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12 changes: 12 additions & 0 deletions .mailmap
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Oscar Esteban <[email protected]>
Christopher J. Markiewicz <[email protected]>
Christopher J. Markiewicz <[email protected]> <[email protected]>
Mathias Goncalves <[email protected]>
Mathias Goncalves <[email protected]> <[email protected]>
Mathias Goncalves <[email protected]> <[email protected]>
Julien Marabotto <[email protected]>
Julien Marabotto <[email protected]> <[email protected]>
Julien Marabotto <[email protected]> <[email protected]>
Stefano Moia <[email protected]>
Basile Pinsard <[email protected]>
Jaume Banús <[email protected]>
50 changes: 0 additions & 50 deletions .zenodo.json

This file was deleted.

100 changes: 100 additions & 0 deletions CITATION.cff
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cff-version: 1.2.0
title: "NiTransforms: A Python tool to read, represent, manipulate, and apply N-dimensional spatial transforms"
license: MIT
type: software
url: https://github.com/nipy/nitransforms/
version: 24.1.1
date-released: 2024-12-18
abstract: |
Spatial transforms formalize mappings between coordinates of objects in biomedical images.
Transforms typically are the outcome of image registration methodologies, which estimate
the alignment between two images.
Image registration is a prominent task present in nearly all standard image processing
and analysis pipelines.
The proliferation of software implementations of image registration methodologies has
resulted in a spread of data structures and file formats used to preserve and communicate
transforms.
This segregation of formats precludes the compatibility between tools and endangers the
reproducibility of results.
We propose a software tool capable of converting between formats and resampling images
to apply transforms generated by the most popular neuroimaging packages and libraries
(AFNI, FSL, FreeSurfer, ITK, and SPM).
The proposed software is subject to continuous integration tests to check the
compatibility with each supported tool after every change to the code base.
Compatibility between software tools and imaging formats is a necessary bridge
to ensure the reproducibility of results and enable the optimization and evaluation
of current image processing and analysis workflows.
keywords:
- neuroimaging
- spatial normalization

authors:
- family-names: Goncalves
given-names: Mathias
orcid: https://orcid.org/0000-0002-7252-7771
affiliation: "Department of Psychology, Stanford University, Stanford, CA, USA"
- family-names: Markiewicz
given-names: Christopher J.
orcid: https://orcid.org/0000-0002-6533-164X
affiliation: "Department of Psychology, Stanford University, Stanford, CA, USA"
- family-names: Moia
given-names: Stefano
orcid: https://orcid.org/0000-0002-2553-3327
affiliation: "Basque Center on Cognition Brain and Language, San Sebastian, Spain"
- family-names: Waller
given-names: Lea
orcid: https://orcid.org/0000-0002-3239-6957
affiliation: Charite Universitatsmedizin Berlin, Germany
- family-names: Pinsard
given-names: Basile
orcid: https://orcid.org/0000-0002-4391-3075
affiliation: University of Montréal, Montréal, Canada
- family-names: Banús
given-names: Jaume
orcid: https://orcid.org/0000-0001-9318-6323
- family-names: Visconti di Oleggio Castello
given-names: Matteo
orcid: https://orcid.org/0000-0001-7931-5272
affiliation: University of California Berkeley, Berkeley, CA, USA
- family-names: Marabotto
given-names: Julien
orcid: https://orcid.org/0009-0003-7070-5217
affiliation: Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
- family-names: Ma
given-names: Feilong
orcid: https://orcid.org/0000-0002-6838-3971
affiliation: Dartmouth College, Hanover, NH, United States
- family-names: Nielson
given-names: Dylan
orcid: https://orcid.org/0000-0003-4613-6643
affiliation: Machine Learning Team, National Institute of Mental Health, USA
- family-names: Cluce
given-names: Jon
orcid: https://orcid.org/0000-0001-7590-5806
affiliation: Child Mind Institute, New York, NY, USA
- family-names: Shain
given-names: Cory
orcid: https://orcid.org/0000-0002-2704-7197
affiliation: Stanford University, Stanford, CA, USA
## When contributing, please copy and uncomment the following lines
# - family-names:
# given-names:
# orcid: https://orcid.org/
# affiliation:
- family-names: Ghosh
given-names: Satrajit
orcid: https://orcid.org/0000-0002-5312-6729
affiliation: "McGovern Institute for Brain Research, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA; and Department of Otolaryngology, Harvard Medical School, Boston, MA, USA"
- family-names: Poldrack
given-names: Russell A.
orcid: https://orcid.org/0000-0001-6755-0259
affiliation: "Department of Psychology, Stanford University, Stanford, CA, USA"
- family-names: Esteban
given-names: Oscar
orcid: https://orcid.org/0000-0001-8435-6191
affiliation: "Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland"

identifiers:
- description: Concept DOI for the software
type: doi
value: 10.5281/zenodo.5499693
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