Reproducible Brain Charts Analysis Template

This repo can be used as a template for creating new repos that will process RBC datasets. It has some useful scripts to get started in the code/ directory.

Getting started

Create a new repository, selecting this repo as a template on the github website. It is required that you include all the branches in your new repo.

Suppose you created a new repo called ReproBrainChart/ExampleAnalysis.git. You will clone this repo with datalad using

datalad clone git@github.com:ReproBrainChart/ExampleAnalysis.git

This will create an ExampleAnalysis directory that is ready to start analyzing RBC data.

Installing RBC datasets

There are some convenience scripts included in this template to get you started. Suppose I want to get the structural and functional from the CCNP study. I could run these commands to get them installed:

cd ExampleAnalysis
./code/install_rbc.py \
    --qc-threshold complete-pass \
    --release 1.0 \
    --bold-studies CCNP \
    --anat-studies CCNP

This will result in two new directories:

• inputs/data/CCNP_FreeSurfer
• inputs/data/CCNP_CPAC

You can cd into these directories to see what sort of data is available. To access the content of any of the files in these directories you will need to datalad get specific files.

Do not attempt to download the entire datasets unless you want to run out of disk space

Running analysis scripts

In the code/ directory you will find an example script that that performs a couple steps:

1. datalad get the tabular data that you want to analyze
2. combines these data into a single tsv file
3. calculates some stats on them