HCP dMRI data download

This section describes how to download and process diffussion MRI (dMRI) data from the Human Connectome Project (HCP) database using various neuroconductor R packages (https://neuroconductor.org/)

HCP dMRI data download

Step 1: Obtain AWS access credential – access key id and secret key: Login ConnectomeDB account and then click the Amazon S3 Access Enabled box. If you do not have an account, you need to first create one.

Wu-Minn HCP Data webpage.

Step 2: Install the neurohcp R package for batch downloading from ConnectomeDB.

Step 3: Obtain subject ID using the hcp_1200_scanning_info function in the neurohcp package.

library(neurohcp)
set_aws_api_key(access_key = "your_access_key", secret_key = "your_secret_key")
hcp_info=hcp_1200_scanning_info # information of the database
hcp_id=hcp_info$id #ID of available subjects

Two functions are used to download data from ConnectomeDB:

  • download_hcp_dir: To download all files in a certain directory

  • download_hcp_file: To download a certain file

For each subject, the following files (approximately, 1.5GB) are relevant to our analysis:

  • T1w_acpc_dc_restore_1.25.nii.gz: T1w image (structural volume sampled at the same resolution as the diffusion data)
  • data.nii.gz: diffusion weighted image
  • bvecs: gradient directions
  • bvals: b-values
  • nodif_brain_mask.nii.gz: T2w extracted brain mask
## Download D-MRI directory of a subject
# "100307" is the subject ID; an output directory should also be specified: default: tempfile()
download_hcp_dir("HCP/100307/T1w/Diffusion",verbose=FALSE, outdir="user_path")  

## Downlaod the T1w image of a subject
# an output file path/name should also be specified: default: NULL
download_hcp_file("HCP/100307/T1w/T1w_acpc_dc_restore_1.25.nii.gz", verbose = FALSE,
                  destfile="user_path/out_file_name")

Notes: Sometimes, the files of a subject found through hcp_1200_scanning_info could not be downloaded through either download_hcp_dir or download_hcp_file function. This problem occurs due to one of the two reasons:

  • Data of this subject have not been registered on ConnectomeDB.
  • Data have not been registered with proper directory path, even though the data are available on ConnectomeDB.

You can check whether data of a subject are available on ConnectomeDB by using the hcp_list_dirs function: If the result from hcp_list_dirs does not have any value in parsed_result$Contents$Key[[1]], it means that you will have to manually check the availability of files.

dir_info=hcp_list_dirs(paste0("HCP/100307/T1w/Diffusion"))

#Check whether D-MRI can be downloaded thorugh the "download_hcp_dir" function.
is.null(dir_info$parsed_result$ListBucketResult$Contents$Key[[1]])