10.5281/zenodo.6658382
https://zenodo.org/records/6658382
oai:zenodo.org:6658382
Brett, Matthew
Matthew
Brett
0000-0001-5500-2546
School of Psychology, University of Birmingham, Birmingham, UK
Markiewicz, Christopher J.
Christopher J.
Markiewicz
0000-0002-6533-164X
Stanford University
Hanke, Michael
Michael
Hanke
0000-0001-6398-6370
Otto-von-Guericke-University Magdeburg, Germany
Côté, Marc-Alexandre
Marc-Alexandre
Côté
0000-0002-5147-7859
Microsoft Research, Montréal, Québec, Canada
Cipollini, Ben
Ben
Cipollini
0000-0002-7782-0790
UC San Diego
McCarthy, Paul
Paul
McCarthy
Jarecka, Dorota
Dorota
Jarecka
0000-0001-8282-2988
MIT
Cheng, Christopher P.
Christopher P.
Cheng
0000-0001-9112-9464
Center for Open Neuroscience, Dartmouth College
Halchenko, Yaroslav O.
Yaroslav O.
Halchenko
0000-0003-3456-2493
Dartmouth College: Hanover, NH, United States
Cottaar, Michiel
Michiel
Cottaar
0000-0003-4679-7724
Wellcome Centre for Integrative Neuroimaging, University of Oxford, UK
Larson, Eric
Eric
Larson
0000-0003-4782-5360
University of Washington: Seattle, WA, United States
Ghosh, Satrajit
Satrajit
Ghosh
0000-0002-5312-6729
MIT, HMS
Wassermann, Demian
Demian
Wassermann
0000-0001-5194-6056
Athena EPI, Inria Sophia-Antipolis
Gerhard, Stephan
Stephan
Gerhard
0000-0003-4454-6171
Institute of Neuroinformatics, ETH/University of Zurich
Lee, Gregory R.
Gregory R.
Lee
0000-0001-8895-2740
Deptartment of Radiology, University of Cincinnati College of Medicine, Cincinnati, OH
Wang, Hao-Ting
Hao-Ting
Wang
0000-0003-4078-2038
Kastman, Erik
Erik
Kastman
0000-0001-7221-9042
Harvard University - Psychology
Kaczmarzyk, Jakub
Jakub
Kaczmarzyk
0000-0002-5544-7577
MIT
Guidotti, Roberto
Roberto
Guidotti
0000-0002-0807-6005
Department of Computer Science, Aalto University, Espoo, Finland and Department of Neuroscience, Imaging and Clinical Sciences, University G. D'Annunzio, Chieti, Italy
Daniel, Jonathan
Jonathan
Daniel
Duek, Or
Or
Duek
Rokem, Ariel
Ariel
Rokem
0000-0003-0679-1985
The University of Washington eScience Institute
Madison, Cindee
Cindee
Madison
Moloney, Brendan
Brendan
Moloney
Morency, Félix C.
Félix C.
Morency
Goncalves, Mathias
Mathias
Goncalves
0000-0002-7252-7771
MIT
Markello, Ross
Ross
Markello
0000-0003-1057-1336
Montreal Neurological Institute and Hospital
Riddell, Cameron
Cameron
Riddell
0000-0001-8950-0375
Department of Psychology, University of California Davis, CA, USA
Sólon, Anibal
Anibal
Sólon
Burns, Christopher
Christopher
Burns
Millman, Jarrod
Jarrod
Millman
0000-0002-5263-5070
Berkeley Institute for Data Science, UC Berkeley
Gramfort, Alexandre
Alexandre
Gramfort
0000-0001-9791-4404
CNRS LTCI, Telecom ParisTech, Université Paris-Saclay
Leppäkangas, Jaakko
Jaakko
Leppäkangas
van den Bosch, Jasper J.F.
Jasper J.F.
van den Bosch
Vincent, Robert D.
Robert D.
Vincent
Braun, Henry
Henry
Braun
0000-0001-7003-9822
Center for Magnetic Resonance Research, University of Minnesota
Subramaniam, Krish
Krish
Subramaniam
Papadopoulos Orfanos, Dimitri
Dimitri
Papadopoulos Orfanos
0000-0002-1242-8990
CEA
Van, Andrew
Andrew
Van
Gorgolewski, Krzysztof J.
Krzysztof J.
