson (EL). > > References like "pr/298" refer to github pull request numbers. > > New features > ------------ > * TRK <=> TCK streamlines conversion CLI tools (pr/606) (MC, reviewed > by CM) > * Image slicing for SpatialImages (pr/550) (CM) > > Enhancements > ------------ > * Simplify MGHImage and add footer fields (pr/569) (CM, reviewed by MB) > * Force sform/qform codes to be ints, rather than numpy types (pr/575) > (Paul > ? McCarthy, reviewed by MB, CM) > * Auto-fill color table in FreeSurfer annotation file (pr/592) (Paul > McCarthy, > ? reviewed by CM, MB) > * Set default intent code for CIFTI2 images (pr/604) (Mathias Goncalves, > ? reviewed by CM, Satra Ghosh, MB, Tim Coalson) > * Raise informative error on empty files (pr/611) (Pradeep Raamana, > reviewed > ? by CM, MB) > * Accept degenerate filenames such as ``.nii`` (pr/621) (Dimitri > ? Papadopoulos-Orfanos, reviewed by Yaroslav Halchenko) > * Take advantage of ``IndexedGzipFile`` ``drop_handles`` flag to release > ? filehandles by default (pr/614) (Paul McCarthy, reviewed by CM, MB) > > Bug fixes > --------- > * Preserve first point of `LazyTractogram` (pr/588) (MC, reviewed by Nil > ? Goyette, CM, MB) > * Stop adding extraneous metadata padding (pr/593) (Jon Stutters, > reviewed by > ? CM, MB) > * Accept lower-case orientation codes in TRK files (pr/600) (Kesshi > Jordan, > ? MB, reviewed by MB, MC, CM) > * Annotation file reading (pr/592) (Paul McCarthy, reviewed by CM, MB) > * Fix buffer size calculation in ArraySequence (pr/597) (Serge Koudoro, > ? reviewed by MC, MB, Eleftherios Garyfallidis, CM) > * Resolve ``UnboundLocalError`` in Python 3 (pr/607) (Jakub Kaczmarzyk, > ? reviewed by MB, CM) > * Do not crash on non-``ImportError`` failures in optional imports > (pr/618) > ? (Yaroslav Halchenko, reviewed by CM) > * Return original array from ``get_fdata`` for array image, if no cast > ? required (pr/638, MB, reviewed by CM) > > Maintenance > ----------- > * Use SSH address to use key-based auth (pr/587) (CM, reviewed by MB) > * Fix doctests for numpy 1.14 array printing (pr/591) (MB, reviewed by CM) > * Refactor for pydicom 1.0 API changes (pr/599) (MB, reviewed by CM) > * Increase test coverage, remove unreachable code (pr/602) (CM, > reviewed by > ? Yaroslav Halchenko, MB) > * Move ``nib-ls`` and other programs to a new cmdline module (pr/601, > pr/615) > ? (Chris Cheng, reviewed by MB, Yaroslav Halchenko) > * Remove deprecated numpy indexing (EL, reviewed by CM) > * Update documentation to encourage ``get_fdata`` over ``get_data`` > (pr/637, > ? MB, reviewed by CM) > > API changes and deprecations > ---------------------------- > * Support for ``keep_file_open = 'auto'`` as a parameter to > ``Opener()`` will > ? be deprecated in 2.4, for removal in 3.0. Accordingly, support for > ? ``openers.KEEP_FILE_OPEN_DEFAULT = 'auto'`` will be dropped on the same > ? schedule. > * Drop-in support for ``indexed_gzip < 0.7`` has been removed. > > > Enjoy, > > -- > > Chris Markiewicz > > 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 gael.varoquaux at normalesup.org Tue Jun 12 16:37:59 2018 From: gael.varoquaux at normalesup.org (Gael Varoquaux) Date: Tue, 12 Jun 2018 22:37:59 +0200 Subject: [Neuroimaging] ANN: Nibabel release 2.3 In-Reply-To: References: Message-ID: <20180612203759.dcgiey7d2foclmin@phare.normalesup.org> Congratulations! Thank you for keeping this crucial part of the ecosystem alive and kicking. On Tue, Jun 12, 2018 at 06:06:01PM +0000, Christopher Markiewicz wrote: > Hi all, > Nibabel 2.3 has been released just in time for OHBM. It's been published to > PyPI and should be available on conda-forge within the next day. > Features to look