Overview for mand
2026-09-13 @Atsushi Kawaguchi
The mand package provides functions for multivariate
analysis for neuroimaging data.
library(mand)
library(msma)## Warning: package 'msma' was built under R version 4.5.3Introduction
Template
One subject image as the template is available in the mand package. The coad to load it is as follows.
data(template)The image is compressed because of storage and computation time. The dimension is confirmed as follows.
dim(template)## Loading required namespace: oro.nifti## [1] 30 36 30The image is plotted by the coat function.
coat(template)
Other options with the plane argument (such as “axial,” “coronal,”
“sagittal,” and “all”) are available. The default setting is “axial”. If
the argument is specified as plane="all", three directional
slices at a certain coordinate are plotted.
coat(x=template, plane="all")
Image Data Matrix
The imgdatamat function reads image files saved in the
nifti format and creates data matrix with subjects in row and voxel in
column (this example does not work).
fnames1 = c("data1.nii", "data2.nii")
imgmat = imgdatamat(fnames1, simscale=1/4)The first argument is file names with the length equaling the number
of subjects (the number of rows in the resulting data matrix). The
second argument simscale is the image resize scale. In this
example, the all sizes (number of voxel) for three direction was reduced
into its quarter size. The output is the list form where the “S” is data
matrix, the “brainpos” is a binary image indicating brain region, and
the “imagedim” is image dimension. The ROI (Region Of Interest) volume
is computed in the “roi” if the ROI argument is TRUE.
imgmat = imgdatamat(fnames1, schange=TRUE, simscale=1/4, ROI=TRUE)Overlay
The resulting map from the statistical analysis such as the t
statistics map from the SPM is represented with overlapping on the
template. For example, the mand package has the average
difference assuming Alzheimer’s disease and healthy subjects with the
array format.
The overlay is implemented by the coat function.
data(diffimg)
coat(template, diffimg)
Atlas
Anatomical brain segmentation region is useful for the plot and the interpretation. For example, the Automated Anatomical Labeling (AAL) atlas is used. The data.frame has two columns (“ROIid” and “ROIname”) format.
data(atlasdatasets)
atlasname = "aal3"
atlasdataset = atlasdatasets[[atlasname]]
head(atlasdataset)## ROIid ROIname
## 1 1 Left Precentral gyrus
## 2 2 Right Precentral gyrus
## 3 3 Left Superior frontal gyrus-dorsolateral
## 4 4 Right Superior frontal gyrus-dorsolateral
## 5 5 Left Middle frontal gyrus
## 6 6 Right Middle frontal gyrusIt is also neccesary to prepare the array data.
data(atlas)
tmpatlas = atlas[[atlasname]]
dim(tmpatlas)## [1] 30 36 30It has the ROIid as the element.
tmpatlas[,15:20,12]## [,1] [,2] [,3] [,4] [,5] [,6]
## [1,] 0 0 0 0 0 0
## [2,] 0 0 0 0 0 0
## [3,] 90 90 90 90 90 90
## [4,] 94 94 90 90 90 90
## [5,] 94 94 90 90 90 90
## [6,] 94 90 90 90 90 90
## [7,] 94 0 0 0 90 90
## [8,] 0 0 0 0 0 0
## [9,] 60 44 42 42 42 0
## [10,] 60 44 42 42 42 42
## [11,] 44 44 42 42 42 42
## [12,] 44 44 44 0 0 42
## [13,] 52 0 0 0 0 0
## [14,] 100 0 0 162 162 164
## [15,] 114 0 0 166 166 0
## [16,] 0 0 0 0 0 0
## [17,] 99 0 0 165 0 0
## [18,] 101 101 0 163 163 163
## [19,] 43 0 0 0 0 41
## [20,] 0 43 41 41 41 41
## [21,] 43 43 41 41 41 41
## [22,] 43 43 41 41 41 41
## [23,] 0 0 0 0 0 0
## [24,] 93 0 0 0 0 0
## [25,] 93 0 0 89 89 89
## [26,] 93 89 89 89 89 89
## [27,] 89 89 89 89 89 89
## [28,] 89 89 89 89 89 89
## [29,] 0 89 89 89 89 0
## [30,] 0 0 0 0 0 0The anatomical region can be plotted by the coat
function with regionplot=TRUE.
coat(template, tmpatlas, regionplot=TRUE,
atlasdataset=atlasdataset, ROIids = c(1:2, 41:44), regionlegend=TRUE)
The resulting map can be converted into the summary of the anatomical regions.
atlastable(tmpatlas, diffimg, atlasdataset, ROIids = c(1:2, 41:44))## $table
## ROIid ROIname sizenum sizepct sumvalue Min. 1st Qu. Median Mean 3rd Qu. Max.
## 1 1 Left Precentral gyrus 116 0.6170213 8.2999981 -0.5675001 0 0 2.561728e-04 0 0.8024999
## 2 2 Right Precentral gyrus 115 0.6318681 -0.3050001 -0.7349999 0 0 -9.413584e-06 0 0.7499998
## 41 41 Left Hippocampus 26 0.5909091 -7.1899993 -1.0000000 0 0 -2.219136e-04 0 0.4475000
## 42 42 Right Hippocampus 33 0.7333333 -12.1099996 -0.9675000 0 0 -3.737654e-04 0 0.5049999
## 43 43 Left Parahippocampal gyrus 30 0.7317073 -5.4949995 -0.8750000 0 0 -1.695988e-04 0 0.5300001
## 44 44 Right Parahippocampal gyrus 27 0.6923077 -3.1474993 -0.7500000 0 0 -9.714504e-05 0 0.6899998
##
## attr(,"class")
## [1] "atlastable"The outputs are the number of voxel in the sizenum
column, the percentage of the voxel in the sizepct column,
and the minimum, mean, and maximum valued of the region of the
overlaying map. The order of the table row is in the larger absolute
value of the minimum or maximum values.
The brain image corresponding to the region of interest can be extracted as follows. First, we create a mask image in which the hippocampal region is represented by 1 and others by 0. Then the product of the template and the mask image is taken for each voxel.
hipmask = (tmpatlas == 41) + (tmpatlas == 42)
template2 = template * hipmaskThe images generated by these processes are plotted from left to right in one slice.
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)
The template image (left) and the mask image (middle) are multiplied voxel by voxel to obtain the only hippocampus region image (right).
The sum of the voxel values in the region is calculated as follows.
sum(template[which(hipmask==1, arr.ind = TRUE)])/1000## [1] 0.07090703Such a value is calculated for each region and a dataset with ROI values is created.
Principal Component Analysis
Generate Simulation Data
The mand package has a function to generate simulation
brain data from the base image, the difference image and the standard
deviation image. These basic images are loaded as follows.
data(baseimg)
data(diffimg)
data(mask)
data(sdevimg)The number of voxels in the original 3D image is as follows.
dim(baseimg)## [1] 30 36 30To understand the result easily, the difference region was restricted to Parahippocampus and Hippocampus.
diffimg2 = diffimg * (tmpatlas %in% 41:44)An image data matrix with subjects in the rows and voxels in the
columns was generated by using the simbrain function.
img1 = simbrain(baseimg = baseimg, diffimg = diffimg2,
sdevimg=sdevimg, mask=mask, n0=20, c1=0.01, sd1=0.05)The base image, the difference image and the standard deviation image were specified in the first three arguments. The out-of-brain region was specified by the mask argument, which was the binary image. The remaining arguments are the number of subjects per group, the coefficient multiplied by the difference image and the standard deviation for the noise.
The data matrix dimension was 40(subject) x 12620(voxel).
dim(img1$S)## [1] 40 12620The rec function creates the 3D image from the
vectorized data (the first subject).
coat(rec(img1$S[1,], img1$imagedim, mask=img1$brainpos))
The standard deviation image is created from the resulting data matrix.
sdimg = apply(img1$S, 2, sd)
coat(template, rec(sdimg, img1$imagedim, mask=img1$brainpos))
Principal Component Analysis
If the input is a matrix, a principal component analysis is
implemented by the msma function of the msma
package. Principal component analysis with the number of components of 2
for the image data matrix is performed as follows.
