initial joss draft

joss/nt.bib

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+@article{cox_software_1997,
+	author = {Cox, Robert W. and Hyde, James S.},
+	copyright = {Copyright © 1997 John Wiley \& Sons, Ltd.},
+	doi = {10.1002/(SICI)1099-1492(199706/08)10:4/5{	extless}171::AID-NBM453{	extgreater}3.0.CO;2-L},
+	issn = {1099-1492},
+	journal = {NMR Biomed},
+	language = {en},
+	number = {4-5},
+	pages = {171-178},
+	title = {Software tools for analysis and visualization of fMRI data},
+	url = {http://onlinelibrary.wiley.com/doi/10.1002/(SICI)1099-1492(199706/08)10:4/5{	extless}171::AID-NBM453{	extgreater}3.0.CO;2-L/abstract},
+	volume = 10,
+	year = 1997
+}
+
+@article{brett_nibabel_2006,
+	author = {Brett, Matthew and Markiewicz, Christopher J. and Hanke, Michael and Cote, Marc-Alexandre and Cipollini, Ben and McCarthy, Paul and Cheng, Chris and Halchenko, Yaroslav O. and Ghosh, Satrajit S. and Larson, Eric and Wassermann, Demian and Gerhard, Stephan},
+	doi = {10.5281/zenodo.591597},
+	journal = {Zenodo},
+	pages = 3458246,
+	title = {{Open Source Software: NiBabel}},
+	url = {https://zenodo.org/record/3458246\#.XaS82-ZKi5M},
+	year = 2006
+}
+
+@article{fischl_freesurfer_2012,
+	author = {Fischl, B.},
+	doi = {10.1016/j.neuroimage.2012.01.021},
+	issn = {1053-8119},
+	journal = {NeuroImage},
+	number = 2,
+	pages = {774-781},
+	title = {{FreeSurfer}},
+	url = {http://www.sciencedirect.com/science/article/pii/S1053811912000389},
+	volume = 62,
+	year = 2012
+}
+
+@article{jenkinson_fsl_2012,
+	author = {Jenkinson, Mark and Beckmann, Christian F. and Behrens, Timothy E.J. and Woolrich, Mark W. and Smith, Stephen M.},
+	doi = {10.1016/j.neuroimage.2011.09.015},
+	issn = {1053-8119},
+	journal = {NeuroImage},
+	number = 2,
+	pages = {782-790},
+	shorttitle = {FSL},
+	title = {{FSL}},
+	url = {http://www.sciencedirect.com/science/article/pii/S1053811911010603},
+	volume = 62,
+	year = 2012
+}
+
+@article{avants_symmetric_2008,
+	author = {Avants, B.B. and Epstein, C.L. and Grossman, M. and Gee, J.C.},
+	doi = {10.1016/j.media.2007.06.004},
+	issn = {1361-8415},
+	journal = {Medical Image Analysis},
+	number = 1,
+	pages = {26-41},
+	shorttitle = {Symmetric diffeomorphic image registration with cross-correlation},
+	title = {Symmetric diffeomorphic image registration with cross-correlation: Evaluating automated labeling of elderly and neurodegenerative brain},
+	url = {http://www.sciencedirect.com/science/article/pii/S1361841507000606},
+	volume = 12,
+	year = 2008
+}
+
+@book{friston_statistical_2006,
+	address = {London},
+	author = {Friston, Karl J. and Ashburner, John and Kiebel, Stefan J. and Nichols, Thomas E. and Penny, William D.},
+	isbn = {978-0-12-372560-8},
+	publisher = {Academic Press},
+	shorttitle = {Statistical parametric mapping},
+	title = {Statistical parametric mapping : the analysis of functional brain images},
+	year = 2006
+}