out for in this release are a new image slicing interface and > TRK/TCK conversion tools. There have also been a number of first-time > contributors, which is always good to see. > As always, thanks to all contributors, reviewers and users. > Please cite using the Zenodo DOI: https://doi.org/10.5281/zenodo.1287921 > The full changelog follows: > New feature release for the 2.3 series. > Most work on NiBabel so far has been by Matthew Brett (MB), Michael Hanke (MH) > Ben Cipollini (BC), Marc-Alexandre C?t? (MC), Chris Markiewicz (CM), Stephan > Gerhard (SG) and Eric Larson (EL). > References like "pr/298" refer to github pull request numbers. > New features > ------------ > * TRK <=> TCK streamlines conversion CLI tools (pr/606) (MC, reviewed by CM) > * Image slicing for SpatialImages (pr/550) (CM) > Enhancements > ------------ > * Simplify MGHImage and add footer fields (pr/569) (CM, reviewed by MB) > * Force sform/qform codes to be ints, rather than numpy types (pr/575) (Paul > McCarthy, reviewed by MB, CM) > * Auto-fill color table in FreeSurfer annotation file (pr/592) (Paul McCarthy, > reviewed by CM, MB) > * Set default intent code for CIFTI2 images (pr/604) (Mathias Goncalves, > reviewed by CM, Satra Ghosh, MB, Tim Coalson) > * Raise informative error on empty files (pr/611) (Pradeep Raamana, reviewed > by CM, MB) > * Accept degenerate filenames such as ``.nii`` (pr/621) (Dimitri > Papadopoulos-Orfanos, reviewed by Yaroslav Halchenko) > * Take advantage of ``IndexedGzipFile`` ``drop_handles`` flag to release > filehandles by default (pr/614) (Paul McCarthy, reviewed by CM, MB) > Bug fixes > --------- > * Preserve first point of `LazyTractogram` (pr/588) (MC, reviewed by Nil > Goyette, CM, MB) > * Stop adding extraneous metadata padding (pr/593) (Jon Stutters, reviewed by > CM, MB) > * Accept lower-case orientation codes in TRK files (pr/600) (Kesshi Jordan, > MB, reviewed by MB, MC, CM) > * Annotation file reading (pr/592) (Paul McCarthy, reviewed by CM, MB) > * Fix buffer size calculation in ArraySequence (pr/597) (Serge Koudoro, > reviewed by MC, MB, Eleftherios Garyfallidis, CM) > * Resolve ``UnboundLocalError`` in Python 3 (pr/607) (Jakub Kaczmarzyk, > reviewed by MB, CM) > * Do not crash on non-``ImportError`` failures in optional imports (pr/618) > (Yaroslav Halchenko, reviewed by CM) > * Return original array from ``get_fdata`` for array image, if no cast > required (pr/638, MB, reviewed by CM) > Maintenance > ----------- > * Use SSH address to use key-based auth (pr/587) (CM, reviewed by MB) > * Fix doctests for numpy 1.14 array printing (pr/591) (MB, reviewed by CM) > * Refactor for pydicom 1.0 API changes (pr/599) (MB, reviewed by CM) > * Increase test coverage, remove unreachable code (pr/602) (CM, reviewed by > Yaroslav Halchenko, MB) > * Move ``nib-ls`` and other programs to a new cmdline module (pr/601, pr/615) > (Chris Cheng, reviewed by MB, Yaroslav Halchenko) > * Remove deprecated numpy indexing (EL, reviewed by CM) > * Update documentation to encourage ``get_fdata`` over ``get_data`` (pr/637, > MB, reviewed by CM) > API changes and deprecations > ---------------------------- > * Support for ``keep_file_open = 'auto'`` as a parameter to ``Opener()`` will > be deprecated in 2.4, for removal in 3.0. Accordingly, support for > ``openers.KEEP_FILE_OPEN_DEFAULT = 'auto'`` will be dropped on the same > schedule. > * Drop-in support for ``indexed_gzip < 0.7`` has been removed. > Enjoy, -- Gael Varoquaux Senior Researcher, INRIA Parietal NeuroSpin/CEA Saclay , Bat 145, 91191 Gif-sur-Yvette France Phone: ++ 33-1-69-08-79-68 http://gael-varoquaux.info http://twitter.com/GaelVaroquaux From pauldmccarthy at