(fit111 = msma(img1$S, comp=2))## Call:
## .msma_default_legacy(X = X, Y = Y, Z = Z_legacy, comp = comp,
## lambdaX = lambdaX, lambdaY = lambdaY, lambdaXsup = lambdaXsup,
## lambdaYsup = lambdaYsup, eta = eta, type = type, inX = inX,
## inY = inY, inXsup = inXsup, inYsup = inYsup, muX = muX, muY = muY,
## defmethod = defmethod, scaling = scaling, verbose = verbose,
## intseed = intseed, ceps = ceps)
##
## Numbers of non-zeros for X block:
## comp1 comp2
## block1 9865 9865
##
## Numbers of non-zeros for X super:
## comp1 comp2
## comp1-1 1 1The scatter plots for the score vectors specified by the argument
v. The argument axes is specified by the two
length vectors on which components are displayed.
plot(fit111, v="score", axes = 1:2, plottype="scatter")
The weight (loading) vectors can be obtained and reconstructed as follows.
midx = 1 ## the index for the modality
vidx = 1 ## the index for the component
Q = fit111$wbX[[midx]][,vidx]
outstat1 = rec(Q, img1$imagedim, mask=img1$brainpos)The reconstructed loadings as image is overlayed on the template.
coat(template, outstat1)
The output is unclear; however, this will be improved later.
Two-steps dimension reduction
Basis Expansion
This is an example of the two-step dimension reduction.
Generate radial basis function.
B1 = rbfunc(imagedim=img1$imagedim, seppix=2, hispec=FALSE, mask=img1$brainpos)Multiplying the basis function to image data matrix.
SB1 = basisprod(img1$S, B1)The original dimension was 12620.
dim(img1$S)## [1] 40 12620The dimension was reduced to 1604.
dim(SB1)## [1] 40 1604Principal Component Analysis
The Principal Component Analysis (PCA) is applied to the dimension-reduced image.
(fit211 = msma(SB1, comp=2))## Call:
## .msma_default_legacy(X = X, Y = Y, Z = Z_legacy, comp = comp,
## lambdaX = lambdaX, lambdaY = lambdaY, lambdaXsup = lambdaXsup,
## lambdaYsup = lambdaYsup, eta = eta, type = type, inX = inX,
## inY = inY, inXsup = inXsup, inYsup = inYsup, muX = muX, muY = muY,
## defmethod = defmethod, scaling = scaling, verbose = verbose,
## intseed = intseed, ceps = ceps)
##
## Numbers of non-zeros for X block:
## comp1 comp2
## block1 1604 1604
##
## Numbers of non-zeros for X super:
## comp1 comp2
## comp1-1 1 1The loading is reconstructed to the original space by using the
rec function.
Q = fit211$wbX[[1]][,1]
outstat1 = rec(Q, img1$imagedim, B=B1, mask=img1$brainpos)The plotted loading is smoother than the one without the dimension reduction by the basis function.
coat(template, outstat1)
Sparse PCA
If lambdaX (>0) is specified, a sparse principal
component analysis is implemented.
(fit112 = msma(SB1, comp=2, lambdaX=0.06))## Call:
## .msma_default_legacy(X = X, Y = Y, Z = Z_legacy, comp = comp,
## lambdaX = lambdaX, lambdaY = lambdaY, lambdaXsup = lambdaXsup,
## lambdaYsup = lambdaYsup, eta = eta, type = type, inX = inX,
## inY = inY, inXsup = inXsup, inYsup = inYsup, muX = muX, muY = muY,
## defmethod = defmethod, scaling = scaling, verbose = verbose,
## intseed = intseed, ceps = ceps)
##
## Numbers of non-zeros for X block:
## comp1 comp2
## block1 53 40
##
## Numbers of non-zeros for X super:
## comp1 comp2
## comp1-1 1 1The plotted loading is narrower than that from the PCA.
Q = fit112$wbX[[midx]][,vidx]
outstat1 = rec(Q, img1$imagedim, B=B1, mask=img1$brainpos)
outstat2 = outstat1
coat(template, outstat2)
The region is reported as follows to be compared with the next method.
atlastable(tmpatlas, outstat2, atlasdataset)## $table
## ROIid ROIname sizenum sizepct sumvalue Min. 1st Qu. Median Mean 3rd Qu. Max.
## 1 1 Left Precentral gyrus 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 2 2 Right Precentral gyrus 56 0.30769231 4.748789e-01 0 0 0 1.465676e-05 0 1.424819e-01
## 3 3 Left Superior frontal gyrus-dorsolateral 180 0.72000000 8.552688e+01 0 0 0 2.639719e-03 0 2.332348e+00
## 4 4 Right Superior frontal gyrus-dorsolateral 207 0.84489796 2.577099e+02 0 0 0 7.954008e-03 0 5.165228e+00
## 5 5 Left Middle frontal gyrus 152 0.60317460 7.292652e+00 0 0 0 2.250818e-04 0 5.065971e-01
## 6 6 Right Middle frontal gyrus 243 0.97590361 1.277586e+02 0 0 0 3.943165e-03 0 3.423288e+00
## 7 7 Left Inferior frontal gyrus-opercular part 7 0.11475410 2.861414e-03 0 0 0 8.831525e-08 0 1.440939e-03
## 8 8 Right Inferior frontal gyrus-opercular part 64 0.94117647 5.151732e+00 0 0 0 1.590041e-04 0 5.929501e-01
## 9 9 Left Inferior frontal gyrus-triangular part 57 0.50892857 6.078731e-01 0 0 0 1.876151e-05 0 1.129497e-01
## 10 10 Right Inferior frontal gyrus-triangular part 115 0.99137931 2.188454e+01 0 0 0 6.754489e-04 0 1.911110e+00
## 11 11 Left IFG pars orbitalis 21 0.58333333 4.266604e-01 0 0 0 1.316853e-05 0 1.065023e-01
## 12 12 Right IFG pars orbitalis 43 0.93478261 2.176215e+00 0 0 0 6.716713e-05 0 5.083335e-01
## 13 13 Left Rolandic operculum 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 14 14 Right Rolandic operculum 12 0.16438356 1.019422e-02 0 0 0 3.146363e-07 0 6.472303e-03
## 15 15 Left Supplementary motor area 35 0.40229885 7.773107e-01 0 0 0 2.399107e-05 0 2.312197e-01
## 16 16 Right Supplementary motor area 58 0.54716981 3.673874e+00 0 0 0 1.133912e-04 0 7.358109e-01
## 17 17 Left Olfactory cortex 11 0.91666667 4.855253e+00 0 0 0 1.498535e-04 0 1.829529e+00
## 18 18 Right Olfactory cortex 11 1.00000000 6.328657e+00 0 0 0 1.953289e-04 0 2.354883e+00
## 19 19 Left Superior frontal gyrus-medial 115 1.00000000 2.375736e+02 0 0 0 7.332519e-03 0 6.165573e+00
## 20 20 Right Superior frontal gyrus-medial 94 1.00000000 2.264148e+02 0 0 0 6.988112e-03 0 6.113931e+00
## 21 21 Left Superior frontal gyrus-medial orbital 32 1.00000000 2.120301e+01 0 0 0 6.544138e-04 0 1.629459e+00
## 22 22 Right Superior frontal gyrus-medial orbital 39 1.00000000 2.970613e+01 0 0 0 9.168558e-04 0 2.010142e+00
## 23 23 Left Gyrus rectus 27 1.00000000 3.744205e+00 0 0 0 1.155619e-04 0 3.113401e-01
## 24 24 Right Gyrus rectus 21 1.00000000 4.476652e+00 0 0 0 1.381683e-04 0 4.301427e-01
## 25 25 Left Medial orbital gyrus 17 1.00000000 1.269704e+00 0 0 0 3.918840e-05 0 1.704211e-01
## 26 26 Right Medial orbital gyrus 15 1.00000000 2.378205e+00 0 0 0 7.340137e-05 0 2.864638e-01
## 27 27 Left Anterior orbital gyrus 9 1.00000000 3.576257e-01 0 0 0 1.103783e-05 0 1.330053e-01
## 28 28 Right Anterior orbital gyrus 21 1.00000000 3.157526e+00 0 0 0 9.745450e-05 0 4.529979e-01
## 29 29 Left Posterior orbital gyrus 11 0.64705882 5.391140e-02 0 0 0 1.663932e-06 0 1.964482e-02
## 30 30 Right Posterior orbital gyrus 17 1.00000000 1.334172e+00 0 0 0 4.117815e-05 0 2.486018e-01
## 31 31 Left Lateral orbital gyrus 2 1.00000000 2.524063e-04 0 0 0 7.790319e-09 0 1.463614e-04
## 32 32 Right Lateral orbital gyrus 0 NaN 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 33 33 Left Insula 38 0.39583333 1.511061e+00 0 0 0 4.663770e-05 0 3.174231e-01
## 34 34 Right Insula 63 0.64948454 7.451335e+00 0 0 0 2.299795e-04 0 1.041648e+00
## 35 35 Left Anterior cingulate & paracingulate gyri 0 NaN 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 36 36 Right Anterior cingulate & paracingulate gyri 0 NaN 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 37 37 Left Middle cingulate & paracingulate gyri 29 0.30851064 6.714268e+00 0 0 0 2.072305e-04 0 1.478810e+00
## 38 38 Right Middle cingulate & paracingulate gyri 45 0.45918367 4.031853e+01 0 0 0 1.244399e-03 0 5.686351e+00
## 39 39 Left Posterior cingulate gyrus 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 40 40 Right Posterior cingulate gyrus 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 