From b9d44504384b3641dbd1d063105cb6eb99713488 Mon Sep 17 00:00:00 2001 From: Hao-Ting Wang <htwangtw@gmail.com> Date: Mon, 19 Jun 2023 17:01:39 -0400 Subject: [PATCH] EHN neurolibre DONE --- CITATION.cff | 66 ++++++++++++++++++++++++++++++++++++++++++++++++++++ README.md | 13 +++++++---- 2 files changed, 74 insertions(+), 5 deletions(-) create mode 100644 CITATION.cff diff --git a/CITATION.cff b/CITATION.cff new file mode 100644 index 0000000..31eec55 --- /dev/null +++ b/CITATION.cff @@ -0,0 +1,66 @@ +cff-version: "1.2.0" +authors: +- family-names: Wang + given-names: Hao-Ting + orcid: "https://orcid.org/0000-0003-4078-2038" +- family-names: Meisler + given-names: Steven L + orcid: "https://orcid.org/0000-0002-8888-1572" +- family-names: Sharmarke + given-names: Hanad +- family-names: Clarke + given-names: Natasha +- family-names: Paugam + given-names: François +- family-names: Gensollen + given-names: Nicolas + orcid: "https://orcid.org/0000-0001-7199-9753" +- family-names: Markiewicz + given-names: Christopher J + orcid: "https://orcid.org/0000-0002-6533-164X" +- family-names: Thirion + given-names: Bertrand + orcid: "https://orcid.org/0000-0001-5018-7895" +- family-names: Bellec + given-names: Pierre + orcid: "https://orcid.org/0000-0002-9111-0699" +doi: 10.5281 +message: To reference this work, please cite our reproducible preprint + in NeuroLibre. +preferred-citation: + authors: + - family-names: Wang + given-names: Hao-Ting + orcid: "https://orcid.org/0000-0003-4078-2038" + - family-names: Meisler + given-names: Steven L + orcid: "https://orcid.org/0000-0002-8888-1572" + - family-names: Sharmarke + given-names: Hanad + - family-names: Clarke + given-names: Natasha + - family-names: Paugam + given-names: François + - family-names: Gensollen + given-names: Nicolas + orcid: "https://orcid.org/0000-0001-7199-9753" + - family-names: Markiewicz + given-names: Christopher J + orcid: "https://orcid.org/0000-0002-6533-164X" + - family-names: Thirion + given-names: Bertrand + orcid: "https://orcid.org/0000-0001-5018-7895" + - family-names: Bellec + given-names: Pierre + orcid: "https://orcid.org/0000-0002-9111-0699" + date-published: 2023-06-19 + doi: 10.55458/neurolibre.00012 + journal: NeuroLibre Reproducible Preprints + publisher: + name: NeuroLibre + title: A reproducible benchmark of resting-state fMRI denoising + strategies using fMRIPrep and Nilearn + type: preprint + url: "https://neurolibre.org/papers/10.55458/neurolibre.00012" +title: A reproducible benchmark of resting-state fMRI denoising + strategies using fMRIPrep and Nilearn \ No newline at end of file diff --git a/README.md b/README.md index bf9f7e4..1e63437 100644 --- a/README.md +++ b/README.md @@ -1,11 +1,12 @@ # Benchmark denoising strategies on fMRIPrep output -[](https://simexp.github.io/fmriprep-denoise-benchmark/) +[](https://doi.org/10.55458/neurolibre.00012) The project is a continuation of [load_confounds](https://github.com/SIMEXP/load_confounds). The aim is to evaluate the impact of denoising strategy on functional connectivity data, using output processed by fMRIPrep LTS in a reproducible workflow. -Preprint of this project is now on [biorxiv](https://www.biorxiv.org/content/10.1101/2023.04.18.537240). +**Preprint of the manuscript is now on [biorxiv](https://www.biorxiv.org/content/10.1101/2023.04.18.537240). +The reporducible Jupyter Book preprint is on [NeuroLibre](https://neurolibre.org/papers/10.55458/neurolibre.00012).** ## Quick start @@ -26,20 +27,22 @@ make book - `content/` is the source of the JupyterBook. -- `data/` is reserved to store data for building the JupyterBook. +- `data/` is reserved to store data for running analysis. To build the book, one will need all the metrics from the study. The metrics are here: [](https://doi.org/10.5281/zenodo.7764979) + The data will be automatically downloaded to `content/notebooks/data`. + You can by pass this step through accessing the Neurolibre preprint [](https://doi.org/10.55458/neurolibre.00012)! - Custom code is located in `fmriprep_denoise/`. This project is installable. -- Preprocessing SLURM scripts are in `script/` +- Preprocessing SLURM scripts, and scripts for creating figure for manuscript are in `scripts/`. ## Poster and presentations The results will be presented at QBIN science day 2023 as a flash talk, and OHBM 2023 Montreal as a poster :tada:. -The preliminary results were be presented at OHBM 2022 as a poster. +The preliminary results were presented at OHBM 2022 as a poster. 