diff --git a/.mailmap b/.mailmap new file mode 100644 index 00000000..dac8efaa --- /dev/null +++ b/.mailmap @@ -0,0 +1,12 @@ +Oscar Esteban +Christopher J. Markiewicz +Christopher J. Markiewicz +Mathias Goncalves +Mathias Goncalves +Mathias Goncalves +Julien Marabotto <166002186+jmarabotto@users.noreply.github.com> +Julien Marabotto <166002186+jmarabotto@users.noreply.github.com> +Julien Marabotto <166002186+jmarabotto@users.noreply.github.com> +Stefano Moia +Basile Pinsard +Jaume Banús diff --git a/.zenodo.json b/.zenodo.json deleted file mode 100644 index 2cea96d1..00000000 --- a/.zenodo.json +++ /dev/null @@ -1,50 +0,0 @@ -{ - "title": "NiTransforms: A Python tool to read, represent, manipulate, and apply $n$-dimensional spatial transforms", - "description": "

A Python package to access a cacophony of neuroimaging file formats representing spatio-temporal, linear-and-nonlinear transformations.

", - "creators": [ - { - "affiliation": "Department of Psychology, Stanford University, Stanford, CA, USA", - "name": "Goncalves, Mathias", - "orcid": "0000-0002-7252-7771" - }, - { - "affiliation": "Department of Psychology, Stanford University, Stanford, CA, USA", - "name": "Markiewicz, Christopher J.", - "orcid": "0000-0002-6533-164X" - }, - { - "affiliation": "Basque Center on Cognition Brain and Language, San Sebastian, Spain", - "name": "Moia, Stefano", - "orcid": "0000-0002-2553-3327" - }, - { - "affiliation": "McGovern Institute for Brain Research, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA; and Department of Otolaryngology, Harvard Medical School, Boston, MA, USA", - "name": "Ghosh, Satrajit", - "orcid": "0000-0002-5312-6729" - }, - { - "affiliation": "Department of Psychology, Stanford University, Stanford, CA, USA", - "name": "Poldrack, Russell A.", - "orcid": "0000-0001-6755-0259" - }, - { - "affiliation": "Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland", - "name": "Esteban, Oscar", - "orcid": "0000-0001-8435-6191" - } - ], - "contributors": [ - { - "affiliation": "Charite Universitatsmedizin Berlin, Germany", - "name": "Waller, Lea", - "orcid": "0000-0002-3239-6957", - "type": "Researcher" - } - ], - "keywords": [ - "neuroimaging", - "spatial normalization" - ], - "license": "mit-license", - "upload_type": "software" -} diff --git a/CITATION.cff b/CITATION.cff new file mode 100644 index 00000000..575132c1 --- /dev/null +++ b/CITATION.cff @@ -0,0 +1,100 @@ +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