gmail.com Tue Jun 12 17:28:41 2018 From: pauldmccarthy at gmail.com (paul mccarthy) Date: Tue, 12 Jun 2018 22:28:41 +0100 Subject: [Neuroimaging] ANN: Nibabel release 2.3 In-Reply-To: <20180612203759.dcgiey7d2foclmin@phare.normalesup.org> References: <20180612203759.dcgiey7d2foclmin@phare.normalesup.org> Message-ID: Thanks for all the hard work Chris! Paul On 12 June 2018 at 21:37, Gael Varoquaux wrote: > Congratulations! Thank you for keeping this crucial part of the ecosystem > alive and kicking. > > On Tue, Jun 12, 2018 at 06:06:01PM +0000, Christopher Markiewicz wrote: > > Hi all, > > > Nibabel 2.3 has been released just in time for OHBM. It's been published > to > > PyPI and should be available on conda-forge within the next day. > > > Features to look out for in this release are a new image slicing > interface and > > TRK/TCK conversion tools. There have also been a number of first-time > > contributors, which is always good to see. > > > As always, thanks to all contributors, reviewers and users. > > > Please cite using the Zenodo DOI: https://doi.org/10.5281/ > zenodo.1287921 > > > The full changelog follows: > > > > New feature release for the 2.3 series. > > > Most work on NiBabel so far has been by Matthew Brett (MB), Michael > Hanke (MH) > > Ben Cipollini (BC), Marc-Alexandre C?t? (MC), Chris Markiewicz (CM), > Stephan > > Gerhard (SG) and Eric Larson (EL). > > > References like "pr/298" refer to github pull request numbers. > > > New features > > ------------ > > * TRK <=> TCK streamlines conversion CLI tools (pr/606) (MC, reviewed by > CM) > > * Image slicing for SpatialImages (pr/550) (CM) > > > Enhancements > > ------------ > > * Simplify MGHImage and add footer fields (pr/569) (CM, reviewed by MB) > > * Force sform/qform codes to be ints, rather than numpy types (pr/575) > (Paul > > McCarthy, reviewed by MB, CM) > > * Auto-fill color table in FreeSurfer annotation file (pr/592) (Paul > McCarthy, > > reviewed by CM, MB) > > * Set default intent code for CIFTI2 images (pr/604) (Mathias Goncalves, > > reviewed by CM, Satra Ghosh, MB, Tim Coalson) > > * Raise informative error on empty files (pr/611) (Pradeep Raamana, > reviewed > > by CM, MB) > > * Accept degenerate filenames such as ``.nii`` (pr/621) (Dimitri > > Papadopoulos-Orfanos, reviewed by Yaroslav Halchenko) > > * Take advantage of ``IndexedGzipFile`` ``drop_handles`` flag to release > > filehandles by default (pr/614) (Paul McCarthy, reviewed by CM, MB) > > > Bug fixes > > --------- > > * Preserve first point of `LazyTractogram` (pr/588) (MC, reviewed by Nil > > Goyette, CM, MB) > > * Stop adding extraneous metadata padding (pr/593) (Jon Stutters, > reviewed by > > CM, MB) > > * Accept lower-case orientation codes in TRK files (pr/600) (Kesshi > Jordan, > > MB, reviewed by MB, MC, CM) > > * Annotation file reading (pr/592) (Paul McCarthy, reviewed by CM, MB) > > * Fix buffer size calculation in ArraySequence (pr/597) (Serge Koudoro, > > reviewed by MC, MB, Eleftherios Garyfallidis, CM) > > * Resolve ``UnboundLocalError`` in Python 3 (pr/607) (Jakub Kaczmarzyk, > > reviewed by MB, CM) > > * Do not crash on non-``ImportError`` failures in optional imports > (pr/618) > > (Yaroslav Halchenko, reviewed by CM) > > * Return original array from ``get_fdata`` for array image, if no cast > > required (pr/638, MB, reviewed by CM) > > > Maintenance > > ----------- > > * Use SSH address to use key-based auth (pr/587) (CM, reviewed by MB) > > * Fix doctests for numpy 1.14 array printing (pr/591) (MB, reviewed by > CM) > > * Refactor for pydicom 1.0 API changes (pr/599) (MB, reviewed by CM) > > * Increase test coverage, remove unreachable code (pr/602) (CM, reviewed > by > > Yaroslav Halchenko, MB) > > * Move ``nib-ls`` and other programs to a new cmdline module (pr/601, > pr/615) > > (Chris Cheng, reviewed by MB, Yaroslav Halchenko) > > * Remove deprecated numpy indexing (EL, reviewed by CM) > > * Update documentation to encourage ``get_fdata`` over ``get_data`` > (pr/637, > > MB, reviewed by CM) > > > API changes and deprecations > > ---------------------------- > > * Support for ``keep_file_open = 'auto'`` as a parameter to ``Opener()`` > will > > be deprecated in 2.4, for removal in 3.0. Accordingly, support for > > ``openers.KEEP_FILE_OPEN_DEFAULT = 'auto'`` will be dropped on the > same > > schedule. > > * Drop-in support for ``indexed_gzip < 0.7`` has been removed. > > > > > Enjoy, > -- > Gael Varoquaux > Senior Researcher, INRIA Parietal > NeuroSpin/CEA Saclay , Bat 145, 91191 Gif-sur-Yvette France > Phone: ++ 33-1-69-08-79-68 > http://gael-varoquaux.info http://twitter.com/GaelVaroquaux > _______________________________________________ > 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 Jun 12 20:28:42 2018 From: satra at mit.edu (Satrajit Ghosh) Date: Wed, 13 Jun 2018 05:58:42 +0530 Subject: [Neuroimaging] ANN: Nibabel release 2.3 In-Reply-To: References: Message-ID: thanks chris for pushing this through! cheers, satra On Wed, Jun 13, 2018 at 12:06 AM Christopher Markiewicz < markiewicz at stanford.edu> wrote: > Hi all, > > Nibabel 2.3 has been released just in time for OHBM. It's been published > to PyPI and should be available on conda-forge within the next day. > > Features to look out for in this release are a new image slicing interface > and TRK/TCK conversion tools. There have also been a number of first-time > contributors, which is always good to see. > > As always, thanks to all contributors, reviewers and users. > > Please cite using the Zenodo DOI: > > https://doi.org/10.5281/zenodo.1287921 > > The full changelog follows: > > > New feature release for the 2.3 series. > > Most work on NiBabel so far has been by Matthew Brett (MB), Michael Hanke > (MH) > Ben Cipollini (BC), Marc-Alexandre C?t? (MC), Chris Markiewicz (CM), > Stephan > Gerhard (SG) and Eric Larson (EL). > > References like "pr/298" refer to github pull request numbers. > > New features > ------------ > * TRK <=> TCK streamlines conversion CLI tools (pr/606) (MC, reviewed by > CM) > * Image slicing for SpatialImages (pr/550) (CM) > > Enhancements > ------------ > * Simplify MGHImage and add footer fields (pr/569) (CM, reviewed by MB) > * Force sform/qform codes to be ints, rather than numpy types (pr/575) > (Paul > McCarthy, reviewed by MB, CM) > * Auto-fill color table in FreeSurfer annotation file (pr/592) (Paul > McCarthy, > reviewed by CM, MB) > * Set default intent code for CIFTI2 images (pr/604) (Mathias Goncalves, > reviewed by CM, Satra Ghosh, MB, Tim Coalson) > * Raise informative error on empty files (pr/611) (Pradeep Raamana, > reviewed > by CM, MB) > * Accept degenerate filenames such as ``.nii`` (pr/621) (Dimitri > Papadopoulos-Orfanos, reviewed by Yaroslav Halchenko) > * Take advantage of ``IndexedGzipFile`` ``drop_handles`` flag to release > filehandles by default (pr/614) (Paul McCarthy, reviewed by CM, MB) > > Bug fixes > --------- > * Preserve first point of `LazyTractogram` (pr/588) (MC, reviewed by Nil > Goyette, CM, MB) > * Stop adding extraneous metadata padding (pr/593) (Jon Stutters, reviewed > by > CM, MB) > * Accept lower-case orientation codes in TRK files (pr/600) (Kesshi Jordan, > MB, reviewed by MB, MC, CM) > * Annotation file reading (pr/592) (Paul McCarthy, reviewed by CM, MB) > * Fix buffer size calculation in ArraySequence (pr/597) (Serge Koudoro, > reviewed