a_overview.R
In mand: Multivariate Analysis for Neuroimaging Data

## ----echo=FALSE-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
options(width = 300)

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library(mand)

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data(template)

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dim(template)

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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, schange=TRUE, simscale=1/4, ROI=TRUE)

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

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data(diffimg)
coat(template, diffimg)

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data(atlasdatasets)
atlasname = "aal3"
atlasdataset = atlasdatasets[[atlasname]]
head(atlasdataset)

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

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tmpatlas[,15:20,12]

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coat(template, tmpatlas, regionplot=TRUE, 
atlasdataset=atlasdataset, ROIids = c(1:2, 41:44), regionlegend=TRUE)

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atlastable(tmpatlas, diffimg, atlasdataset, ROIids = c(1:2, 41:44))

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hipmask = (tmpatlas == 41) + (tmpatlas == 42)
template2 = template * hipmask

## ----fig.width = 5, fig.height = 2------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
par(mfrow=c(1,3), mar=rep(1,4))
coat(template, pseq=12, paron=FALSE)
coat(hipmask, pseq=12, paron=FALSE)
coat(template2, pseq=12, paron=FALSE)

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

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data(baseimg)
data(diffimg)
data(mask)
data(sdevimg)

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dim(baseimg)

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diffimg2 = diffimg * (tmpatlas %in% 41:44)

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img1 = simbrain(baseimg = baseimg, diffimg = diffimg2, 
sdevimg=sdevimg, mask=mask, n0=20, c1=0.01, sd1=0.05)

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dim(img1$S)

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coat(rec(img1$S[1,], img1$imagedim, mask=img1$brainpos))

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sdimg = apply(img1$S, 2, sd)
coat(template, rec(sdimg, img1$imagedim, mask=img1$brainpos))

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(fit111 = msma(img1$S, comp=2))

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plot(fit111, v="score", axes = 1:2, plottype="scatter")

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midx = 1 ## the index for the modality
vidx = 1 ## the index for the component
Q = fit111$wbX[[midx]][,vidx]
outstat1 = rec(Q, img1$imagedim, mask=img1$brainpos)

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coat(template, outstat1)

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B1 = rbfunc(imagedim=img1$imagedim, seppix=2, hispec=FALSE, mask=img1$brainpos)

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SB1 = basisprod(img1$S, B1)

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dim(img1$S)

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dim(SB1)

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(fit211 = msma(SB1, comp=2))

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Q = fit211$wbX[[1]][,1]
outstat1 = rec(Q, img1$imagedim, B=B1, mask=img1$brainpos)

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coat(template, outstat1)

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(fit112 = msma(SB1, comp=2, lambdaX=0.06))

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Q = fit112$wbX[[midx]][,vidx]
outstat1 = rec(Q, img1$imagedim, B=B1, mask=img1$brainpos)
outstat2 = outstat1
coat(template, outstat2)

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atlastable(tmpatlas, outstat2, atlasdataset)

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Z = img1$Z

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(fit113 = msma(SB1, Z=Z, comp=2, lambdaX=0.06, muX=0.5))

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Q = fit113$wbX[[1]][,1]
outstat1 = rec(Q, img1$imagedim, B=B1, mask=img1$brainpos)
outstat2 = -outstat1
coat(template, outstat2)

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atlastable(tmpatlas, outstat2, atlasdataset)

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Q = fit113$wbX[[1]][,2]
outstat1 = rec(Q, img1$imagedim, B=B1, mask=img1$brainpos)
outstat2 = -outstat1
coat(template, outstat2)

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atlastable(tmpatlas, outstat2, atlasdataset)

## ----fig.width = 7, fig.height = 6.5----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
ws = multirec(fit113, imagedim=img1$imagedim, B=B1, mask=img1$brainpos)
multicompplot(ws, template, col4comp=4)