Gorgolewski
0000-0003-3321-7583
Google
Raamana, Pradeep Reddy
Pradeep Reddy
Raamana
0000-0003-4662-0558
Rotman Research Institute, Baycrest Health Sciences, Toronto, ON, Canada
Klug, Julian
Julian
Klug
0000-0002-4849-9811
University of Geneva, Switzerland
Nichols, B. Nolan
B. Nolan
Nichols
0000-0003-1099-3328
SRI International
Baker, Eric M.
Eric M.
Baker
Hayashi, Soichi
Soichi
Hayashi
Pinsard, Basile
Basile
Pinsard
Haselgrove, Christian
Christian
Haselgrove
Hymers, Mark
Mark
Hymers
Esteban, Oscar
Oscar
Esteban
0000-0001-8435-6191
Department of Psychology, Stanford University, CA, USA
Koudoro, Serge
Serge
Koudoro
Pérez-García, Fernando
Fernando
Pérez-García
0000-0001-9090-3024
University College London
Dockès, Jérôme
Jérôme
Dockès
Oosterhof, Nikolaas N.
Nikolaas N.
Oosterhof
Amirbekian, Bago
Bago
Amirbekian
Nimmo-Smith, Ian
Ian
Nimmo-Smith
Nguyen, Ly
Ly
Nguyen
Reddigari, Samir
Samir
Reddigari
0000-0003-1472-5881
BrainSpec, Boston, MA
St-Jean, Samuel
Samuel
St-Jean
Panfilov, Egor
Egor
Panfilov
0000-0002-2500-6375
Garyfallidis, Eleftherios
Eleftherios
Garyfallidis
Varoquaux, Gael
Gael
Varoquaux
0000-0003-1076-5122
INRIA
Legarreta, Jon Haitz
Jon Haitz
Legarreta
0000-0002-9661-1396
Université de Sherbrooke
Hahn, Kevin S.
Kevin S.
Hahn
Waller, Lea
Lea
Waller
0000-0002-3239-6957
Charite Universitatsmedizin Berlin, Germany
Hinds, Oliver P.
Oliver P.
Hinds
Fauber, Bennet
Bennet
Fauber
Roberts, Jacob
Jacob
Roberts
Poline, Jean-Baptiste
Jean-Baptiste
Poline
0000-0002-9794-749X
McGill University
Stutters, Jon
Jon
Stutters
0000-0002-9151-0844
University College London, London, UK
Jordan, Kesshi
Kesshi
Jordan
0000-0001-6313-0580
University of California, San Francisco
Cieslak, Matthew
Matthew
Cieslak
0000-0002-1931-4734
Department of Neuropsychiatry, University of Pennsylvania
Moreno, Miguel Estevan
Miguel Estevan
Moreno
Hrnčiar, Tomáš
Tomáš
Hrnčiar
Haenel, Valentin
Valentin
Haenel
Schwartz, Yannick
Yannick
Schwartz
Baratz, Zvi
Zvi
Baratz
Darwin, Benjamin C
Benjamin C
Darwin
Hospital for Sick Children
Thirion, Bertrand
Bertrand
Thirion
0000-0001-5018-7895
INRIA
Gauthier, Carl
Carl
Gauthier
Solovey, Igor
Igor
Solovey
Gonzalez, Ivan
Ivan
Gonzalez
0000-0002-6451-6909
Athinoula A. Martinos Center for Biomedical Imaging, Charlestown, MA
Palasubramaniam, Jath
Jath
Palasubramaniam
Lecher, Justin
Justin
Lecher
Leinweber, Katrin
Katrin
Leinweber
0000-0001-5135-5758
TIB – Leibniz Information Centre for Science and Technology and University Library, Hannover, Germany
Raktivan, Konstantinos
Konstantinos
Raktivan
National Technical University of Athens, Greece
Calábková, Markéta
Markéta
Calábková
Fischer, Peter
Peter
Fischer
0000-0003-3242-9867
Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
Gervais, Philippe
Philippe
Gervais
Gadde, Syam
Syam
Gadde
Ballinger, Thomas
Thomas
Ballinger
Roos, Thomas
Thomas
Roos
Reddam, Venkateswara Reddy
Venkateswara Reddy
Reddam
0000-0001-6817-2966
National Institute of Mental Health and Neuro-Sciences, India
freec84
freec84
nipy/nibabel:
Zenodo
2022
neuroimaging
2022-06-17
https://github.com/nipy/nibabel/tree/4.0.0
10.5281/zenodo.591597
4.0.0
MIT License
Most work on NiBabel so far has been by Matthew Brett (MB), Chris Markiewicz
(CM), Michael Hanke (MH), Marc-Alexandre Côté (MC), Ben Cipollini (BC), Paul
McCarthy (PM), Chris Cheng (CC), Yaroslav Halchenko (YOH), Satra Ghosh (SG),
Eric Larson (EL), Demian Wassermann, Stephan Gerhard and Ross Markello (RM).