by MC, MB, Eleftherios Garyfallidis, CM) > * Resolve ``UnboundLocalError`` in Python 3 (pr/607) (Jakub Kaczmarzyk, > reviewed by MB, CM) > * Do not crash on non-``ImportError`` failures in optional imports (pr/618) > (Yaroslav Halchenko, reviewed by CM) > * Return original array from ``get_fdata`` for array image, if no cast > required (pr/638, MB, reviewed by CM) > > Maintenance > ----------- > * Use SSH address to use key-based auth (pr/587) (CM, reviewed by MB) > * Fix doctests for numpy 1.14 array printing (pr/591) (MB, reviewed by CM) > * Refactor for pydicom 1.0 API changes (pr/599) (MB, reviewed by CM) > * Increase test coverage, remove unreachable code (pr/602) (CM, reviewed > by > Yaroslav Halchenko, MB) > * Move ``nib-ls`` and other programs to a new cmdline module (pr/601, > pr/615) > (Chris Cheng, reviewed by MB, Yaroslav Halchenko) > * Remove deprecated numpy indexing (EL, reviewed by CM) > * Update documentation to encourage ``get_fdata`` over ``get_data`` > (pr/637, > MB, reviewed by CM) > > API changes and deprecations > ---------------------------- > * Support for ``keep_file_open = 'auto'`` as a parameter to ``Opener()`` > will > be deprecated in 2.4, for removal in 3.0. Accordingly, support for > ``openers.KEEP_FILE_OPEN_DEFAULT = 'auto'`` will be dropped on the same > schedule. > * Drop-in support for ``indexed_gzip < 0.7`` has been removed. > > > Enjoy, > > -- > > Chris Markiewicz > > 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 arnaud.bore at gmail.com Wed Jun 13 15:55:17 2018 From: arnaud.bore at gmail.com (=?UTF-8?B?QXJuYXVkIEJvcsOp?=) Date: Wed, 13 Jun 2018 15:55:17 -0400 Subject: [Neuroimaging] Postdoctoral Fellowship in Spinal Cord and Parkinson's Disease Message-ID: *Postdoctoral Fellowship in Spinal Cord and Parkinson's Disease* We are looking to recruit a post-doctoral fellow in Dr. Julien Doyon?s *Motor Learning and Plasticity Laboratory*, at McGill University. The suitable candidate will join a team of post-doctoral fellows and PhD students who are conducting neuroimaging research in motor learning, both fundamental and clinical. For the current job opening, we seek to recruit a post-doctoral fellow who will *conduct neuroimaging and behavioral studies on healthy individuals and Parkinson?s Disease (PD) patients*. These studies are part of a research program aiming to characterize motor learning related plasticity in both brain and spinal cord, as well as to identify neuronal correlates of early stages of PD at both spinal and supra-spinal levels. The position is based at the Montreal Neurological Institute (MNI). The ideal candidate is expected to take the lead in regards to the methodological aspects of the study, addressing specifically the challenges related to the functional neuroimaging of the spinal cord, and to the analysis of complex data sets. The fellow will be involved in all stages of the research projects, from experimental design to data analysis and manuscript writing. The following requirements are mandatory: - PhD degree in neuroscience or a related field; - Experience with functional neuroimaging in human participants and with neuroimaging data analysis techniques and software (i.e. SPM, FSL or similar); - Ability to work independently and to collaborate with other team members; - Excellent organizational and social skills, especially when dealing with patient participants; - Established publication record attesting the above-mentioned requirements; - Good English proficiency (especially scientific writing and oral communication). The following requirements are assets: - Experience with spinal cord imaging; - Experience with multivariate data analysis