---
title: "Examples to build region-level connectivity network"
author: "Xubo Yue, Chia-Wei Hsu, Jian Kang"
date: "`r Sys.Date()`"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Examples to build region-level connectivity network}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r setup, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
```

## Vignette Info

This vignette provides you a simple example to construct region-level connectivity network. In example below, when the programming is running, the progress bar will be generated.

```{r, fig.show='hold'}
require(brainKCCA)
require(oro.nifti)
# write data into temp file. The generated NIfTI
# provide you a general structure of fMRI data.
filePath <- tempdir()
# the nii.gz fMRI imaging file is created (toy example)
oro.nifti::writeNIfTI(brainKCCA::input_img, paste(filePath, "/",  "temp", sep=""))
#read fMRI data
testcase1 <- nii2RData(niiFile1 = "temp", resolution = "3mm", imgPath = filePath)
result1<-permkCCA_multipleRegion(imageDat = testcase1, region = c(1,5,10))
summary_kcca(result1)
```