41 41 Left Hippocampus 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 42 42 Right Hippocampus 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 43 43 Left Parahippocampal gyrus 1 0.02439024 8.086059e-06 0 0 0 2.495697e-10 0 8.086059e-06
## 44 44 Right Parahippocampal gyrus 1 0.02564103 1.728440e-04 0 0 0 5.334690e-09 0 1.728440e-04
## 45 45 Left Amygdala 1 0.09090909 3.870510e-05 0 0 0 1.194602e-09 0 3.870510e-05
## 46 46 Right Amygdala 7 0.53846154 7.060743e-03 0 0 0 2.179242e-07 0 3.596136e-03
## 47 47 Left Calcarine fissure and surrounding cortex 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 48 48 Right Calcarine fissure and surrounding cortex 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 49 49 Left Cuneus 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 50 50 Right Cuneus 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 51 51 Left Lingual gyrus 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 52 52 Right Lingual gyrus 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 53 53 Left Superior occipital gyrus 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 54 54 Right Superior occipital gyrus 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 55 55 Left Middle occipital gyrus 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 56 56 Right Middle occipital gyrus 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 57 57 Left Inferior occipital gyrus 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 58 58 Right Inferior occipital gyrus 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 59 59 Left Fusiform gyrus 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 60 60 Right Fusiform gyrus 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 61 61 Left Postcentral gyrus 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 62 62 Right Postcentral gyrus 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 63 63 Left Superior parietal gyrus 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 64 64 Right Superior parietal gyrus 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 65 65 Left Inferior parietal gyrus-excluding supramarginal and angular gyri 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 66 66 Right Inferior parietal gyrus-excluding supramarginal and angular gyri 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 67 67 Left SupraMarginal gyrus 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 68 68 Right SupraMarginal gyrus 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 69 69 Left Angular gyrus 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 70 70 Right Angular gyrus 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 71 71 Left Precuneus 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 72 72 Right Precuneus 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 73 73 Left Paracentral lobule 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 74 74 Right Paracentral lobule 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 75 75 Left Caudate nucleus 35 0.94594595 1.575101e+01 0 0 0 4.861422e-04 0 1.417868e+00
## 76 76 Right Caudate nucleus 48 0.96000000 4.136425e+01 0 0 0 1.276674e-03 0 2.408496e+00
## 77 77 Left Lenticular nucleus-Putamen 37 0.68518519 1.955917e+00 0 0 0 6.036782e-05 0 3.002033e-01
## 78 78 Right Lenticular nucleus-Putamen 50 0.86206897 6.975001e+00 0 0 0 2.152778e-04 0 7.603229e-01
## 79 79 Left Lenticular nucleus-Pallidum 11 1.00000000 1.607813e-01 0 0 0 4.962386e-06 0 5.541498e-02
## 80 80 Right Lenticular nucleus-Pallidum 10 0.90909091 6.973981e-01 0 0 0 2.152463e-05 0 2.784539e-01
## 81 81 Left Thalamus 0 NaN 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 82 82 Right Thalamus 0 NaN 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 83 83 Left Heschls gyrus 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 84 84 Right Heschls gyrus 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 85 85 Left Superior temporal gyrus 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 86 86 Right Superior temporal gyrus 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 87 87 Left Temporal pole: superior temporal gyrus 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 88 88 Right Temporal pole: superior temporal gyrus 15 0.22058824 2.735908e-03 0 0 0 8.444162e-08 0 1.032239e-03
## 89 89 Left Middle temporal gyrus 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 90 90 Right Middle temporal gyrus 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 91 91 Left Temporal pole: middle temporal gyrus 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 92 92 Right Temporal pole: middle temporal gyrus 1 0.01886792 4.699404e-06 0 0 0 1.450433e-10 0 4.699404e-06
## 93 93 Left Inferior temporal gyrus 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 94 94 Right Inferior temporal gyrus 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 95 95 Left Crus I of cerebellar hemisphere 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 96 96 Right Crus I of cerebellar hemisphere 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 97 97 Left Crus II of cerebellar hemisphere 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 98 98 Right Crus II of cerebellar hemisphere 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 99 99 Left Lobule III of cerebellar hemisphere 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 100 100 Right Lobule III of cerebellar hemisphere 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 101 101 Left Lobule IV-V of cerebellar hemisphere 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 102 102 Right Lobule IV-V of cerebellar hemisphere 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 103 103 Left Lobule VI of cerebellar hemisphere 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 104 104 Right Lobule VI of cerebellar hemisphere 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 105 105 Left Lobule VIIB of cerebellar hemisphere 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 106 106 Right Lobule VIIB of cerebellar hemisphere 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 107 107 Left Lobule VIII of cerebellar hemisphere 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 108 108 Right Lobule VIII of cerebellar hemisphere 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 109 109 Left Lobule IX of cerebellar hemisphere 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 110 110 Right Lobule IX of cerebellar hemisphere 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 111 111 Left Lobule X of cerebellar hemisphere 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 112 112 Right Lobule X of cerebellar hemisphere 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 113 113 Lobule I-II of vermis 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 114 114 Lobule III of vermis 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 115 115 Lobule IV-V of vermis 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 116 116 Lobule VI of vermis 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 117 117 Lobule VII of vermis 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 118 118 Lobule VIII of vermis 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 119 119 Lobule IX of vermis 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 120 120 Lobule X of vermis 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 121 121 Left Thalamus-Anteroventral Nucleus 1 1.00000000 3.233869e-03 0 0 0 9.981077e-08 0 3.233869e-03
## 122 122 Right