approaches as implemented in established neuroimaging data analysis software; - Good proficiency with programming (such as Python or Matlab); - French proficiency; - Research experience with PD patients (or other movement-related disorders); - Availability to start as soon as possible. If you are interested in this position, please send your CV, a cover letter and the contact information of two individuals who can provide references at the following e-mail address: *francine.belanger at mcgill.ca * -------------- next part -------------- An HTML attachment was scrubbed... URL: From elef at indiana.edu Fri Jun 15 16:55:54 2018 From: elef at indiana.edu (Eleftherios Garyfallidis) Date: Fri, 15 Jun 2018 22:55:54 +0200 Subject: [Neuroimaging] DIPY developers and users meetings at ISMRM 2018, Paris Message-ID: Hello all, Serge, Ariel, Rafael, Mic, Mauro, Max, Gab, ...., and many other DIPY contributors are this year in ISMRM in Paris! Tomorrow Saturday will have a short lunch meeting near the conference center. Send me a quick email if you want to join. Then we plan to organize some drinks during the conference. Monday night seems reasonable right now. Let me know if you have other suggestions for a day or if you have suggestions for a nice bar. Will be really happy to see you all! :) Cheers, Eleftherios -------------- next part -------------- An HTML attachment was scrubbed... URL: From jbpoline at gmail.com Sun Jun 17 13:07:52 2018 From: jbpoline at gmail.com (JB Poline) Date: Mon, 18 Jun 2018 01:07:52 +0800 Subject: [Neuroimaging] Developers and Post-Doc positions at the MNI Message-ID: The Montreal Neurological Institute (MNI) is working to become the first institution to develop and implement an institutional open science framework with the Tanenbaum Open Science Initiative. We hope open science will help trigger a paradigm shift in how we do science in academia. Over time, the MNI has developed platforms for data dissemination, pipeline executions (cf the MNI atlases, the LORIS and CBRAIN projects), becoming a vibrant neuroimaging community. Recently, the Canadian Open Neuroscience Platform and NeuroHub -the neuroinformatics platform for the Healthy Brains for Healthy Lives program at McGill- are two large initiatives aiming at building the next generation of research platforms. The MNI is looking for post-doctoral fellows and developers who are interested in neuroinformatics and/or running neuroimaging and neuroscience data analyses to develop reproducible and collaborative data management and processing platforms, leveraging projects such as DataLad and ReproNim. If you know either neuroimaging, genomics, or know scientific computing or databasing, and like to develop in python, or javascript, etc, and if you are interested in constructing a platform to make science more reproducible, interoperable, efficient, open, reusable, please contact us. We are a vibrant, diverse, innovative and welcoming scientific community and wish to make progress in the understanding, diagnosis or treatment of brain diseases. You can send expression of interest and CV to jbpoline at gmail.com and samirdas99 at gmail.com, we are at OHBM in Singapore and would be happy to meet with you there or in Montreal. -------------- next part -------------- An HTML attachment was scrubbed... URL: From tracygilliam5 at gmail.com Mon Jun 18 15:04:12 2018 From: tracygilliam5 at gmail.com (tracy gilliam) Date: Mon, 18 Jun 2018 14:04:12 -0500 Subject: [Neuroimaging] Call for Expressions of Interest on Collaborative Research Message-ID: Our start up The Neurographics Group is applying for America's Seed Fund (a.k.a., the National Science Foundation Small