[Neuroimaging] ANN: NiBabel 5.0

[Christopher Markiewicz]

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 <neuroimaging-bounces+markiewicz=stanford.edu at python.org> on behalf of JB Poline <jbpoline at gmail.com>
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 <bertrand.thirion at inria.fr<mailto:bertrand.thirion at inria.fr>> wrote:
Congrats indeed !

Bertrand Thirion
Head of science (délégué 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" <z.baratz at gmail.com<mailto:z.baratz at gmail.com>>
To: "Neuroimaging analysis in Python" <neuroimaging at python.org<mailto:neuroimaging at python.org>>
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<mailto: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>.

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
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