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humanconnectome

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Getting Data from the Human Connectome Project (HCP)

Public Connectome Data

Installing the neurohcp package

Command:

source("http://neuroconductor.org/neurocLite.R")

Error:

'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
    CRAN: https://cran.rstudio.com/
Bioconductor version 3.18 (BiocManager 1.30.22), R 4.3.3 (2024-02-29 ucrt)
Using neurocLite version: # neurocInstall package version: 0.12.0

Refactor command per error:

getOption("http://neuroconductor.org/neurocLite.R")

Output:

NULL

Retry:

source("http://neuroconductor.org/neurocLite.R")
'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
    CRAN: https://cran.rstudio.com/
Bioconductor version 3.18 (BiocManager 1.30.22), R 4.3.3 (2024-02-29 ucrt)
Using neurocLite version: # neurocInstall package version: 0.12.0
 neuro_install("neurohcp", release = "stable")
Installing package
(aslibis unspecified)
Warning: unable to access index for repository https://neuroconductor.org/releases/2020/05/bin/windows/contrib/4.3:
  cannot open URL 'https://neuroconductor.org/releases/2020/05/bin/windows/contrib/4.3/PACKAGES'
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.3/neurohcp_0.9.0.zip'
Content type 'application/zip' length 624303 bytes (609 KB)
downloaded 609 KB

packageneurohcpsuccessfully unpacked and MD5 sums checked

Note: the current markdown document records the progress made while following along with the following document:

Getting Data from the Human Connectome Project (HCP)


Note: added command:

library(neurohcp)

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

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

Command:

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

Error: [Resolved]

  could not find function "%>%"

[Fix]:

Part 1: install 2 packages:
install.packages("magrittr") # package installations are only needed the first time you use it
install.packages("dplyr")    # alternative installation of the %>%
library(magrittr) # needs to be run every time you start R and want to use %>%
library(dplyr)    # alternatively, this also loads %>%
Part 2: Repaste original code correctly formatted (remove +):
ids_with_dwi = hcp_900_scanning_info %>% 
    filter(scan_type %in% "dMRI") %>%
    select(id) %>%
    unique

Reference: stackoverflow: Error: could not find function "%>%"

Bug Fixed [Resolved]


Continuing with: Getting Data from the Human Connectome Project (HCP)

head(ids_with_dwi)

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

r = download_hcp_dir("HCP/100307/T1w/Diffusion", verbose = FALSE)

From above: "complete directory"

There is a wait here (minute(s)).

print(basename(r$output_files))
ids_with_dwi = ids_with_dwi %>% 
  mutate(id_dir = paste0("HCP/", id, "/T1w/Diffusion"))
if (have_aws_key()) {
  ret = download_hcp_file("HCP/100307/T1w/Diffusion/bvals", verbose = FALSE)
}

End of webpage document.


Note: from start of webpage document:

All code for this document is located at here.

Note: This version untried as used the version in original webpage.