joss/paper.md

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+---
+title: 'NiTransforms: A Python tool to read, represent, manipulate, and apply $n$-dimensional spatial transforms'
+tags:
+  - Python
+  - neuroimaging
+  - image processing
+  - spatial transform
+  - nibabel
+authors:
+  - name: Mathias Goncalves
+    orcid: 0000-0002-7252-7771
+    affiliation: 1
+  - name: Christopher J. Markiewicz
+    orcid: 0000-0002-6533-164X
+    affiliation: "1, 2"
+  - name: Satrajit S. Ghosh
+    orcid: 0000-0002-5312-6729
+    affiliation: "2, 3"
+  - name: Russell A. Poldrack
+    orcid: 0000-0001-6755-0259
+    affiliation: 1
+  - name: Oscar Esteban
+    orcid: 0000-0001-8435-6191
+    affiliation: 1
+affiliations:
+ - name: Department of Psychology, Stanford University, Stanford, CA, USA
+   index: 1
+ - name: McGovern Institute for Brain Research, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
+   index: 2
+ - name: Department of Otolaryngology, Harvard Medical School, Boston, MA, USA
+   index: 3
+date: 04 November 2019
+bibliography: nt.bib
+---
+
+# Summary
+
+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 image processing.
+In neuroimaging, the proliferation of image registration software implementations has resulted in a disparate collection of structures and file formats used to preserve and communicate the transformation.
+This assortment of formats presents the challenge of compatibility between tools and endangers the reproducibility of results.
+
+_NiTransforms_ is a Python tool capable of reading and writing tranforms produced by the most popular neuroimaging software (AFNI [@cox_software_1997], FSL [@jenkinson_fsl_2012], FreeSurfer [@fischl_freesurfer_2012], ITK via ANTs [@avants_symmetric_2008], and SPM [@friston_statistical_2006]).
+Additionally, the tool provides seamless conversion between these formats, as well as the ability of applying the transforms to other images.
+_NiTransforms_ is inspired by `NiBabel` [@brett_nibabel_2006], a Python package with a collection of tools to read, write and handle neuroimaging data, and will be included as a new module.
+
+# Spatial transforms
+
+Let $\vec{x}$ represent the coordinates of a point in the reference coordinate system $R$, and $\vec{x}'$ its projection on to another coordinate system $M$:
+
+$T\colon R \subset \mathbb{R}^n \to M \subset \mathbb{R}^n$
+
+$\vec{x} \mapsto \vec{x}' = f(\vec{x}).$
+
+In an image registration problem, $M$ is a moving image from which we want to sample data in order to bring the image into spatial alignment with the reference image $R$.
+Hence, $f$ here is the spatial transformation function that maps from coordinates in $R$ to coordinates in $M$.
+There are a multiplicity of image registration algorithms and corresponding image transformation models to estimate linear and nonlinear transforms.
+
+The problem has been traditionally confused by the need of _transforming_ or mapping one image (generally referred to as _moving_) into another that serves as reference, with the goal of _fusing_ the information from both.
+An example of image fusion application would be the alignment of functional data from one individual's brain to the same individual's corresponding anatomical MRI scan for visualization.
+Therefore, "applying a transform" entails two operations: first, transforming the coordinates of the samples in the reference image $R$ to find their mapping $\vec{x}'$ on $M$ via $T\{\cdot\}$, and second an interpolation step as $\vec{x}'$ will likely fall off-the-grid of the moving image $M$.
+These two operations are confusing because, while the spatial transformation projects from $R$ to $M$, the data flows in reversed way after the interpolation of the values of $M$ at the mapped coordinates $\vec{x}'$.
+
+# Software Architecture
+
+There are four main components within the tool: an `io` submodule to handle the structure of the various file formats, a `base` submodule where abstract classes are defined, a `linear` submodule implementing $n$-dimensional linear transforms, and a `nonlinear` submodule for both parametric and non-parametric nonlinear transforms.
+Furthermore, _NiTranforms_ provides a straightforward _Application Programming Interface_ (API) that allows researchers to map point sets via transforms, as well as apply transforms (i.e., mapping the coordinates and interpolating the data) to data structures with ease.
+
+To ensure the consistency and uniformity of internal operations, all transforms are defined using a left-handed coordinate system of physical coordinates.
+In words from the neuroimaging domain, the coordinate system of transforms is _RAS+_ (or positive directions point to the Righthand for the first axis, Anterior for the second, and Superior for the third axis).
+The internal representation of transform coordinates is the most relevant design decision, and implies that a conversion of coordinate system is necessary to correctly interpret transforms generated by other software.
+When a transform that is defined in another coordinate system is loaded, it is automatically converted into _RAS+_ space.
+
+_NiTransforms_ was developed using a test-driven development paradigm, with the
+battery of tests being written prior to the software implementations.
+Two categories of tests were used: unit tests and cross-tool comparison tests.
+Unit tests evaluate the formal correctness of the implementation, while cross-tool
+comparison tests assess the correct implementation of third-party software.
+The testing suite is incorporated into a continuous integration framework, which assesses the continuity of the implementation along the development life and ensures that code changes and additions do not break existing functionalities.
+
+# Examples
+
+# References