Thalamus-Anteroventral Nucleus 2 1.00000000 6.359419e-02 0 0 0 1.962784e-06 0 5.889710e-02
## 123 123 Left Lateral posterior 0 NaN 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 124 124 Right Lateral posterior 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 125 125 Left Ventral anterior 3 1.00000000 4.623904e-02 0 0 0 1.427131e-06 0 2.640670e-02
## 126 126 Right Ventral anterior 5 1.00000000 1.761699e-01 0 0 0 5.437343e-06 0 4.988060e-02
## 127 127 Left Ventral lateral 4 0.26666667 4.858415e-03 0 0 0 1.499511e-07 0 1.955612e-03
## 128 128 Right Ventral lateral 6 0.54545455 1.652199e-02 0 0 0 5.099380e-07 0 3.867090e-03
## 129 129 Left Ventral posterolateral 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 130 130 Right Ventral posterolateral 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 131 131 Left Intralaminar 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 132 132 Right Intralaminar 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 133 133 Left Reuniens 0 NaN 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 134 134 Right Reuniens 0 NaN 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 135 135 Left Mediodorsal medial magnocellular 1 0.11111111 1.916387e-03 0 0 0 5.914774e-08 0 1.916387e-03
## 136 136 Right Mediodorsal medial magnocellular 1 0.11111111 3.580514e-03 0 0 0 1.105097e-07 0 3.580514e-03
## 137 137 Left Mediodorsal lateral parvocellular 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 138 138 Right Mediodorsal lateral parvocellular 1 0.25000000 4.886574e-03 0 0 0 1.508202e-07 0 4.886574e-03
## 139 139 Left Lateral geniculate 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 140 140 Right Lateral geniculate 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 141 141 Left Medial Geniculate 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 142 142 Right Medial Geniculate 0 NaN 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 143 143 Left Pulvinar anterior 0 NaN 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 144 144 Right Pulvinar anterior 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 145 145 Left Pulvinar medial 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 146 146 Right Pulvinar medial 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 147 147 Left Pulvinar lateral 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 148 148 Right Pulvinar lateral 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 149 149 Left Pulvinar inferior 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 150 150 Right Pulvinar inferior 0 NaN 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 151 151 Left Anterior cingulate cortex-subgenual 10 1.00000000 1.522313e+01 0 0 0 4.698496e-04 0 2.916240e+00
## 152 152 Right Anterior cingulate cortex-subgenual 6 1.00000000 1.353748e+01 0 0 0 4.178233e-04 0 3.413513e+00
## 153 153 Left Anterior cingulate cortex-pregenual 35 1.00000000 1.331032e+02 0 0 0 4.108123e-03 0 6.943993e+00
## 154 154 Right Anterior cingulate cortex-pregenual 36 1.00000000 2.089043e+02 0 0 0 6.447665e-03 0 7.480375e+00
## 155 155 Left Anterior cingulate cortex-supracallosal 39 1.00000000 1.069481e+02 0 0 0 3.300868e-03 0 6.448857e+00
## 156 156 Right Anterior cingulate cortex-supracallosal 31 1.00000000 1.361975e+02 0 0 0 4.203627e-03 0 6.880439e+00
## 157 157 Left Nucleus accumbens 7 1.00000000 1.878194e+00 0 0 0 5.796894e-05 0 6.456946e-01
## 158 158 Right Nucleus accumbens 7 1.00000000 3.141609e+00 0 0 0 9.696323e-05 0 8.745726e-01
## 159 159 Left Ventral tegmental area 0 NaN 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 160 160 Right Ventral tegmental area 0 NaN 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 161 161 Left Substantia nigra-pars compacta 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 162 162 Right Substantia nigra-pars compacta 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 163 163 Left Substantia nigra-pars reticulata 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 164 164 Right Substantia nigra-pars reticulata 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 165 165 Left Red nucleus 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 166 166 Right Red nucleus 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 167 167 Left Locus coeruleus 0 NaN 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 168 168 Right Locus coeruleus 0 NaN 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 169 169 Raphe nucleus-dorsal 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 170 170 Raphe nucleus-median 0 NaN 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
##
## attr(,"class")
## [1] "atlastable"Supervised Sparse PCA
The simbrain generates the synthetic brain image data
and the binary outcome. The outcome Z is obtained.
Z = img1$ZIf the outcome Z is specified in the msma function, a
supervised sparse principal component analysis is implemented.
(fit113 = msma(SB1, Z=Z, comp=2, lambdaX=0.06, muX=0.5))## Call:
## .msma_default_legacy(X = X, Y = Y, Z = Z_legacy, comp = comp,
## lambdaX = lambdaX, lambdaY = lambdaY, lambdaXsup = lambdaXsup,
## lambdaYsup = lambdaYsup, eta = eta, type = type, inX = inX,
## inY = inY, inXsup = inXsup, inYsup = inYsup, muX = muX, muY = muY,
## defmethod = defmethod, scaling = scaling, verbose = verbose,
## intseed = intseed, ceps = ceps)
##
## Numbers of non-zeros for X block:
## comp1 comp2
## block1 48 38
##
## Numbers of non-zeros for X super:
## comp1 comp2
## comp1-1 1 1The plotted loading is located differently from the sparse PCA.
Q = fit113$wbX[[1]][,1]
outstat1 = rec(Q, img1$imagedim, B=B1, mask=img1$brainpos)
outstat2 = -outstat1
coat(template, outstat2)
The region near the hippocampus, which differs from the sparse PCA (without supervision).
atlastable(tmpatlas, outstat2, atlasdataset)## $table
## ROIid ROIname sizenum sizepct sumvalue Min. 1st Qu. Median Mean 3rd Qu. Max.
## 1 1 Left Precentral gyrus 124 0.65957447 1.062377e+01 0 0 0 3.278941e-04 0 8.569300e-01
## 2 2 Right Precentral gyrus 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 3 3 Left Superior frontal gyrus-dorsolateral 1 0.00400000 3.337561e-05 0 0 0 1.030111e-09 0 3.337561e-05
## 4 4 Right Superior frontal gyrus-dorsolateral 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 5 5 Left Middle frontal gyrus 17 0.06746032 3.876795e-02 0 0 0 1.196542e-06 0 1.360439e-02
## 6 6 Right Middle frontal gyrus 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 7 7 Left Inferior frontal gyrus-opercular part 59 0.96721311 2.314522e+00 0 0 0 7.143586e-05 0 2.362614e-01
## 8 8 Right Inferior frontal gyrus-opercular part 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 9 9 Left Inferior frontal gyrus-triangular part 9 0.08035714 6.248256e-02 0 0 0 1.928474e-06 0 2.964117e-02
## 10 10 Right Inferior frontal gyrus-triangular part 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 11 11 Left IFG pars orbitalis 7 0.19444444 1.908029e-03 0 0 0 5.888979e-08 0 6.357083e-04
## 12 12 Right IFG pars orbitalis 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 13 13 Left Rolandic operculum 56 1.00000000 1.254762e+02 0 0 0 3.872724e-03 0 5.222454e+00
## 14 14 Right Rolandic operculum 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 15 15 Left Supplementary motor area 1 0.01149425 6.998475e-06 0 0 0 2.160023e-10 0 6.998475e-06
## 16 16 Right Supplementary motor area 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 17 17 Left Olfactory cortex 10 0.83333333 3.775781e-01 0 0 0 1.165364e-05 0 1.950686e-01
## 