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.

require(brainKCCA)
#> Loading required package: brainKCCA
require(oro.nifti)
#> Loading required package: oro.nifti
#> oro.nifti 0.10.1
# 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)
#> Reading nii files...this progress may take a long time... 
#> 
  |                                                                       
  |                                                                 |   0%
  |                                                                       
  |=                                                                |   1%
  |                                                                       
  |=                                                                |   2%
  |                                                                       
  |==                                                               |   3%
  |                                                                       
  |===                                                              |   4%
  |                                                                       
  |===                                                              |   5%
  |                                                                       
  |====                                                             |   6%
  |                                                                       
  |====                                                             |   7%
  |                                                                       
  |=====                                                            |   8%
  |                                                                       
  |======                                                           |   9%
  |                                                                       
  |=======                                                          |  10%
  |                                                                       
  |=======                                                          |  11%
  |                                                                       
  |========                                                         |  12%
  |                                                                       
  |========                                                         |  13%
  |                                                                       
  |=========                                                        |  14%
  |                                                                       
  |==========                                                       |  15%
  |                                                                       
  |==========                                                       |  16%
  |                                                                       
  |===========                                                      |  16%
  |                                                                       
  |===========                                                      |  17%
  |                                                                       
  |============                                                     |  18%
  |                                                                       
  |============                                                     |  19%
  |                                                                       
  |=============                                                    |  20%
  |                                                                       
  |=============                                                    |  21%
  |                                                                       
  |==============                                                   |  22%
  |                                                                       
  |===============                                                  |  22%
  |                                                                       
  |===============                                                  |  23%
  |                                                                       
  |================                                                 |  24%
  |                                                                       
  |================                                                 |  25%
  |                                                                       
  |=================                                                |  26%
  |                                                                       
  |=================                                                |  27%
  |                                                                       
  |==================                                               |  28%
  |                                                                       
  |===================                                              |  29%
  |                                                                       
  |====================                                             |  30%
  |                                                                       
  |====================                                             |  31%
  |                                                                       
  |=====================                                            |  32%
  |                                                                       
  |=====================                                            |  33%
  |                                                                       
  |======================                                           |  34%
  |                                                                       
  |=======================                                          |  35%
  |                                                                       
  |========================                                         |  36%
  |                                                                       
  |========================                                         |  37%
  |                                                                       
  |=========================                                        |  38%
  |                                                                       
  |=========================                                        |  39%
  |                                                                       
  |==========================                                       |  40%
  |                                                                       
  |==========================                                       |  41%
  |                                                                       
  |===========================                                      |  41%
  |                                                                       
  |===========================                                      |  42%
  |                                                                       
  |============================                                     |  43%
  |                                                                       
  |=============================                                    |  44%
  |                                                                       
  |=============================                                    |  45%
  |                                                                       
  |==============================                                   |  46%
  |                                                                       
  |==============================                                   |  47%
  |                                                                       
  |===============================                                  |  47%
  |                                                                       
  |===============================                                  |  48%
  |                                                                       
  |================================                                 |  49%
  |                                                                       
  |================================                                 |  50%
  |                                                                       
  |=================================                                |  51%
  |                                                                       
  |==================================                               |  52%
  |                                                                       
  |==================================                               |  53%
  |                                                                       
  |===================================                              |  53%
  |                                                                       
  |===================================                              |  54%
  |                                                                       
  |====================================                             |  55%
  |                                                                       
  |====================================                             |  56%
  |                                                                       
  |=====================================                            |  57%
  |                                                                       
  |======================================                           |  58%
  |                                                                       
  |======================================                           |  59%
  |                                                                       
  |=======================================                          |  59%
  |                                                                       
  |=======================================                          |  60%
  |                                                                       
  |========================================                         |  61%
  |                                                                       
  |========================================                         |  62%
  |                                                                       
  |=========================================                        |  63%
  |                                                                       
  |=========================================                        |  64%
  |                                                                       
  |==========================================                       |  65%
  |                                                                       
  |===========================================                      |  66%
  |                                                                       
  |============================================                     |  67%
  |                                                                       
  |============================================                     |  68%
  |                                                                       
  |=============================================                    |  69%
  |                                                                       
  |=============================================                    |  70%
  |                                                                       
  |==============================================                   |  71%
  |                                                                       
  |===============================================                  |  72%
  |                                                                       
  |================================================                 |  73%
  |                                                                       
  |================================================                 |  74%
  |                                                                       
  |=================================================                |  75%
  |                                                                       
  |=================================================                |  76%
  |                                                                       
  |==================================================               |  77%
  |                                                                       
  |==================================================               |  78%
  |                                                                       
  |===================================================              |  78%
  |                                                                       
  |====================================================             |  79%
  |                                                                       
  |====================================================             |  80%
  |                                                                       
  |=====================================================            |  81%
  |                                                                       
  |=====================================================            |  82%
  |                                                                       
  |======================================================           |  83%
  |                                                                       
  |======================================================           |  84%
  |                                                                       
  |=======================================================          |  84%
  |                                                                       
  |=======================================================          |  85%
  |                                                                       
  |========================================================         |  86%
  |                                                                       
  |=========================================================        |  87%
  |                                                                       
  |=========================================================        |  88%
  |                                                                       
  |==========================================================       |  89%
  |                                                                       
  |==========================================================       |  90%
  |                                                                       
  |===========================================================      |  91%
  |                                                                       
  |============================================================     |  92%
  |                                                                       
  |=============================================================    |  93%
  |                                                                       
  |=============================================================    |  94%
  |                                                                       
  |==============================================================   |  95%
  |                                                                       
  |==============================================================   |  96%
  |                                                                       
  |===============================================================  |  97%
  |                                                                       
  |================================================================ |  98%
  |                                                                       
  |================================================================ |  99%
  |                                                                       
  |=================================================================| 100%
#>  reading data  1 
#> 
  |                                                                       
  |                                                                 |   0%
  |                                                                       
  |=============                                                    |  20%
  |                                                                       
  |==========================                                       |  40%
  |                                                                       
  |=======================================                          |  60%
  |                                                                       
  |====================================================             |  80%
  |                                                                       
  |=================================================================| 100%
#>  Completed...
result1<-permkCCA_multipleRegion(imageDat = testcase1, region = c(1,5,10))
#> 
#>  Checking data format... 
#> 
#>  processed image data detected, do not need to read nii data again... 
#> Calculating KCC... 
#> 
  |                                                                       
  |                                                                 |   0%
  |                                                                       
  |=                                                                |   2%
  |                                                                       
  |===                                                              |   4%
  |                                                                       
  |====                                                             |   6%
  |                                                                       
  |=====                                                            |   8%
  |                                                                       
  |======                                                           |  10%
  |                                                                       
  |========                                                         |  12%
  |                                                                       
  |=========                                                        |  14%
  |                                                                       
  |==========                                                       |  16%
  |                                                                       
  |============                                                     |  18%
  |                                                                       
  |=============                                                    |  20%
  |                                                                       
  |==============                                                   |  22%
  |                                                                       
  |================                                                 |  24%
  |                                                                       
  |=================                                                |  26%
  |                                                                       
  |==================                                               |  28%
  |                                                                       
  |====================                                             |  30%
  |                                                                       
  |=====================                                            |  32%
  |                                                                       
  |======================                                           |  34%
  |                                                                       
  |=======================                                          |  36%
  |                                                                       
  |=========================                                        |  38%
  |                                                                       
  |==========================                                       |  40%
  |                                                                       
  |===========================                                      |  42%
  |                                                                       
  |=============================                                    |  44%
  |                                                                       
  |==============================                                   |  46%
  |                                                                       
  |===============================                                  |  48%
  |                                                                       
  |================================                                 |  50%
  |                                                                       
  |==================================                               |  52%
  |                                                                       
  |===================================                              |  54%
  |                                                                       
  |====================================                             |  56%
  |                                                                       
  |======================================                           |  58%
  |                                                                       
  |=======================================                          |  60%
  |                                                                       
  |========================================                         |  62%
  |                                                                       
  |==========================================                       |  64%
  |                                                                       
  |===========================================                      |  66%
  |                                                                       
  |============================================                     |  68%
  |                                                                       
  |==============================================                   |  70%
  |                                                                       
  |===============================================                  |  72%
  |                                                                       
  |================================================                 |  74%
  |                                                                       
  |=================================================                |  76%
  |                                                                       
  |===================================================              |  78%
  |                                                                       
  |====================================================             |  80%
  |                                                                       
  |=====================================================            |  82%
  |                                                                       
  |=======================================================          |  84%
  |                                                                       
  |========================================================         |  86%
  |                                                                       
  |=========================================================        |  88%
  |                                                                       
  |==========================================================       |  90%
  |                                                                       
  |============================================================     |  92%
  |                                                                       
  |=============================================================    |  94%
  |                                                                       
  |==============================================================   |  96%
  |                                                                       
  |================================================================ |  98%
  |                                                                       
  |=================================================================| 100%
#> 
  |                                                                       
  |                                                                 |   0%
  |                                                                       
  |=                                                                |   2%
  |                                                                       
  |===                                                              |   4%
  |                                                                       
  |====                                                             |   6%
  |                                                                       
  |=====                                                            |   8%
  |                                                                       
  |======                                                           |  10%
  |                                                                       
  |========                                                         |  12%
  |                                                                       
  |=========                                                        |  14%
  |                                                                       
  |==========                                                       |  16%
  |                                                                       
  |============                                                     |  18%
  |                                                                       
  |=============                                                    |  20%
  |                                                                       
  |==============                                                   |  22%
  |                                                                       
  |================                                                 |  24%
  |                                                                       
  |=================                                                |  26%
  |                                                                       
  |==================                                               |  28%
  |                                                                       
  |====================                                             |  30%
  |                                                                       
  |=====================                                            |  32%
  |                                                                       
  |======================                                           |  34%
  |                                                                       
  |=======================                                          |  36%
  |                                                                       
  |=========================                                        |  38%
  |                                                                       
  |==========================                                       |  40%
  |                                                                       
  |===========================                                      |  42%
  |                                                                       
  |=============================                                    |  44%
  |                                                                       
  |==============================                                   |  46%
  |                                                                       
  |===============================                                  |  48%
  |                                                                       
