do.neurocdf: Aggregate values in ROI

In kkholst/neurocdf: Various utilities for handling neuroimaging data

Description

Aggregate values in ROI

Usage

  ## S3 method for class 'neurocdf'
 do(object, roi, fun, type = 1,
    margin = 2, na.rm = TRUE, na.rm.margin = 2,
    slice = NULL, plane = 3, x, y, z, realworld = FALSE,
    atlas = 2, var = "GlobalImage", mc.cores = 4,
    chunksize = 1000/mc.cores, exclude, ...)

Arguments

object	Filename of (neuro-)netcdf file
roi	Region of interest. Either a string or number defining the region in the atlas of 'x', or a nx3 matrix with voxel positions defining the region. If an attribute type="mm" is set, the voxel positions are treated as real world coordinates, and in the other case as voxel indices (vx).
fun	Optional function to apply. If missing the actual image values in each voxel is returned.
type	The image type number (if 0 all images will be used)
margin	Function applied row-wise (1) or column-wise (2). If 0 only the ROI coordinates are returned.
na.rm	Should NA values be removed (complete-cases)
na.rm.margin	Complete-cases defined from columns (2) or rows (1)
slice	Slice number
plane	Coordinate (row 1, column 2, slice 3)
x	row
y	column
z	slice
realworld	If TRUE real world coordinates are returned as the element mm.
atlas	Position of atlas among 'var' images
var	The variable in the neuro netCDF file from which the atlas is chosen.
mc.cores	Number of cores to be used in parallel computing
chunksize	Chunk size (parallel computing)
exclude	Index of subjects to exclude
...	Additional arguments parsed to lower level functions

Details

A kxn matrix is extracted where n is the number of voxels in the region, and k is the number of subjects/images. Optionally a function can be applied over columns of rows of this matrix.

Value

A list with voxel coordinates (vx), real world coordinates (mm) if realworld=TRUE, and aggregated image values val.

Author(s)

Klaus K. Holst

kkholst/neurocdf documentation built on May 20, 2019, 10:59 a.m.