From 2f40cf1085765825cbae9fa072cd220b06d36023 Mon Sep 17 00:00:00 2001 From: Andrew Van Date: Fri, 29 May 2026 23:33:14 -0500 Subject: [PATCH 1/2] :memo: Update citation to published Imaging Neuroscience paper Switch all references from the bioRxiv pre-print to the published Imaging Neuroscience article (doi: 10.1162/IMAG.a.1262). - LICENSE: replace pre-print URL with full official citation - README.md: point intro to the published paper; add Citation section - CLAUDE.md: update pre-print reference to the published paper - pyproject.toml: add a `paper` project URL pointing to the DOI --- CLAUDE.md | 2 +- LICENSE | 5 ++++- README.md | 11 ++++++++++- pyproject.toml | 2 +- 4 files changed, 16 insertions(+), 4 deletions(-) diff --git a/CLAUDE.md b/CLAUDE.md index ef6d6ac..d68bcbf 100644 --- a/CLAUDE.md +++ b/CLAUDE.md @@ -10,7 +10,7 @@ DIstortion Correction). Phase unwrapping uses a self-contained C++17 port of **no Julia runtime is involved**; do not reintroduce one (no `julia.py`, no conda recipe, no `FindJulia.cmake`). -Pre-print: . +Paper (Imaging Neuroscience): . ## Layout diff --git a/LICENSE b/LICENSE index c9fcd15..1e8b852 100644 --- a/LICENSE +++ b/LICENSE @@ -1,7 +1,10 @@ Copyright (c) 2022 Washington University. Authored by: Andrew Van -Please cite https://www.biorxiv.org/content/10.1101/2023.11.28.568744v1 +Please cite: +Van AN, Montez DF, Laumann TO, Cho PN, Suljic V, Madison T, et al. +Frame-wise multi-echo distortion correction for superior functional MRI. +Imaging Neuroscience 2026; 4 IMAG.a.1262. doi: https://doi.org/10.1162/IMAG.a.1262 warpkit is free for non-commercial use by academic, government, and non-profit/not-for-profit institutions. A commercial version of the software is diff --git a/README.md b/README.md index 5a45ea4..dc12867 100644 --- a/README.md +++ b/README.md @@ -5,7 +5,7 @@ [![docker](https://ghcr-badge.egpl.dev/vanandrew/warpkit/latest_tag?trim=major&label=ghcr latest)](https://github.com/vanandrew/warpkit/pkgs/container/warpkit) [![codecov](https://codecov.io/gh/vanandrew/warpkit/graph/badge.svg?token=S6ZZKOAF8V)](https://codecov.io/gh/vanandrew/warpkit) -A Python library for neuroimaging transforms, focused on the Multi-Echo DIstortion Correction (MEDIC) algorithm. The pre-print is available at . +A Python library for neuroimaging transforms, focused on the Multi-Echo DIstortion Correction (MEDIC) algorithm. The paper is published in *Imaging Neuroscience* at . The phase-unwrapping core is a self-contained C++17 port of [ROMEO](https://github.com/korbinian90/ROMEO) — there is no Julia runtime to install, and binary wheels ship with the ITK pieces statically linked. If you used an older release of warpkit that required `julia` on `PATH`, that step is gone. @@ -194,6 +194,15 @@ wk-convert-fieldmap \ --output sub-01_run-01_fieldmap.nii ``` +## Citation + +If you use warpkit, please cite: + +> Van AN, Montez DF, Laumann TO, Cho PN, Suljic V, Madison T, et al. +> Frame-wise multi-echo distortion correction for superior functional MRI. +> *Imaging Neuroscience* 2026; 4 IMAG.a.1262. +> doi: + ## Authors Vahdeta Suljic <suljic@wustl.edu>, Andrew Van <vanandrew77@gmail.com> diff --git a/pyproject.toml b/pyproject.toml index 88bc4d1..9b15fef 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -6,7 +6,7 @@ requires-python = ">=3.11" authors = [{ name = "Andrew Van", email = "vanandrew77@gmail.com" }] keywords = ["neuroimaging"] classifiers = ["Programming Language :: Python :: 3"] -urls = { github = "https://github.com/vanandrew/warpkit" } +urls = { github = "https://github.com/vanandrew/warpkit", paper = "https://doi.org/10.1162/IMAG.a.1262" } # include/romeo/LICENSE is the upstream MIT notice for the ROMEO C++ port; it # travels with the headers in source distributions and (via PEP 639 # license-files) gets bundled into wheels under *.dist-info/licenses/. From 89463a077d598f9a82ddf8426b9b621de076049c Mon Sep 17 00:00:00 2001 From: Andrew Van Date: Fri, 29 May 2026 23:38:11 -0500 Subject: [PATCH 2/2] :fire: Remove broken Docker badge from README --- README.md | 1 - 1 file changed, 1 deletion(-) diff --git a/README.md b/README.md index dc12867..d0aaf11 100644 --- a/README.md +++ b/README.md @@ -2,7 +2,6 @@ [![Build](https://github.com/vanandrew/warpkit/actions/workflows/build.yml/badge.svg)](https://github.com/vanandrew/warpkit/actions) [![PyPI](https://img.shields.io/pypi/v/warpkit)](https://pypi.org/project/warpkit/) -[![docker](https://ghcr-badge.egpl.dev/vanandrew/warpkit/latest_tag?trim=major&label=ghcr latest)](https://github.com/vanandrew/warpkit/pkgs/container/warpkit) [![codecov](https://codecov.io/gh/vanandrew/warpkit/graph/badge.svg?token=S6ZZKOAF8V)](https://codecov.io/gh/vanandrew/warpkit) A Python library for neuroimaging transforms, focused on the Multi-Echo DIstortion Correction (MEDIC) algorithm. The paper is published in *Imaging Neuroscience* at .