18 18 Right Olfactory cortex 2 0.18181818 1.446679e-05 0 0 0 4.465060e-10 0 1.120140e-05
## 19 19 Left Superior frontal gyrus-medial 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 20 20 Right Superior frontal gyrus-medial 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 21 21 Left Superior frontal gyrus-medial orbital 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 22 22 Right Superior frontal gyrus-medial orbital 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 23 23 Left Gyrus rectus 6 0.22222222 2.310631e-02 0 0 0 7.131576e-07 0 1.401455e-02
## 24 24 Right Gyrus rectus 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 25 25 Left Medial orbital gyrus 4 0.23529412 2.750149e-02 0 0 0 8.488115e-07 0 1.585314e-02
## 26 26 Right Medial orbital gyrus 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 27 27 Left Anterior orbital gyrus 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 28 28 Right Anterior orbital gyrus 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 29 29 Left Posterior orbital gyrus 12 0.70588235 2.083022e-01 0 0 0 6.429081e-06 0 6.971438e-02
## 30 30 Right Posterior orbital gyrus 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 31 31 Left Lateral orbital gyrus 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 32 32 Right Lateral orbital gyrus 0 NaN 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 33 33 Left Insula 88 0.91666667 1.009409e+02 0 0 0 3.115460e-03 0 5.909930e+00
## 34 34 Right Insula 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 35 35 Left Anterior cingulate & paracingulate gyri 0 NaN 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 36 36 Right Anterior cingulate & paracingulate gyri 0 NaN 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 37 37 Left Middle cingulate & paracingulate gyri 63 0.67021277 2.582099e+00 0 0 0 7.969440e-05 0 3.027063e-01
## 38 38 Right Middle cingulate & paracingulate gyri 32 0.32653061 1.769562e-01 0 0 0 5.461610e-06 0 2.593513e-02
## 39 39 Left Posterior cingulate gyrus 17 1.00000000 6.040326e+00 0 0 0 1.864298e-04 0 1.881986e+00
## 40 40 Right Posterior cingulate gyrus 11 1.00000000 4.148732e-01 0 0 0 1.280473e-05 0 1.291099e-01
## 41 41 Left Hippocampus 44 1.00000000 1.290294e+02 0 0 0 3.982388e-03 0 6.665653e+00
## 42 42 Right Hippocampus 1 0.02222222 5.363438e-03 0 0 0 1.655382e-07 0 5.363438e-03
## 43 43 Left Parahippocampal gyrus 41 1.00000000 7.173206e+01 0 0 0 2.213952e-03 0 5.094835e+00
## 44 44 Right Parahippocampal gyrus 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 45 45 Left Amygdala 11 1.00000000 5.659849e+00 0 0 0 1.746867e-04 0 9.840613e-01
## 46 46 Right Amygdala 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 47 47 Left Calcarine fissure and surrounding cortex 52 0.58426966 1.290853e+01 0 0 0 3.984116e-04 0 1.525031e+00
## 48 48 Right Calcarine fissure and surrounding cortex 12 0.12371134 1.814160e-02 0 0 0 5.599260e-07 0 7.291375e-03
## 49 49 Left Cuneus 28 0.42424242 1.251272e+00 0 0 0 3.861951e-05 0 3.980086e-01
## 50 50 Right Cuneus 3 0.03750000 3.970363e-03 0 0 0 1.225421e-07 0 3.636119e-03
## 51 51 Left Lingual gyrus 81 0.85263158 6.654842e+01 0 0 0 2.053964e-03 0 4.584649e+00
## 52 52 Right Lingual gyrus 36 0.36734694 9.150443e-02 0 0 0 2.824211e-06 0 2.880567e-02
## 53 53 Left Superior occipital gyrus 36 0.52941176 3.233000e-01 0 0 0 9.978396e-06 0 9.194631e-02
## 54 54 Right Superior occipital gyrus 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 55 55 Left Middle occipital gyrus 146 0.90123457 4.034731e+00 0 0 0 1.245287e-04 0 6.797666e-01
## 56 56 Right Middle occipital gyrus 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 57 57 Left Inferior occipital gyrus 36 0.76595745 1.245488e+00 0 0 0 3.844098e-05 0 4.904622e-01
## 58 58 Right Inferior occipital gyrus 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 59 59 Left Fusiform gyrus 102 0.99029126 7.356566e+01 0 0 0 2.270545e-03 0 2.946326e+00
## 60 60 Right Fusiform gyrus 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 61 61 Left Postcentral gyrus 133 0.70370370 5.293517e+01 0 0 0 1.633801e-03 0 2.473056e+00
## 62 62 Right Postcentral gyrus 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 63 63 Left Superior parietal gyrus 23 0.18852459 3.733082e-02 0 0 0 1.152186e-06 0 1.124865e-02
## 64 64 Right Superior parietal gyrus 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 65 65 Left Inferior parietal gyrus-excluding supramarginal and angular gyri 121 0.98373984 2.318386e+01 0 0 0 7.155511e-04 0 1.431804e+00
## 66 66 Right Inferior parietal gyrus-excluding supramarginal and angular gyri 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 67 67 Left SupraMarginal gyrus 61 1.00000000 5.920034e+01 0 0 0 1.827171e-03 0 3.497201e+00
## 68 68 Right SupraMarginal gyrus 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 69 69 Left Angular gyrus 67 1.00000000 9.352486e+00 0 0 0 2.886570e-04 0 8.777804e-01
## 70 70 Right Angular gyrus 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 71 71 Left Precuneus 56 0.42424242 1.657144e+01 0 0 0 5.114642e-04 0 3.322482e+00
## 72 72 Right Precuneus 31 0.19375000 2.497502e-01 0 0 0 7.708341e-06 0 7.140275e-02
## 73 73 Left Paracentral lobule 1 0.01886792 3.264002e-04 0 0 0 1.007408e-08 0 3.264002e-04
## 74 74 Right Paracentral lobule 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 75 75 Left Caudate nucleus 28 0.75675676 1.499540e+00 0 0 0 4.628209e-05 0 6.526606e-01
## 76 76 Right Caudate nucleus 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 77 77 Left Lenticular nucleus-Putamen 54 1.00000000 4.070004e+01 0 0 0 1.256174e-03 0 4.204569e+00
## 78 78 Right Lenticular nucleus-Putamen 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 79 79 Left Lenticular nucleus-Pallidum 11 1.00000000 3.803091e+00 0 0 0 1.173794e-04 0 1.013942e+00
## 80 80 Right Lenticular nucleus-Pallidum 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 81 81 Left Thalamus 0 NaN 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 82 82 Right Thalamus 0 NaN 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 83 83 Left Heschls gyrus 14 1.00000000 6.325236e+01 0 0 0 1.952233e-03 0 6.877505e+00
## 84 84 Right Heschls gyrus 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 85 85 Left Superior temporal gyrus 150 1.00000000 2.973087e+02 0 0 0 9.176193e-03 0 6.196454e+00
## 86 86 Right Superior temporal gyrus 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 87 87 Left Temporal pole: superior temporal gyrus 67 1.00000000 1.842698e+00 0 0 0 5.687340e-05 0 2.115854e-01
## 88 88 Right Temporal pole: superior temporal gyrus 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 89 89 Left Middle temporal gyrus 247 1.00000000 1.489357e+02 0 0 0 4.596781e-03 0 3.752971e+00
## 90 90 Right Middle temporal gyrus 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 91 91 Left Temporal pole: middle temporal gyrus 35 1.00000000 2.670591e-01 0 0 0 8.242563e-06 0 4.321610e-02
## 92 92 Right Temporal pole: middle temporal gyrus 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 93 93 Left Inferior temporal gyrus 120 1.00000000 2.735250e+01 0 0 0 8.442131e-04 0 1.996966e+00
## 94 94 Right Inferior temporal gyrus 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 95 95 Left Crus I of cerebellar hemisphere 100 0.75757576 1.193042e+00 0 0 0 3.682229e-05 0 1.406105e-01
## 96 96 Right Crus I of cerebellar hemisphere 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 97 97 Left Crus II of cerebellar hemisphere 