Advanced NeuroVec Patterns

This article is now the deeper companion to vignette("VolumesAndVectors"). Read that first if you want the compact introduction to NeuroVec. Stay here when you want more detail on multi-file reads, manual construction, matrix views, and dense/sparse conversions for 4D data.

Working with neuroimaging time-series data

This vignette focuses on the parts of the 4D workflow that remain useful after you already understand the basic container model:

reading many 4D files into a NeuroVecSeq
creating NeuroVec objects from arrays or matrices
time-series transforms and concatenation
dense/sparse conversion patterns
writing vectors back to disk

Reading multiple four-dimensional images

file_name <- system.file("extdata", "global_mask_v4.nii", package = "neuroim2")
vec <- read_vec(file_name)
vec_multi <- read_vec(c(file_name, file_name, file_name))
dim(vec_multi)
#> [1] 64 64 25 12

vec2 <- read_vec(rep(file_name, 10))
vec2
#> <NeuroVecSeq> [10 vectors] 
#> ── Sequence ──────────────────────────────────────────────────────────────────── 
#>     [1]         : DenseNeuroVec 64x64x25 x 4t
#>     [2]         : DenseNeuroVec 64x64x25 x 4t
#>     [3]         : DenseNeuroVec 64x64x25 x 4t
#>     [4]         : DenseNeuroVec 64x64x25 x 4t
#>     [5]         : DenseNeuroVec 64x64x25 x 4t
#>   ... and 5 more

Creating a NeuroVec from an in-memory array

You can build a NeuroVec directly from arrays or matrices:

set.seed(1)
dims <- c(24, 24, 24, 5)
arr  <- array(rnorm(prod(dims)), dims)
sp4  <- NeuroSpace(dims, spacing = c(2,2,2))
dvec <- NeuroVec(arr, sp4)
dim(dvec)
#> [1] 24 24 24  5

You can also start from a matrix (voxels × time or time × voxels) using DenseNeuroVec:

mat  <- matrix(rnorm(prod(dims)), nrow = prod(dims[1:3]), ncol = dims[4])
dvec2 <- DenseNeuroVec(mat, sp4)
all.equal(dim(dvec), dim(dvec2))
#> [1] TRUE

Time-series transforms: z-scoring and summary volumes

Z-score each voxel’s time-series (center and scale across time):

vec_z <- scale_series(dvec, center = TRUE, scale = TRUE)
dim(vec_z)
#> [1] 24 24 24  5

Compute a mean volume across time and return a 3D NeuroVol:

M      <- as.matrix(dvec)              # voxels × time
vmean  <- rowMeans(M)                  # per-voxel mean
mean3d <- NeuroVol(vmean, drop_dim(space(dvec)))
mean3d
#> <DenseNeuroVol> [114.6 Kb] 
#> ── Spatial ───────────────────────────────────────────────────────────────────── 
#>   Dimensions    : 24 x 24 x 24
#>   Spacing       : 2 x 2 x 2 mm
#>   Origin        : 0, 0, 0
#>   Orientation   : RAS
#> ── Data ──────────────────────────────────────────────────────────────────────── 
#>   Range         : [-1.643, 1.756]

Concatenating along time

Append time points by concatenating vectors or volumes:

dvec_more <- concat(dvec, dvec)        # doubles the time dimension
dim(dvec_more)
#> [1] 24 24 24 10

Dense ↔︎ sparse workflows

Sparse representations store only voxels within a mask. This is handy for large ROIs or brain masks.

# Build a random mask and convert a dense vec to sparse
mask_arr <- array(runif(prod(dims[1:3])) > 0.7, dims[1:3])
mask_vol <- LogicalNeuroVol(mask_arr, drop_dim(sp4))

svec <- as.sparse(dvec, mask_vol)     # SparseNeuroVec with explicit mask
svec                                 # note the stored mask and cardinality
#> <SparseNeuroVec> [306.2 Kb] 
#> ── Spatial ───────────────────────────────────────────────────────────────────── 
#>   Dimensions    : 24 x 24 x 24
#>   Time Points   : 5
#>   Spacing       : 2 x 2 x 2
#>   Origin        : 0, 0, 0
#> ── Sparse ────────────────────────────────────────────────────────────────────── 
#>   Cardinality   : 4128

# Convert back to dense if needed
dense_again <- as.dense(svec)
all.equal(dim(dense_again), dim(dvec))
#> [1] TRUE

Tip: For file-backed or memory-mapped vectors, convert to DenseNeuroVec via a matrix if you need dense-only operations:

dv_dense <- DenseNeuroVec(as.matrix(vec), space(vec))

Writing vectors to disk

You can write NeuroVec and NeuroVol objects as NIfTI files:

tmp_vec <- tempfile(fileext = ".nii.gz")
write_vec(sub_vector(vec, 1:3), tmp_vec)
file.exists(tmp_vec)
#> [1] TRUE
unlink(tmp_vec)

Putting it together with an ROI

Combine ROI extraction with time-series transforms:

vol3d <- read_vol(system.file("extdata", "global_mask_v4.nii", package="neuroim2"))
roi   <- spherical_roi(vol3d, c(12,12,12), radius = 6)
rts   <- series_roi(vec, roi)          # ROIVec (T × N with coords)

# z-score each column (voxel) across time, then average within ROI
mat_roi  <- values(rts)                # T × N
mat_z    <- base::scale(mat_roi, center=TRUE, scale=TRUE)
roi_mean <- rowMeans(mat_z)
length(roi_mean)                       # matches time dimension
#> [1] 4

This article now complements the core path rather than replacing it. Use vignette("VolumesAndVectors") for the basic 4D container model and come back here when you need denser transformation and conversion patterns.