Getting an Access/API Key

Once logged into http://db.humanconnectome.org and the terms are accepted, the user must enable Amazon S3 access for their Amazon account. The user will then be provided an access key identifier (ID), which is required to authenticate a user to Amazon as well as a secret key. These access and secret keys are necessary for the neurohcp package, and will be referred to as access keys or API (application program interface) keys.

Setting the API key

In the neurohcp package, set_aws_api_key will set the AWS access keys:

set_aws_api_key(access_key = "ACCESS_KEY", secret_key = "SECRET_KEY")

or these can be stored in AWS_ACCESS_KEY_ID, AWS_SECRET_ACCESS_KEY environment variables, respectively.

Once these are set, the functions of neurohcp are ready to use. To test that the API keys are set correctly, one can run bucketlist:

if (have_aws_key()) {
  neurohcp::bucketlist()
}

                     Bucket             CreationDate
1 jh-jmusche1-awscloudtrail 2020-08-07T12:40:48.000Z
2     jh-jmusche1-awsconfig 2020-08-07T12:38:23.000Z
3  jh-jmusche1-s3accesslogs 2020-08-07T12:45:03.000Z

We see that hcp-openaccess is a bucket that we have access to, and therefore have access to the data.

Getting Data: Downloading a Directory of Data

In the neurohcp package, there is a data set indicating the scans read for each subject, named hcp_900_scanning_info. We can subset those subjects that have diffusion tensor imaging:

ids_with_dwi = hcp_900_scanning_info %>% 
  filter(scan_type %in% "dMRI") %>% 
  select(id) %>% 
  unique
head(ids_with_dwi)

# A tibble: 6 x 1
  id    
  <chr> 
1 100307
2 100408
3 101006
4 101107
5 101309
6 101410

Let us download the complete directory of diffusion data using download_hcp_dir:

r = download_hcp_dir("HCP/100307/T1w/Diffusion", verbose = FALSE)
print(basename(r$output_files))

[1] "bvals"                   "bvecs"                  
[3] "data.nii.gz"             "grad_dev.nii.gz"        
[5] "nodif_brain_mask.nii.gz"

This diffusion data is the data that can be used to create summaries such as fractional anisotropy and mean diffusivity.

If we create a new column with all the directories, we can iterate over these to download all the diffusion data for these subjects from the HCP database.

ids_with_dwi = ids_with_dwi %>% 
  mutate(id_dir = paste0("HCP/", id, "/T1w/Diffusion"))

Getting Data: Downloading a Single File

We can also download a single file using download_hcp_file. Here we will simply download the bvals file:

if (have_aws_key()) {
  ret = download_hcp_file("HCP/100307/T1w/Diffusion/bvals", verbose = FALSE)
}