From 4a666688f5801339b236f741c6ee227413bb28b9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jon=20Haitz=20Legarreta=20Gorro=C3=B1o?= Date: Thu, 21 Mar 2024 09:52:59 -0400 Subject: [PATCH 1/3] DOC: Add status badges to `README` file Add miscellaneous status badges to `README` file: - License - PyPI version - Documentation - Python package --- README.rst | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) diff --git a/README.rst b/README.rst index 8dce225e..9a77a3d0 100644 --- a/README.rst +++ b/README.rst @@ -6,6 +6,22 @@ :target: https://doi.org/10.5281/zenodo.4680599 :alt: DOI +.. image:: https://img.shields.io/pypi/l/eddymotion.svg + :target: https://pypi.python.org/pypi/eddymotion/ + :alt: License + +.. image:: https://img.shields.io/pypi/v/eddymotion.svg + :target: https://pypi.python.org/pypi/eddymotion/ + :alt: Latest Version + +.. image:: https://github.com/nipreps/eddymotion/actions/workflows/pages/pages-build-deployment/badge.svg + :target: https://www.nipreps.org/eddymotion/main/index.html + :alt: Documentation + +.. image:: https://github.com/nipreps/eddymotion/actions/workflows/pythonpackage.yml/badge.svg + :target: https://github.com/nipreps/eddymotion/actions/workflows/pythonpackage.yml + :alt: Python package + Retrospective estimation of head-motion between diffusion-weighted images (DWI) acquired within diffusion MRI (dMRI) experiments renders exceptionally challenging1 for datasets including high-diffusivity (or “high b”) images. From 62a669b1b3df958d758320909ce4bf3fb8c1461a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jon=20Haitz=20Legarreta=20Gorro=C3=B1o?= Date: Fri, 22 Mar 2024 10:24:36 -0400 Subject: [PATCH 2/3] DOC: Make `README` refs be considered as citations instead of footnotes Make references in README be considered as citations instead of footnotes. Fixes: ``` Warning, treated as error: /home/runner/work/eddymotion/eddymotion/README.rst:17:Footnote [1] is not referenced. make: *** [Makefile:65: html] Error 2 ``` raised for example in: https://github.com/nipreps/eddymotion/actions/runs/8376155506/job/22935185353?pr=138#step:6:54 --- README.rst | 20 ++++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/README.rst b/README.rst index 9a77a3d0..d002e84f 100644 --- a/README.rst +++ b/README.rst @@ -27,34 +27,34 @@ diffusion MRI (dMRI) experiments renders exceptionally challenging1 for datasets high-diffusivity (or “high b”) images. These “high b” (b > 1000s/mm2) DWIs enable higher angular resolution, as compared to more traditional diffusion tensor imaging (DTI) schemes. -UNDISTORT [1]_ (Using NonDistorted Images to Simulate a Template Of the Registration Target) +UNDISTORT [#r1]_ (Using NonDistorted Images to Simulate a Template Of the Registration Target) was the earliest method addressing this issue, by simulating a target DW image without motion or distortion from a DTI (b=1000s/mm2) scan of the same subject. -Later, Andersson and Sotiropoulos [2]_ proposed a similar approach (widely available within the +Later, Andersson and Sotiropoulos [#r2]_ proposed a similar approach (widely available within the FSL ``eddy`` tool), by predicting the target DW image to be registered from the remainder of the dMRI dataset and modeled with a Gaussian process. Besides the need for less data, ``eddy`` has the advantage of implicitly modeling distortions due to Eddy currents. -More recently, Cieslak et al. [3]_ integrated both approaches in *SHORELine*, by +More recently, Cieslak et al. [#r3]_ integrated both approaches in *SHORELine*, by (i) setting up a leave-one-out prediction framework as in eddy; and -(ii) replacing eddy’s general-purpose Gaussian process prediction with the SHORE [4]_ diffusion model. +(ii) replacing eddy’s general-purpose Gaussian process prediction with the SHORE [#r4]_ diffusion model. *Eddymotion* is an open implementation of eddy-current and head-motion correction that builds upon the work of ``eddy`` and *SHORELine*, while generalizing these methods to multiple acquisition schemes -(single-shell, multi-shell, and diffusion spectrum imaging) using diffusion models available with DIPY [5]_. +(single-shell, multi-shell, and diffusion spectrum imaging) using diffusion models available with DIPY [#r5]_. .. image:: docs/_static/eddymotion-flowchart.svg :alt: The eddymotion flowchart -.. [1] S. Ben-Amitay et al., Motion correction and registration of high b-value diffusion weighted images, Magnetic +.. [#r1] S. Ben-Amitay et al., Motion correction and registration of high b-value diffusion weighted images, Magnetic Resonance in Medicine 67:1694–1702 (2012) -.. [2] J. L. R. Andersson. et al., An integrated approach to correction for off-resonance effects and subject movement +.. [#r2] J. L. R. Andersson. et al., An integrated approach to correction for off-resonance effects and subject movement in diffusion MR imaging, NeuroImage 125 (2016) 1063–1078 -.. [3] M. Cieslak et al., QSIPrep: An integrative platform for preprocessing and reconstructing diffusion MRI data. +.. [#r3] M. Cieslak et al., QSIPrep: An integrative platform for preprocessing and reconstructing diffusion MRI data. Nature Methods, 18(7), 775–778 (2021) -.. [4] E. Ozarslan et al., Simple Harmonic Oscillator Based Reconstruction and Estimation for Three-Dimensional Q-Space +.. [#r4] E. Ozarslan et al., Simple Harmonic Oscillator Based Reconstruction and Estimation for Three-Dimensional Q-Space MRI. in Proc. Intl. Soc. Mag. Reson. Med. vol. 17 1396 (2009) -.. [5] E. Garyfallidis et al., Dipy, a library for the analysis of diffusion MRI data. Front. Neuroinformatics 8, 8 +.. [#r5] E. Garyfallidis et al., Dipy, a library for the analysis of diffusion MRI data. Front. Neuroinformatics 8, 8 (2014) From d3a6b0a2211c8e694bee1bd83c51c374aa5545ce Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jon=20Haitz=20Legarreta=20Gorro=C3=B1o?= Date: Fri, 22 Mar 2024 10:43:46 -0400 Subject: [PATCH 3/3] DOC: Use URL as path to static content in `README` Use commit raw content URL as path to static content in `README`. Fixes: ``` Warning, treated as error: /home/runner/work/eddymotion/eddymotion/README.rst::image file not readable: docs/_static/eddymotion-flowchart.svg make: *** [Makefile:65: html] Error 2 ``` raised for example in: https://github.com/nipreps/eddymotion/actions/runs/8391856943/job/22983140234#step:6:54 --- README.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.rst b/README.rst index d002e84f..3ac109a5 100644 --- a/README.rst +++ b/README.rst @@ -44,7 +44,7 @@ the work of ``eddy`` and *SHORELine*, while generalizing these methods to multip (single-shell, multi-shell, and diffusion spectrum imaging) using diffusion models available with DIPY [#r5]_. -.. image:: docs/_static/eddymotion-flowchart.svg +.. image:: https://raw.githubusercontent.com/nipreps/eddymotion/507fc9bab86696d5330fd6a86c3870968243aea8/docs/_static/eddymotion-flowchart.svg :alt: The eddymotion flowchart