3 0.03571429 1.822986e-05 0 0 0 5.626499e-10 0 6.250557e-06
## 98 98 Right Crus II of cerebellar hemisphere 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 99 99 Left Lobule III of cerebellar hemisphere 7 1.00000000 5.503356e+00 0 0 0 1.698567e-04 0 1.160132e+00
## 100 100 Right Lobule III of cerebellar hemisphere 6 1.00000000 7.662559e-02 0 0 0 2.364987e-06 0 3.410214e-02
## 101 101 Left Lobule IV-V of cerebellar hemisphere 57 1.00000000 3.741270e+01 0 0 0 1.154713e-03 0 1.880591e+00
## 102 102 Right Lobule IV-V of cerebellar hemisphere 22 0.62857143 1.570715e-01 0 0 0 4.847887e-06 0 4.244862e-02
## 103 103 Left Lobule VI of cerebellar hemisphere 74 1.00000000 1.056744e+01 0 0 0 3.261556e-04 0 6.981526e-01
## 104 104 Right Lobule VI of cerebellar hemisphere 6 0.08823529 1.592300e-03 0 0 0 4.914505e-08 0 1.017942e-03
## 105 105 Left Lobule VIIB of cerebellar hemisphere 3 0.12500000 9.149168e-04 0 0 0 2.823817e-08 0 8.037689e-04
## 106 106 Right Lobule VIIB of cerebellar hemisphere 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 107 107 Left Lobule VIII of cerebellar hemisphere 17 0.24285714 1.404709e-02 0 0 0 4.335523e-07 0 5.640267e-03
## 108 108 Right Lobule VIII of cerebellar hemisphere 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 109 109 Left Lobule IX of cerebellar hemisphere 8 0.25806452 1.616005e-02 0 0 0 4.987670e-07 0 9.674748e-03
## 110 110 Right Lobule IX of cerebellar hemisphere 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 111 111 Left Lobule X of cerebellar hemisphere 1 1.00000000 5.597982e-03 0 0 0 1.727772e-07 0 5.597982e-03
## 112 112 Right Lobule X of cerebellar hemisphere 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 113 113 Lobule I-II of vermis 1 1.00000000 7.959824e-02 0 0 0 2.456736e-06 0 7.959824e-02
## 114 114 Lobule III of vermis 8 1.00000000 2.267892e+00 0 0 0 6.999668e-05 0 6.248655e-01
## 115 115 Lobule IV-V of vermis 34 1.00000000 3.894355e+00 0 0 0 1.201961e-04 0 7.620944e-01
## 116 116 Lobule VI of vermis 16 1.00000000 6.076200e-02 0 0 0 1.875370e-06 0 1.646879e-02
## 117 117 Lobule VII of vermis 6 0.54545455 3.528699e-03 0 0 0 1.089105e-07 0 2.468348e-03
## 118 118 Lobule VIII of vermis 5 0.50000000 3.548390e-03 0 0 0 1.095182e-07 0 2.781213e-03
## 119 119 Lobule IX of vermis 3 0.42857143 8.760055e-04 0 0 0 2.703721e-08 0 8.215907e-04
## 120 120 Lobule X of vermis 3 1.00000000 2.255844e-02 0 0 0 6.962480e-07 0 1.990642e-02
## 121 121 Left Thalamus-Anteroventral Nucleus 1 1.00000000 1.350460e-01 0 0 0 4.168086e-06 0 1.350460e-01
## 122 122 Right Thalamus-Anteroventral Nucleus 2 1.00000000 8.629559e-03 0 0 0 2.663444e-07 0 8.044917e-03
## 123 123 Left Lateral posterior 0 NaN 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 124 124 Right Lateral posterior 3 1.00000000 2.297779e-02 0 0 0 7.091911e-07 0 1.557184e-02
## 125 125 Left Ventral anterior 3 1.00000000 5.555910e-01 0 0 0 1.714787e-05 0 3.475474e-01
## 126 126 Right Ventral anterior 1 0.20000000 3.770724e-04 0 0 0 1.163804e-08 0 3.770724e-04
## 127 127 Left Ventral lateral 15 1.00000000 1.225426e+01 0 0 0 3.782180e-04 0 2.347056e+00
## 128 128 Right Ventral lateral 8 0.72727273 6.158087e-03 0 0 0 1.900644e-07 0 4.478616e-03
## 129 129 Left Ventral posterolateral 12 1.00000000 3.992214e+01 0 0 0 1.232165e-03 0 5.808750e+00
## 130 130 Right Ventral posterolateral 5 0.41666667 5.039269e-03 0 0 0 1.555330e-07 0 1.906710e-03
## 131 131 Left Intralaminar 4 1.00000000 7.303360e+00 0 0 0 2.254124e-04 0 2.250353e+00
## 132 132 Right Intralaminar 3 1.00000000 6.681360e-02 0 0 0 2.062148e-06 0 3.244947e-02
## 133 133 Left Reuniens 0 NaN 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 134 134 Right Reuniens 0 NaN 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 135 135 Left Mediodorsal medial magnocellular 9 1.00000000 5.968962e+00 0 0 0 1.842272e-04 0 1.215673e+00
## 136 136 Right Mediodorsal medial magnocellular 9 1.00000000 7.136350e-01 0 0 0 2.202577e-05 0 1.772179e-01
## 137 137 Left Mediodorsal lateral parvocellular 2 1.00000000 1.709580e+00 0 0 0 5.276481e-05 0 1.350485e+00
## 138 138 Right Mediodorsal lateral parvocellular 4 1.00000000 4.448508e-02 0 0 0 1.372996e-06 0 2.024112e-02
## 139 139 Left Lateral geniculate 1 1.00000000 3.964922e+00 0 0 0 1.223741e-04 0 3.964922e+00
## 140 140 Right Lateral geniculate 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 141 141 Left Medial Geniculate 1 1.00000000 4.273022e+00 0 0 0 1.318834e-04 0 4.273022e+00
## 142 142 Right Medial Geniculate 0 NaN 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 143 143 Left Pulvinar anterior 0 NaN 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 144 144 Right Pulvinar anterior 1 0.50000000 3.704953e-03 0 0 0 1.143504e-07 0 3.704953e-03
## 145 145 Left Pulvinar medial 10 1.00000000 3.544561e+01 0 0 0 1.094000e-03 0 6.039709e+00
## 146 146 Right Pulvinar medial 9 0.81818182 2.456256e-01 0 0 0 7.581036e-06 0 6.200280e-02
## 147 147 Left Pulvinar lateral 3 1.00000000 8.792075e+00 0 0 0 2.713603e-04 0 3.534778e+00
## 148 148 Right Pulvinar lateral 2 1.00000000 5.806060e-03 0 0 0 1.791994e-07 0 2.908921e-03
## 149 149 Left Pulvinar inferior 1 1.00000000 5.285981e+00 0 0 0 1.631476e-04 0 5.285981e+00
## 150 150 Right Pulvinar inferior 0 NaN 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 151 151 Left Anterior cingulate cortex-subgenual 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 152 152 Right Anterior cingulate cortex-subgenual 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 153 153 Left Anterior cingulate cortex-pregenual 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 154 154 Right Anterior cingulate cortex-pregenual 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 155 155 Left Anterior cingulate cortex-supracallosal 1 0.02564103 1.149136e-04 0 0 0 3.546718e-09 0 1.149136e-04
## 156 156 Right Anterior cingulate cortex-supracallosal 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 157 157 Left Nucleus accumbens 7 1.00000000 4.723677e-02 0 0 0 1.457925e-06 0 2.107174e-02
## 158 158 Right Nucleus accumbens 0 0.00000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 159 159 Left Ventral tegmental area 0 NaN 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 160 160 Right Ventral tegmental area 0 NaN 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 161 161 Left Substantia nigra-pars compacta 1 1.00000000 3.716791e-01 0 0 0 1.147158e-05 0 3.716791e-01
## 162 162 Right Substantia nigra-pars compacta 2 1.00000000 1.113302e-02 0 0 0 3.436118e-07 0 8.883362e-03
## 163 163 Left Substantia nigra-pars reticulata 4 1.00000000 2.914534e+00 0 0 0 8.995476e-05 0 1.300334e+00
## 164 164 Right Substantia nigra-pars reticulata 1 1.00000000 2.145111e-04 0 0 0 6.620714e-09 0 2.145111e-04
## 165 165 Left Red nucleus 3 1.00000000 2.115039e+00 0 0 0 6.527899e-05 0 9.159293e-01
## 166 166 Right Red nucleus 4 1.00000000 2.482625e-01 0 0 0 7.662423e-06 0 1.084301e-01
## 167 167 Left Locus coeruleus 0 NaN 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 168 168 Right Locus coeruleus 0 NaN 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 169 169 Raphe nucleus-dorsal 1 1.00000000 5.300409e-01 0 0 0 1.635929e-05 0 5.300409e-01
## 170 170 Raphe nucleus-median 0 NaN 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
##
## attr(,"class")
## [1] "atlastable"The loading for the second component
Q = fit113$wbX[[1]][,2]
outstat1 = rec(Q, img1$imagedim, B=B1, mask=img1$brainpos)
outstat2 = -outstat1
coat(template, outstat2)