Business Innovation Research program). We are seeking assistance from the neuroscience community on collaborative research for our proof-of-concept. As a potential benefit corporation, we segment markets by cognitive identities while partitioning citizen science research/open data for the study of the collective neural signature. See more information on our vision at Linkedin: https://www.linkedin.com/in/tracy-gilliam-mba-1ba4789a/ Please contact me if you have interests in consumer neuroscience, social consumerism, and data philanthropy. Thank you in advance! Tracy Gilliam The Neurographics Group TracyGilliam5 at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From AiWern.Chung at childrens.harvard.edu Fri Jun 29 04:19:44 2018 From: AiWern.Chung at childrens.harvard.edu (Chung, Ai Wern) Date: Fri, 29 Jun 2018 08:19:44 +0000 Subject: [Neuroimaging] Call for late-breaking abstracts - MICCAI 2018 Connectomics in NeuroImaging Workshop In-Reply-To: <1528731433339.33564@childrens.harvard.edu> References: <1525146658594.86048@childrens.harvard.edu>, <1525184505400.41354@childrens.harvard.edu>, <1528731433339.33564@childrens.harvard.edu> Message-ID: <1530260387260.78778@childrens.harvard.edu> << Apologies for cross-posting >> Dear all, Do you have late-breaking research in connectomics you want to share with the MICCAI community? Our full paper submission deadline may have passed but there's still time to submit your work and participate in the 2nd workshop on Connectomics in NeuroImaging (CNI 2018) at the International Conference on Medical Image Computing and Computer-assisted Intervention (MICCAI 2018) in Granada, Spain! CNI is now accepting single-page abstracts for poster and power-pitch presentations! Please see our website for further information: http://munsellb.people.cofc.edu/cni.html CNI 2018 is a full day workshop that will take place on September 20th, 2018. Our topics of interest cover all things connectomic, including: (1) New developments in connectome construction from different imaging modalities; (2) Development of data driven techniques to identify biomarkers; (3) Brain network modeling and formal conceptual models of connectome data; (4) Machine learning algorithms and connectome data analysis; (5) Evaluation and validation of connectome models. ** Why submit an abstract to the CNI workshop? ** - Three great keynote speakers, presentations and poster sessions with accompanying power pitches for notable submissions will provide you with ample opportunity for exchanges and discussions with international computational neuroscientists and clinicians; - Accepted abstracts, and their posters, will be published in ArXiv as a special abstract proceeding; - There will be a Best Poster Award. ** Single-page abstract submission - important dates ** Submissions are via https://cmt3.research.microsoft.com/CNI2018 Abstract submission deadline: 11:59 PM PST, July 16th, 2018 Notification of acceptance: Aug 8th, 2018 Workshop date: Sept 20th, 2018 For submission guidelines visit http://munsellb.people.cofc.edu/cnisub.html We look forward to your participation! If you have any additional questions, feel free to contact Ai Chung (aiwern.chung at childrens.harvard.edu) or Brent Munsell (munsellb at cofc.edu) ============================= CNI 2018 Chairs ----------------------------- Ai Wern Chung, Boston Children's Hospital, Harvard Medical School Islem Rekik, University of Dundee Markus Schirmer, Massachusetts General Hospital, Harvard Medical School Guorong Wu, University of North Carolina, Chapel Hill Brent Munsell, College of Charleston -------------- next part -------------- An HTML attachment was scrubbed... URL: