From 8a38385bab12b115aacad5ca0d48ab2e370d9c33 Mon Sep 17 00:00:00 2001 From: James Kent Date: Tue, 3 Dec 2024 13:02:18 -0600 Subject: [PATCH 1/2] rephrase the intro --- docs/source/index.rst | 16 +++++++++------- 1 file changed, 9 insertions(+), 7 deletions(-) diff --git a/docs/source/index.rst b/docs/source/index.rst index ff1c051..524273c 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -6,13 +6,15 @@ Welcome to giga_connectome's documentation! =========================================== -Functional connectivity is a common approach in analysing resting state fMRI data. Python tool Nilearn -provides utilities to extract, denoise time-series on a parcellation and compute functional connectivity. -Currently there's no standalone one stop solution to generate connectomes from fMRIPrep outputs. -This BIDS-app combines Nilearn, TemplateFlow to denoise the data and generate timeseries and functional -connectomes directly from fMRIPrep outputs. -The workflow comes with several built in denoising strategies and several choices of atlases -(MIST, Schaefer 7 networks, DiFuMo, Harvard-Oxford). +Functional connectivity is a common approach in analysing resting state fMRI data. +The Python tool Nilearn provides utilities to extract and denoise time-series on a parcellation. +Nilearn also has methods to compute functional connectivity. +While Nilearn provides useful methods to generate connectomes, +there is no standalone one stop solution to generate connectomes from fMRIPrep outputs. +Giga_connectome (a BIDS-app!) combines Nilearn and TemplateFlow to denoise the data, generate timeseries, +and most critically giga_connectome generates functional connectomes directly from fMRIPrep outputs. +The workflow comes with several built-in denoising strategies and +there are several choices of atlases (MIST, Schaefer 7 networks, DiFuMo, Harvard-Oxford). Users can customise their own strategies and atlases using the configuration json files. .. toctree:: From 7f53a2b168a3beef46b6e50acf63599558c06535 Mon Sep 17 00:00:00 2001 From: James Kent Date: Tue, 3 Dec 2024 13:02:33 -0600 Subject: [PATCH 2/2] add instructions on adding ssh key --- docs/source/contributing.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source/contributing.md b/docs/source/contributing.md index 0abd235..b242a5a 100644 --- a/docs/source/contributing.md +++ b/docs/source/contributing.md @@ -2,7 +2,7 @@ ## Setting up your environment for development -1. Fork the repository from github and clone your fork locally +1. Fork the repository from github and clone your fork locally (see [here](https://docs.github.com/en/authentication/connecting-to-github-with-ssh/adding-a-new-ssh-key-to-your-github-account) to setup your ssh key): ```bash git clone git@github.com:/giga_connectome.git