atlastable(tmpatlas, outstat2, atlasdataset)## $table
## ROIid ROIname sizenum sizepct sumvalue Min. 1st Qu. Median Mean 3rd Qu. Max.
## 1 1 Left Precentral gyrus 60 0.319148936 6.385419e-01 0 0 0 1.970808e-05 0 1.433462e-01
## 2 2 Right Precentral gyrus 85 0.467032967 1.926003e+00 0 0 0 5.944455e-05 0 1.679313e-01
## 3 3 Left Superior frontal gyrus-dorsolateral 39 0.156000000 1.324599e-01 0 0 0 4.088268e-06 0 1.744149e-02
## 4 4 Right Superior frontal gyrus-dorsolateral 63 0.257142857 1.351160e+00 0 0 0 4.170248e-05 0 1.497747e-01
## 5 5 Left Middle frontal gyrus 0 0.000000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 6 6 Right Middle frontal gyrus 7 0.028112450 1.936774e-02 0 0 0 5.977698e-07 0 1.308377e-02
## 7 7 Left Inferior frontal gyrus-opercular part 0 0.000000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 8 8 Right Inferior frontal gyrus-opercular part 0 0.000000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 9 9 Left Inferior frontal gyrus-triangular part 0 0.000000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 10 10 Right Inferior frontal gyrus-triangular part 0 0.000000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 11 11 Left IFG pars orbitalis 0 0.000000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 12 12 Right IFG pars orbitalis 0 0.000000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 13 13 Left Rolandic operculum 22 0.392857143 1.231418e+00 0 0 0 3.800674e-05 0 2.863178e-01
## 14 14 Right Rolandic operculum 0 0.000000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 15 15 Left Supplementary motor area 66 0.758620690 2.787698e+00 0 0 0 8.604008e-05 0 2.070768e-01
## 16 16 Right Supplementary motor area 90 0.849056604 9.594453e+00 0 0 0 2.961251e-04 0 3.159231e-01
## 17 17 Left Olfactory cortex 0 0.000000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 18 18 Right Olfactory cortex 0 0.000000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 19 19 Left Superior frontal gyrus-medial 0 0.000000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 20 20 Right Superior frontal gyrus-medial 0 0.000000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 21 21 Left Superior frontal gyrus-medial orbital 0 0.000000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 22 22 Right Superior frontal gyrus-medial orbital 0 0.000000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 23 23 Left Gyrus rectus 0 0.000000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 24 24 Right Gyrus rectus 0 0.000000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 25 25 Left Medial orbital gyrus 0 0.000000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 26 26 Right Medial orbital gyrus 0 0.000000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 27 27 Left Anterior orbital gyrus 0 0.000000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 28 28 Right Anterior orbital gyrus 0 0.000000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 29 29 Left Posterior orbital gyrus 0 0.000000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 30 30 Right Posterior orbital gyrus 0 0.000000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 31 31 Left Lateral orbital gyrus 0 0.000000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 32 32 Right Lateral orbital gyrus 0 NaN 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 33 33 Left Insula 11 0.114583333 1.418258e-01 0 0 0 4.377340e-06 0 9.389534e-02
## 34 34 Right Insula 0 0.000000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 35 35 Left Anterior cingulate & paracingulate gyri 0 NaN 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 36 36 Right Anterior cingulate & paracingulate gyri 0 NaN 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 37 37 Left Middle cingulate & paracingulate gyri 84 0.893617021 3.524396e+01 0 0 0 1.087776e-03 0 5.265023e+00
## 38 38 Right Middle cingulate & paracingulate gyri 80 0.816326531 6.559560e+00 0 0 0 2.024556e-04 0 4.413128e-01
## 39 39 Left Posterior cingulate gyrus 17 1.000000000 2.340084e+01 0 0 0 7.222482e-04 0 3.521056e+00
## 40 40 Right Posterior cingulate gyrus 11 1.000000000 2.407464e+00 0 0 0 7.430446e-05 0 7.584434e-01
## 41 41 Left Hippocampus 11 0.250000000 2.137798e-01 0 0 0 6.598142e-06 0 8.066659e-02
## 42 42 Right Hippocampus 1 0.022222222 3.744927e-05 0 0 0 1.155842e-09 0 3.744927e-05
## 43 43 Left Parahippocampal gyrus 7 0.170731707 4.851080e-03 0 0 0 1.497247e-07 0 1.558628e-03
## 44 44 Right Parahippocampal gyrus 0 0.000000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 45 45 Left Amygdala 0 0.000000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 46 46 Right Amygdala 0 0.000000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 47 47 Left Calcarine fissure and surrounding cortex 89 1.000000000 4.533484e+01 0 0 0 1.399224e-03 0 2.301207e+00
## 48 48 Right Calcarine fissure and surrounding cortex 83 0.855670103 5.167356e+00 0 0 0 1.594863e-04 0 5.326529e-01
## 49 49 Left Cuneus 66 1.000000000 1.185381e+02 0 0 0 3.658584e-03 0 5.685272e+00
## 50 50 Right Cuneus 79 0.987500000 1.647293e+01 0 0 0 5.084238e-04 0 1.075869e+00
## 51 51 Left Lingual gyrus 90 0.947368421 3.306905e+00 0 0 0 1.020650e-04 0 3.884172e-01
## 52 52 Right Lingual gyrus 62 0.632653061 5.955825e-01 0 0 0 1.838217e-05 0 2.219980e-01
## 53 53 Left Superior occipital gyrus 68 1.000000000 1.167450e+02 0 0 0 3.603241e-03 0 7.709361e+00
## 54 54 Right Superior occipital gyrus 56 0.823529412 4.994497e-01 0 0 0 1.541511e-05 0 5.536336e-02
## 55 55 Left Middle occipital gyrus 160 0.987654321 1.863647e+02 0 0 0 5.751997e-03 0 7.967722e+00
## 56 56 Right Middle occipital gyrus 3 0.027272727 3.191678e-04 0 0 0 9.850857e-09 0 2.662634e-04
## 57 57 Left Inferior occipital gyrus 31 0.659574468 2.694271e-02 0 0 0 8.315653e-07 0 6.630163e-03
## 58 58 Right Inferior occipital gyrus 0 0.000000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 59 59 Left Fusiform gyrus 26 0.252427184 4.028398e-02 0 0 0 1.243333e-06 0 8.009797e-03
## 60 60 Right Fusiform gyrus 0 0.000000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 61 61 Left Postcentral gyrus 135 0.714285714 1.691043e+01 0 0 0 5.219268e-04 0 1.420441e+00
## 62 62 Right Postcentral gyrus 67 0.374301676 6.972058e-01 0 0 0 2.151870e-05 0 1.049028e-01
## 63 63 Left Superior parietal gyrus 122 1.000000000 3.224538e+02 0 0 0 9.952277e-03 0 7.645856e+00
## 64 64 Right Superior parietal gyrus 68 0.576271186 9.121250e-01 0 0 0 2.815201e-05 0 1.654363e-01
## 65 65 Left Inferior parietal gyrus-excluding supramarginal and angular gyri 123 1.000000000 1.798702e+02 0 0 0 5.551549e-03 0 6.837754e+00
## 66 66 Right Inferior parietal gyrus-excluding supramarginal and angular gyri 2 0.024390244 3.471351e-04 0 0 0 1.071405e-08 0 1.883311e-04
## 67 67 Left SupraMarginal gyrus 56 0.918032787 4.065460e+00 0 0 0 1.254771e-04 0 5.827098e-01
## 68 68 Right SupraMarginal gyrus 1 0.010752688 1.763923e-06 0 0 0 5.444207e-11 0 1.763923e-06
## 69 69 Left Angular gyrus 67 1.000000000 1.200552e+02 0 0 0 3.705407e-03 0 6.088266e+00
## 70 70 Right Angular gyrus 2 0.020408163 3.772943e-03 0 0 0 1.164489e-07 0 2.341176e-03
## 71 71 Left Precuneus 132 1.000000000 3.072416e+02 0 0 0 9.482766e-03 0 7.466646e+00
## 72 72 Right Precuneus 160 1.000000000 4.222704e+01 0 0 0 1.303304e-03 0 1.282177e+00
## 73 73 Left Paracentral lobule 53 1.000000000 4.682815e+00 0 0 0 1.445313e-04 0 4.062110e-01
## 74 74 Right Paracentral lobule 44 1.000000000 3.437726e+00 0 0 0 1.061027e-04 0 2.065649e-01
## 75 75 Left Caudate nucleus 6 0.162162162 6.971127e-03 0 0 0 2.151582e-07 0 5.209895e-03
## 76 76 Right Caudate nucleus 14 0.280000000 1.967139e-02 0 0 0 6.071415e-07 0 4.787706e-03
## 77 77 Left Lenticular nucleus-Putamen 1 0.018518519 1.748245e-05 0 0 0 5.395817e-10 0 1.748245e-05
## 78 78 Right Lenticular nucleus-Putamen 0 0.000000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 79 79 Left Lenticular nucleus-Pallidum 0 0.000000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 80 80 Right Lenticular nucleus-Pallidum 0 0.000000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 81 81 Left Thalamus 0 NaN 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 82 82 Right Thalamus 0 NaN 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 83 83 Left Heschls gyrus 8 0.571428571 9.520539e-02 0 0 0 2.938438e-06 0 4.355492e-02
## 84 84 Right Heschls gyrus 0 0.000000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 85 85 Left Superior temporal gyrus 57 0.380000000 3.125891e+00 0 0 0 9.647810e-05 0 3.858545e-01
## 86 86 Right Superior temporal gyrus 0 0.000000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 87 87 Left Temporal pole: superior temporal gyrus 0 0.000000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 88 88 Right Temporal pole: superior temporal gyrus 0 0.000000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 