knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) library(Rxnat)
XNAT is an open source imaging informatics platform developed by the Neuroinformatics Research Group at Washington University. XNAT was originally developed in the Buckner Lab at Washington University, now at Harvard University. It facilitates common management, productivity, and quality assurance tasks for imaging and associated data. Thanks to its extensibility, XNAT can be used to support a wide range of imaging-based projects.
There are several projects that currently use XNAT to manage a vast number of datasets.
For a more complete list of XNAT implementations around the world you can click here.
You can install Rxnat
from github with:
``` {r, eval = FALSE}
library(devtools) devtools::install_github("adigherman/Rxnat")
## Accessing XNAT Data ### How to get a username/password for a XNAT project XNAT projects can be public or private. In order to access a private repository a set of credentials are required. To obtain a user name and password combo you will need to visit: * HCP (Human Connectome Project) - [new account request](https://db.humanconnectome.org) and click on the Register button * NITRC - [new account request](https://www.nitrc.org/account/register.php). Some of the NITRC hosted projects will require additional access requests but this can be easily requested using the NITRC web interface for each project. * XNAT Central - this is mostly public, but you can also perform a [new account request](https://central.xnat.org/app/template/Register.vm) if any of the projects require it. ### Establishing a XNAT connection with the `Rxnat` package The `Rxnat` package will accept credentials provided in the function call or read from the system environment. #### Function parameters To establish a connection using the credentials as function parameters we can call the `xnat_connect` function: ``` {r, eval = FALSE} nitrc <- xnat_connect('https://nitrc.org/ir', username='XXXX', password='YYYY', xnat_name=NULL)
To use system environment variables we need to add them to the .Renviron
file located in the user's home folder. Use Sys.getenv("HOME")
to get the path (for unix/osx users the location can be easily accessed with ~, eg. vi ~/.Renviron
).
The Rxnat
package will be able to automatically read / use a system environment variable provided the following format is used: XXXX_RXNAT_USER
and XXXX_RXNAT_PASS
. XXXX
is provided as an argument when an XNAT connection is initiated.
As an example NITRC
is used as argument and the system environment variables names should be NITRC_RXNAT_USER
, and NITRC_RXNAT_PASS
.
``` {r, eval = FALSE}
nitrc <- xnat_connect('https://nitrc.org/ir', xnat_name='NITRC')
NITRC has some public image repositories, a username and password are not required to connect/query them. To create a connection to the public NITRC resources we call the `xnat_connect` function. ``` {r} nitrc <- xnat_connect('https://nitrc.org/ir')
Once a connection is established using the xnat_connect
function a list of available projects can be easily retrieved by using the class internal function projects
:
nitrc_projects <- nitrc$projects() head(nitrc_projects[c('ID','name')])
A full list of subjects for each XNAT connection can be retrieved using the subjects
function:
nitrc_subjects <- nitrc$subjects() head(nitrc_subjects)
To obtain a full list of experiments the experiments
function will be used:
nitrc_experiments <- nitrc$experiments() head(nitrc_experiments)
The scan resources for an experiment can be retrieved using the get_xnat_experiment_resources
function:
xnat_E00026_resources <- nitrc$get_xnat_experiment_resources('xnat_E00026') head(xnat_E00026_resources[c('Name','URI')])
If you are interested just in a subset of subjects/experiments that match a certain criteria you can use the query_scan_resources
function. Accepted query parameters are:
To retrieve a list of all subject IDs and associated experiment IDs we can use the query_scan_resources
function. In the example below, we are querying the HCP XNAT database for all subjects belonging the the HCP_500 project with scans taken at age 26.
nitrc_age_26 <- query_scan_resources(nitrc,age='26') head(nitrc_age_26[c("subject_ID","experiment_ID", "Project", "Age")])
To download a single file we will use the download_file
function. Using the first experiment_ID
from the above example, we will get all scan resources associated with it first.
``` {r, eval = FALSE} scan_resources <- get_scan_resources(nitrc,'xnat_E00026') scan_resources[1,c("Name","URI")]
To download the resource file (100307_3T_BIAS_BC.nii.gz) we will do: ``` {r, eval = FALSE} > download_xnat_file(nitrc,"/data/experiments/xnat_E00026/scans/anat_mprage_anonymized/resources/3967/files/scan_mprage_anonymized.nii.gz", file_dir = tempdir()) [1] "/var/folders/kr/05bm5krj0r3fpwxfdmx4xthm0000gn/T//RtmpTNSN5E/scan_mprage_anonymized.nii.gz"
To download all the T1 type images from experiment ConnectomeDB_E03657 we will use the download_xnat_dir
function.
{r, eval = FALSE}
download_xnat_dir(nitrc, experiment_ID='NITRC_IR_E10507',scan_type='T2', file_dir = tempdir(), verbose=TRUE)
/var/folders/kr/05bm5krj0r3fpwxfdmx4xthm0000gn/T//RtmpTNSN5E/NITRC_IR_E10507.zip
Downloading: 5.2 MB [1] "/var/folders/kr/05bm5krj0r3fpwxfdmx4xthm0000gn/T//RtmpTNSN5E/NITRC_IR_E10507.zip"
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.