References like "pr/298" refer to github pull request numbers.
4.0.0 (Saturday 18 June 2022)
New feature release in the 4.0.x series.
New features
Add 'mask', 'compat' and 'smallest' dtype aliases to NIfTI images
to allow for dtype specifications that can depend on the contents of the data.
'mask' is a synonym for uint8. 'compat' will find the nearest
Analyze-compatible (therefore widely supported) dtype that will not truncate
the data. 'smallest' attempts to find the smallest integer dtype that will
contain the data. (pr/1096) (CM, reviewed by Chris Rorden and Josh Teves)
Add dtype arguments to Cifti2Image (pr/1111) (CM)
Allow dtypes to be passed to Analyze-like images at __init__() and
to_filename() to provide better control over output images. (pr/1082)
(CM, following discussions with Chris Rorden, Josh Teves, Jerome Dockes, and MB)
Allow compressed GIFTI images (MB, reviewed by CM)
Add zstd compression support (pr/1005) (Andrew Van, reviewed by CM)
Support ExternalFileBinary GIFTI data arrays (PM, reviewed by CM)
Enhancements
Document InTemporaryDirectory as non-thread-safe (pr/1103) (Jacob Roberts,
reviewed by MB)
Unify Caret-XML-style metadata structure (GiftiMetaData, Cifti2MetaData)
as dict-like (pr/1091) (CM, reviewed by Josh Teves and Hao-Ting Wang)
Add __repr__ methods to GIFTI objects (pr/1092) (CM,
reviewed by Josh Teves and Hao-Ting Wang)
Create gzip header deterministically by default (pr/1024) (CM, reviewed by YOH)
Provide clear error message when files with zip extensions don't match
file contents (pr/1013) (Jérôme Dockès, reviewed by CM)
Bug fixes
Re-import externals/netcdf.py from scipy to resolve numpy API change (pr/1110)
(CM)
Resize ArraySequence.data without helper function to avoid reference increment
(pr/1093) (MC, reviewed by CM)
Maintenance
Update submodule URLs to use https over git protocol (pr/1097) (CM)
Published BIAP 9: CoordinateImage API (pr/1084) (CM)
Drop uses of deprecated distutils (pr/1073) (CM, reviewed by MB)
Suppress LGTM false alarm "Clear-text logging of sensitive information"
(pr/1052) (Dimitri Papadopoulos, reviewed by CM)
Test on Python 3.10 (pr/1047) (CM)
Fix typos found by codespell (pr/1040, pr/1044)
(Dimitri Papadopoulos, reviewed by CM)
Run stable tests weekly, pre-release tests nightly (pr/1025) (CM)
Documentation updates to establish/clarify governance and decision
making (pr/1019, pr/1020, pr/1022, pr/1018, pr/1017, pr/1016) (MB and CM)
API changes and deprecations
Writing NIfTIs with 64-bit integer dtypes is getting harder.
Passing (u)int64 arrays to Nifti1Image and subclasses will warn unless
a header or dtype option is passed; in the future this will become an
error.
Additionally, passing int or 'int' to set_data_dtype() now raises
an error, requiring an explicit numpy dtype to make 64-bit integer images.
(pr/1082) (CM, following discussions with Chris Rorden, Josh Teves, Jerome Dockes,
and MB)
Drop support for Python 3.6, Numpy < 1.17 (pr/1079) (CM)
Fully removed the following APIs, which have raised errors on use
since 3.0 (pr/980) (CM, reviewed by Jonathan Daniel)
nibabel.trackvis
nibabel.volumeutils.calculate_scale
nibabel.volumeutils.can_cast
nibabel.volumeutils.scale_min_max
nibabel.dataobj_images.DataobjImage.get_shape
nibabel.minc1.MincImage (use Minc1Image)
nibabel.minc1.MincFile (use Minc1File)
nibabel.filebasedimages.FileBasedImage.from_files
nibabel.filebasedimages.FileBasedImage.filespec_to_files
nibabel.filebasedimages.FileBasedImage.to_filespec
nibabel.filebasedimages.FileBasedImage.to_files
nibabel.arrayproxy.ArrayProxy.header
keep_file_open=="auto" parameter to load method (now must be boolean)