89 89 Left Middle temporal gyrus 86 0.348178138 1.687835e+01 0 0 0 5.209368e-04 0 1.572207e+00
## 90 90 Right Middle temporal gyrus 0 0.000000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 91 91 Left Temporal pole: middle temporal gyrus 0 0.000000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 92 92 Right Temporal pole: middle temporal gyrus 0 0.000000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 93 93 Left Inferior temporal gyrus 3 0.025000000 7.071638e-05 0 0 0 2.182604e-09 0 3.775154e-05
## 94 94 Right Inferior temporal gyrus 0 0.000000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 95 95 Left Crus I of cerebellar hemisphere 1 0.007575758 6.192189e-07 0 0 0 1.911169e-11 0 6.192189e-07
## 96 96 Right Crus I of cerebellar hemisphere 0 0.000000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 97 97 Left Crus II of cerebellar hemisphere 0 0.000000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 98 98 Right Crus II of cerebellar hemisphere 0 0.000000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 99 99 Left Lobule III of cerebellar hemisphere 2 0.285714286 6.496359e-05 0 0 0 2.005049e-09 0 6.051280e-05
## 100 100 Right Lobule III of cerebellar hemisphere 0 0.000000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 101 101 Left Lobule IV-V of cerebellar hemisphere 26 0.456140351 2.928493e-01 0 0 0 9.038558e-06 0 8.762974e-02
## 102 102 Right Lobule IV-V of cerebellar hemisphere 10 0.285714286 5.891954e-03 0 0 0 1.818504e-07 0 2.567740e-03
## 103 103 Left Lobule VI of cerebellar hemisphere 23 0.310810811 1.406813e-02 0 0 0 4.342014e-07 0 3.208548e-03
## 104 104 Right Lobule VI of cerebellar hemisphere 2 0.029411765 5.748270e-06 0 0 0 1.774157e-10 0 4.450791e-06
## 105 105 Left Lobule VIIB of cerebellar hemisphere 0 0.000000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 106 106 Right Lobule VIIB of cerebellar hemisphere 0 0.000000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 107 107 Left Lobule VIII of cerebellar hemisphere 0 0.000000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 108 108 Right Lobule VIII of cerebellar hemisphere 0 0.000000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 109 109 Left Lobule IX of cerebellar hemisphere 0 0.000000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 110 110 Right Lobule IX of cerebellar hemisphere 0 0.000000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 111 111 Left Lobule X of cerebellar hemisphere 0 0.000000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 112 112 Right Lobule X of cerebellar hemisphere 0 0.000000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 113 113 Lobule I-II of vermis 0 0.000000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 114 114 Lobule III of vermis 7 0.875000000 4.230594e-03 0 0 0 1.305739e-07 0 2.577779e-03
## 115 115 Lobule IV-V of vermis 31 0.911764706 5.932546e-01 0 0 0 1.831033e-05 0 1.629019e-01
## 116 116 Lobule VI of vermis 10 0.625000000 6.898923e-03 0 0 0 2.129297e-07 0 2.378809e-03
## 117 117 Lobule VII of vermis 0 0.000000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 118 118 Lobule VIII of vermis 0 0.000000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 119 119 Lobule IX of vermis 0 0.000000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 120 120 Lobule X of vermis 0 0.000000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 121 121 Left Thalamus-Anteroventral Nucleus 0 0.000000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 122 122 Right Thalamus-Anteroventral Nucleus 1 0.500000000 1.249982e-04 0 0 0 3.857969e-09 0 1.249982e-04
## 123 123 Left Lateral posterior 0 NaN 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 124 124 Right Lateral posterior 3 1.000000000 3.549411e-03 0 0 0 1.095497e-07 0 2.952804e-03
## 125 125 Left Ventral anterior 0 0.000000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 126 126 Right Ventral anterior 1 0.200000000 1.763923e-06 0 0 0 5.444207e-11 0 1.763923e-06
## 127 127 Left Ventral lateral 4 0.266666667 1.116103e-03 0 0 0 3.444764e-08 0 5.891870e-04
## 128 128 Right Ventral lateral 4 0.363636364 1.915057e-03 0 0 0 5.910669e-08 0 1.735941e-03
## 129 129 Left Ventral posterolateral 8 0.666666667 4.772350e-02 0 0 0 1.472947e-06 0 1.574355e-02
## 130 130 Right Ventral posterolateral 3 0.250000000 1.328130e-04 0 0 0 4.099166e-09 0 1.249982e-04
## 131 131 Left Intralaminar 1 0.250000000 2.897462e-04 0 0 0 8.942783e-09 0 2.897462e-04
## 132 132 Right Intralaminar 0 0.000000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 133 133 Left Reuniens 0 NaN 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 134 134 Right Reuniens 0 NaN 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 135 135 Left Mediodorsal medial magnocellular 3 0.333333333 1.683435e-03 0 0 0 5.195787e-08 0 1.441014e-03
## 136 136 Right Mediodorsal medial magnocellular 1 0.111111111 3.434015e-04 0 0 0 1.059881e-08 0 3.434015e-04
## 137 137 Left Mediodorsal lateral parvocellular 1 0.500000000 1.003863e-05 0 0 0 3.098344e-10 0 1.003863e-05
## 138 138 Right Mediodorsal lateral parvocellular 0 0.000000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 139 139 Left Lateral geniculate 0 0.000000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 140 140 Right Lateral geniculate 0 0.000000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 141 141 Left Medial Geniculate 1 1.000000000 4.856719e-04 0 0 0 1.498987e-08 0 4.856719e-04
## 142 142 Right Medial Geniculate 0 NaN 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 143 143 Left Pulvinar anterior 0 NaN 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 144 144 Right Pulvinar anterior 0 0.000000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 145 145 Left Pulvinar medial 10 1.000000000 3.709338e-01 0 0 0 1.144857e-05 0 9.919363e-02
## 146 146 Right Pulvinar medial 4 0.363636364 3.513521e-04 0 0 0 1.084420e-08 0 2.532056e-04
## 147 147 Left Pulvinar lateral 3 1.000000000 8.926384e-03 0 0 0 2.755057e-07 0 5.003917e-03
## 148 148 Right Pulvinar lateral 0 0.000000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 149 149 Left Pulvinar inferior 1 1.000000000 3.071638e-02 0 0 0 9.480364e-07 0 3.071638e-02
## 150 150 Right Pulvinar inferior 0 NaN 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 151 151 Left Anterior cingulate cortex-subgenual 0 0.000000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 152 152 Right Anterior cingulate cortex-subgenual 0 0.000000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 153 153 Left Anterior cingulate cortex-pregenual 0 0.000000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 154 154 Right Anterior cingulate cortex-pregenual 0 0.000000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 155 155 Left Anterior cingulate cortex-supracallosal 5 0.128205128 1.779044e-02 0 0 0 5.490877e-07 0 1.122857e-02
## 156 156 Right Anterior cingulate cortex-supracallosal 2 0.064516129 7.567588e-04 0 0 0 2.335675e-08 0 7.507080e-04
## 157 157 Left Nucleus accumbens 0 0.000000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 158 158 Right Nucleus accumbens 0 0.000000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 159 159 Left Ventral tegmental area 0 NaN 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 160 160 Right Ventral tegmental area 0 NaN 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 161 161 Left Substantia nigra-pars compacta 0 0.000000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 162 162 Right Substantia nigra-pars compacta 0 0.000000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 163 163 Left Substantia nigra-pars reticulata 0 0.000000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 164 164 Right Substantia nigra-pars reticulata 0 0.000000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 165 165 Left Red nucleus 0 0.000000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 166 166 Right Red nucleus 0 0.000000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 167 167 Left Locus coeruleus 0 NaN 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 168 168 Right Locus coeruleus 0 NaN 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 169 169 Raphe nucleus-dorsal 0 0.000000000 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
## 170 170 Raphe nucleus-median 0 NaN 0.000000e+00 0 0 0 0.000000e+00 0 0.000000e+00
##
## attr(,"class")
## [1] "atlastable"This is similar to the result from the sparse PCA (without supervision).
The following method can be used to plot the weights of several
components simultaneously. It is first reconstructed in three dimensions
with the multirec function and then plotted with the
multicompplot function. It is set to display four columns
per component.
ws = multirec(fit113, imagedim=img1$imagedim, B=B1, mask=img1$brainpos)
multicompplot(ws, template, col4comp=4)