## ----echo=FALSE, error=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
options(warn=-1)
knitr::opts_chunk$set(eval = FALSE)

## ----eval=FALSE-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# if(!require("mand")) install.packages("mand")

## ----eval=TRUE, echo=TRUE, message=FALSE, error=FALSE-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
library(mand)

## ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# library(oro.nifti)
# library(oro.dicom)
# library("imager")

## ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# data(template)

## ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# dim(template)

## ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# coat(template)

## ----fig.width = 5, fig.height = 2------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# coat(x=template, plane="all")

## ----eval=FALSE-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# fnames1 = c("data1.nii", "data2.nii")
# imgmat = imgdatamat(fnames1, simscale=1/4)

## ----eval=FALSE-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# imgmat = imgdatamat(fnames1, simscale=1/4, ROI=TRUE)

## ----echo=FALSE, eval=FALSE-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# '

## ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# data(diffimg)
# coat(template, diffimg)

## ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# data(atlasdatasets)
# atlasname = "aal"
# atlasdataset = atlasdatasets[[atlasname]]
# head(atlasdataset)

## ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# data(atlas)
# tmpatlas = atlas[[atlasname]]
# dim(tmpatlas)

## ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# tmpatlas[11:15,11:15,10]

## ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# coat(template, tmpatlas, regionplot=TRUE,
# atlasdataset=atlasdataset, ROIids = c(1:2, 37:40),
# regionlegend=TRUE)

## ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# atlastable(tmpatlas, diffimg, atlasdataset, ROIids = c(1:2,
# 37:40))

## ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# hipmask = (tmpatlas == 37) + (tmpatlas == 38)
# template2 = template * hipmask

## ----fig.width = 5, fig.height = 2------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# par(mfrow=c(1,3), mar=rep(1,4))
# coat(template, pseq=11, paron=FALSE)
# coat(hipmask, pseq=11, paron=FALSE)
# coat(template2, pseq=11, paron=FALSE)

## ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# sum(template[which(hipmask==1, arr.ind = TRUE)])/1000