  |================================                                 |  50%
  |                                                                       
  |==================================                               |  52%
  |                                                                       
  |===================================                              |  54%
  |                                                                       
  |====================================                             |  56%
  |                                                                       
  |======================================                           |  58%
  |                                                                       
  |=======================================                          |  60%
  |                                                                       
  |========================================                         |  62%
  |                                                                       
  |==========================================                       |  64%
  |                                                                       
  |===========================================                      |  66%
  |                                                                       
  |============================================                     |  68%
  |                                                                       
  |==============================================                   |  70%
  |                                                                       
  |===============================================                  |  72%
  |                                                                       
  |================================================                 |  74%
  |                                                                       
  |=================================================                |  76%
  |                                                                       
  |===================================================              |  78%
  |                                                                       
  |====================================================             |  80%
  |                                                                       
  |=====================================================            |  82%
  |                                                                       
  |=======================================================          |  84%
  |                                                                       
  |========================================================         |  86%
  |                                                                       
  |=========================================================        |  88%
  |                                                                       
  |==========================================================       |  90%
  |                                                                       
  |============================================================     |  92%
  |                                                                       
  |=============================================================    |  94%
  |                                                                       
  |==============================================================   |  96%
  |                                                                       
  |================================================================ |  98%
  |                                                                       
  |=================================================================| 100%
#> 
  |                                                                       
  |                                                                 |   0%
  |                                                                       
  |=                                                                |   2%
  |                                                                       
  |===                                                              |   4%
  |                                                                       
  |====                                                             |   6%
  |                                                                       
  |=====                                                            |   8%
  |                                                                       
  |======                                                           |  10%
  |                                                                       
  |========                                                         |  12%
  |                                                                       
  |=========                                                        |  14%
  |                                                                       
  |==========                                                       |  16%
  |                                                                       
  |============                                                     |  18%
  |                                                                       
  |=============                                                    |  20%
  |                                                                       
  |==============                                                   |  22%
  |                                                                       
  |================                                                 |  24%
  |                                                                       
  |=================                                                |  26%
  |                                                                       
  |==================                                               |  28%
  |                                                                       
  |====================                                             |  30%
  |                                                                       
  |=====================                                            |  32%
  |                                                                       
  |======================                                           |  34%
  |                                                                       
  |=======================                                          |  36%
  |                                                                       
  |=========================                                        |  38%
  |                                                                       
  |==========================                                       |  40%
  |                                                                       
  |===========================                                      |  42%
  |                                                                       
  |=============================                                    |  44%
  |                                                                       
  |==============================                                   |  46%
  |                                                                       
  |===============================                                  |  48%
  |                                                                       
  |================================                                 |  50%
  |                                                                       
  |==================================                               |  52%
  |                                                                       
  |===================================                              |  54%
  |                                                                       
  |====================================                             |  56%
  |                                                                       
  |======================================                           |  58%
  |                                                                       
  |=======================================                          |  60%
  |                                                                       
  |========================================                         |  62%
  |                                                                       
  |==========================================                       |  64%
  |                                                                       
  |===========================================                      |  66%
  |                                                                       
  |============================================                     |  68%
  |                                                                       
  |==============================================                   |  70%
  |                                                                       
  |===============================================                  |  72%
  |                                                                       
  |================================================                 |  74%
  |                                                                       
  |=================================================                |  76%
  |                                                                       
  |===================================================              |  78%
  |                                                                       
  |====================================================             |  80%
  |                                                                       
  |=====================================================            |  82%
  |                                                                       
  |=======================================================          |  84%
  |                                                                       
  |========================================================         |  86%
  |                                                                       
  |=========================================================        |  88%
  |                                                                       
  |==========================================================       |  90%
  |                                                                       
  |============================================================     |  92%
  |                                                                       
  |=============================================================    |  94%
  |                                                                       
  |==============================================================   |  96%
  |                                                                       
  |================================================================ |  98%
  |                                                                       
  |=================================================================| 100%
summary_kcca(result1)
#> 
#>  summary of kcca object  1  generated by 'permkCCA_multipleRegion' function:
index1 index2 region1 region2 pvalue
1 5 PreCG.L ORBsup.L 1
1 10 PreCG.L ORBmid.R 0.275
5 10 ORBsup.L ORBmid.R 0