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| 1 | +cff-version: 1.2.0 |
| 2 | +title: "NiTransforms: A Python tool to read, represent, manipulate, and apply N-dimensional spatial transforms" |
| 3 | +license: MIT |
| 4 | +type: software |
| 5 | +url: https://github.com/nipy/nitransforms/ |
| 6 | +version: 24.1.1 |
| 7 | +date-released: 2024-12-18 |
| 8 | +abstract: | |
| 9 | + Spatial transforms formalize mappings between coordinates of objects in biomedical images. |
| 10 | + Transforms typically are the outcome of image registration methodologies, which estimate |
| 11 | + the alignment between two images. |
| 12 | + Image registration is a prominent task present in nearly all standard image processing |
| 13 | + and analysis pipelines. |
| 14 | + The proliferation of software implementations of image registration methodologies has |
| 15 | + resulted in a spread of data structures and file formats used to preserve and communicate |
| 16 | + transforms. |
| 17 | + This segregation of formats precludes the compatibility between tools and endangers the |
| 18 | + reproducibility of results. |
| 19 | + We propose a software tool capable of converting between formats and resampling images |
| 20 | + to apply transforms generated by the most popular neuroimaging packages and libraries |
| 21 | + (AFNI, FSL, FreeSurfer, ITK, and SPM). |
| 22 | + The proposed software is subject to continuous integration tests to check the |
| 23 | + compatibility with each supported tool after every change to the code base. |
| 24 | + Compatibility between software tools and imaging formats is a necessary bridge |
| 25 | + to ensure the reproducibility of results and enable the optimization and evaluation |
| 26 | + of current image processing and analysis workflows. |
| 27 | +keywords: |
| 28 | + - neuroimaging |
| 29 | + - spatial normalization |
| 30 | + |
| 31 | +authors: |
| 32 | + - family-names: Goncalves |
| 33 | + given-names: Mathias |
| 34 | + orcid: https://orcid.org/0000-0002-7252-7771 |
| 35 | + affiliation: "Department of Psychology, Stanford University, Stanford, CA, USA" |
| 36 | + - family-names: Markiewicz |
| 37 | + given-names: Christopher J. |
| 38 | + orcid: https://orcid.org/0000-0002-6533-164X |
| 39 | + affiliation: "Department of Psychology, Stanford University, Stanford, CA, USA" |
| 40 | + - family-names: Moia |
| 41 | + given-names: Stefano |
| 42 | + orcid: https://orcid.org/0000-0002-2553-3327 |
| 43 | + affiliation: "Basque Center on Cognition Brain and Language, San Sebastian, Spain" |
| 44 | + - family-names: Waller |
| 45 | + given-names: Lea |
| 46 | + orcid: https://orcid.org/0000-0002-3239-6957 |
| 47 | + affiliation: Charite Universitatsmedizin Berlin, Germany |
| 48 | + - family-names: Pinsard |
| 49 | + given-names: Basile |
| 50 | + orcid: https://orcid.org/0000-0002-4391-3075 |
| 51 | + affiliation: University of Montréal, Montréal, Canada |
| 52 | + - family-names: Banús |
| 53 | + given-names: Jaume |
| 54 | + orcid: https://orcid.org/0000-0001-9318-6323 |
| 55 | + - family-names: Visconti di Oleggio Castello |
| 56 | + given-names: Matteo |
| 57 | + orcid: https://orcid.org/0000-0001-7931-5272 |
| 58 | + affiliation: University of California Berkeley, Berkeley, CA, USA |
| 59 | + - family-names: Marabotto |
| 60 | + given-names: Julien |
| 61 | + orcid: https://orcid.org/0009-0003-7070-5217 |
| 62 | + affiliation: Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland |
| 63 | + - family-names: Ma |
| 64 | + given-names: Feilong |
| 65 | + orcid: https://orcid.org/0000-0002-6838-3971 |
| 66 | + affiliation: Dartmouth College, Hanover, NH, United States |
| 67 | + - family-names: Nielson |
| 68 | + given-names: Dylan |
| 69 | + orcid: https://orcid.org/0000-0003-4613-6643 |
| 70 | + affiliation: Machine Learning Team, National Institute of Mental Health, USA |
| 71 | + - family-names: Cluce |
| 72 | + given-names: Jon |
| 73 | + orcid: https://orcid.org/0000-0001-7590-5806 |
| 74 | + affiliation: Child Mind Institute, New York, NY, USA |
| 75 | + - family-names: Shain |
| 76 | + given-names: Cory |
| 77 | + orcid: https://orcid.org/0000-0002-2704-7197 |
| 78 | + affiliation: Stanford University, Stanford, CA, USA |
| 79 | + ## When contributing, please copy and uncomment the following lines |
| 80 | + # - family-names: |
| 81 | + # given-names: |
| 82 | + # orcid: https://orcid.org/ |
| 83 | + # affiliation: |
| 84 | + - family-names: Ghosh |
| 85 | + given-names: Satrajit |
| 86 | + orcid: https://orcid.org/0000-0002-5312-6729 |
| 87 | + affiliation: "McGovern Institute for Brain Research, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA; and Department of Otolaryngology, Harvard Medical School, Boston, MA, USA" |
| 88 | + - family-names: Poldrack |
| 89 | + given-names: Russell A. |
| 90 | + orcid: https://orcid.org/0000-0001-6755-0259 |
| 91 | + affiliation: "Department of Psychology, Stanford University, Stanford, CA, USA" |
| 92 | + - family-names: Esteban |
| 93 | + given-names: Oscar |
| 94 | + orcid: https://orcid.org/0000-0001-8435-6191 |
| 95 | + affiliation: "Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland" |
| 96 | + |
| 97 | +identifiers: |
| 98 | + - description: Concept DOI for the software |
| 99 | + type: doi |
| 100 | + value: 10.5281/zenodo.5499693 |
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