In adigherman/Rxnat: Queries and Extracts Images from Extensible Neuroimaging Archive Toolkit Public/Private Datasets
knitr::opts_chunk$set(echo = TRUE)
Download a full set of data for a specific subject from the NITRC XNAT repository
The following tutorial will provide a fully functional example on how to download a full set of images for a specific subject, using the Rxnat package functionality.
Install the Rxnat package
You can install Rxnat from Neuroconductor with:
``` {r, eval = FALSE}
source("https://neuroconductor.org/neurocLite.R")
neuro_install('Rxnat')
### Setting up system environment variables
To use system environment variables we need to add them to the `.Renviron` file located in the user's home folder. Use `Sys.getenv("HOME")` to get the path (for unix/osx users the location can be easily accessed with ~, eg. `vi ~/.Renviron`).
The `Rxnat` package will be able to automatically read / use a system environment variable provided the following format is used: `XXXX_RXNAT_USER` and `XXXX_RXNAT_PASS`. `XXXX` is provided as an argument when an XNAT connection is initiated.
As an example `NITRC` is used as argument and the system environment variables names should be `NITRC_RXNAT_USER`, and `NITRC_RXNAT_PASS`.
``` {r, eval = TRUE}
library(Rxnat)
library(dplyr)
nitrc <- xnat_connect('https://nitrc.org/ir', xnat_name='NITRC')
Retrieve list of subjects
To retrieve the full list of subjects for the nitrc XNAT connection, we will use the nitrc$subjects() function.
``` {r, eval = TRUE}
nitrc_subjects <- nitrc$subjects()
head(nitrc_subjects)
### Retrieve list of experiments
To retrieve the full list of experiments for the `nitrc` XNAT connection, we will use the `nitrc$experiments()` function.
``` {r, eval = TRUE}
nitrc_experiments <- nitrc$experiments()
head(nitrc_experiments)
Get list of all experiments associated with a subject
For the purpose of this example, we would like to identify a subject that has more than one experiments associated with his id. In order to figure out a good subject ID example, we will filter and select all subjects with more than 1 experiment associated.
``` {r, eval = TRUE}
multi_session = nitrc_experiments %>%
group_by(subject) %>%
mutate(n_sessions = n()) %>%
filter(n_sessions > 1)
head(multi_session)
We will select the first subject ID (`UCLA_51209`) to continue our example.
``` {r, eval = TRUE}
subject_id <- "UCLA_51209"
subject_experiments = nitrc_experiments[ nitrc_experiments$subject %in% subject_id, ]
head(subject_experiments)
adigherman/Rxnat documentation built on Oct. 7, 2021, 2:53 p.m.
knitr::opts_chunk$set(echo = TRUE)
Download a full set of data for a specific subject from the NITRC XNAT repository
The following tutorial will provide a fully functional example on how to download a full set of images for a specific subject, using the Rxnat package functionality.
Install the Rxnat package
You can install Rxnat from Neuroconductor with:
``` {r, eval = FALSE}
source("https://neuroconductor.org/neurocLite.R")
neuro_install('Rxnat')
### Setting up system environment variables To use system environment variables we need to add them to the `.Renviron` file located in the user's home folder. Use `Sys.getenv("HOME")` to get the path (for unix/osx users the location can be easily accessed with ~, eg. `vi ~/.Renviron`). The `Rxnat` package will be able to automatically read / use a system environment variable provided the following format is used: `XXXX_RXNAT_USER` and `XXXX_RXNAT_PASS`. `XXXX` is provided as an argument when an XNAT connection is initiated. As an example `NITRC` is used as argument and the system environment variables names should be `NITRC_RXNAT_USER`, and `NITRC_RXNAT_PASS`. ``` {r, eval = TRUE} library(Rxnat) library(dplyr) nitrc <- xnat_connect('https://nitrc.org/ir', xnat_name='NITRC')
Retrieve list of subjects
To retrieve the full list of subjects for the nitrc XNAT connection, we will use the nitrc$subjects() function.
``` {r, eval = TRUE}
nitrc_subjects <- nitrc$subjects()
head(nitrc_subjects)
### Retrieve list of experiments To retrieve the full list of experiments for the `nitrc` XNAT connection, we will use the `nitrc$experiments()` function. ``` {r, eval = TRUE} nitrc_experiments <- nitrc$experiments() head(nitrc_experiments)
Get list of all experiments associated with a subject
For the purpose of this example, we would like to identify a subject that has more than one experiments associated with his id. In order to figure out a good subject ID example, we will filter and select all subjects with more than 1 experiment associated. ``` {r, eval = TRUE} multi_session = nitrc_experiments %>% group_by(subject) %>% mutate(n_sessions = n()) %>% filter(n_sessions > 1) head(multi_session)
We will select the first subject ID (`UCLA_51209`) to continue our example. ``` {r, eval = TRUE} subject_id <- "UCLA_51209" subject_experiments = nitrc_experiments[ nitrc_experiments$subject %in% subject_id, ] head(subject_experiments)
