ABCD_scripts

This folder provides the scripts used to download and process ABCD minimally processed data

USAGE

• download/ folder

  This folder provides scripts and instructions to download the ABCD phenotypic and imaging data

• brain_mask/ folder

  This folder provides scripts to mask the raw data using the brain mask so we can save the space

• config/ folder

  • CBIG_ABCD_proc_tested_config.sh To replicate the ABCD processing pipeline, you need to follow $CBIG_CODE_DIR/setup/README.md to setup the config file. Instead of using CBIG/setup/CBIG_sample_config.sh, you need to use this file
  • CBIG_ABCD_paths_t1_fMRI.sh This file defines the paths that will be used in all the other scripts in this folder. Please change the paths if you want different input or output directories

• folders 2020_ABCD_T1_recon_all/,2020_ABCD_rsfMRI_process/,2020_ABCD_taskfMRI_process/

  These 3 folders contain the scripts to retrieve the recon-all, rest-fMRI processing and task-fMRI processing results

• utilities folder

  This folder contains the scripts that are commonly used by other scripts in this folder

Replicate the ABCD release2.0 image processing

This is for CBIG lab only and the replication steps require sensitive data not allowed to be made public. Steps to replicate the processing are:

1. [optional] Change the paths in the config file CBIG_ABCD_paths_t1_fMRI.sh
2. Go to the download folder to retrieve the ABCD tabular and imaging data. Place the data according to the config file in step1.
3. Go to the brain_mask folder to generate the brain mask of raw fMRI images and mask the raw images
4. Upon successfully completing step3, go to 2020_ABCD_T1_recon_all folder and retrieve the recon-all results
5. Upon successfully completing step4, go to 2020_ABCD_rsfMRI_process folder to retrieve the rest fMRI processing results
6. Upon successfully completing step4, go to 2020_ABCD_taskfMRI_process folder to retrieve the task fMRI processing results