anatGetAll_old: Get values given a set of files and an atlas

In Mouse-Imaging-Centre/RMINC: Statistical Tools for Medical Imaging NetCDF (MINC) Files

Get values given a set of files and an atlas

Description

Computes volumes, means, sums, and similar values across a segmented atlas

Usage

anatGetAll_old(
  filenames,
  atlas,
  method = "jacobians",
  defs = getOption("RMINC_LABEL_DEFINITIONS"),
  dropLabels = TRUE,
  side = "both"
)

Arguments

filenames	A vector of filenames (strings) which contain the information to be extracted at every structure in the atlas.
atlas	A single filename containing the atlas definitions. This MINC volume has to be of the same sampling (sizes and dimension order) as the filenames specified in the first argument and use a separate integer for each atlas label.
method	A string specifying the way information is to be computed at every voxel. See the details section for the possible options and what they mean.
defs	A string pointing to the filename containing the label definitions. Used to map the integers in the atlas to a proper name for the structure and contains additional information for laterality of each structure. See voxel_atlas_defs for details.
dropLabels	Whether to return a value for every structure in the defs or just for the ones actually contained in each file.
side	Three choices, "right", "left", and "both" (the default) which specify what labels to obtain.

Details

anatGetAll needs a set of files along with an atlas and a set of atlas definitions. In the end it will produce one value per label in the atlas for each of the input files. How that value is computed depends on the methods argument:

• jacobians - Each file contains log jacobians, and the volume for each atlas label is computed by multiplying the jacobian with the voxel volume at each voxel.

• labels - Each file contains integer labels (i.e. same as the atlas). The volume is computed by counting the number of voxels with each label and multiplying by the voxel volume.

• means - Each file contains an arbitrary number and the mean of all voxels inside each label is computed.

• sums - Each file contains an aribtrary number and the sum of all voxels inside each label is computed.

• text - Each file is a comma separated values text file and is simply read in.

Value

A matrix with ncols equal to the number of labels in the atlas and nrows equal to the number of files.

See Also

anatLm,anatCombineStructures

Examples

## Not run: 
getRMINCTestData()
filenames <- read.csv("/tmp/rminctestdata/filenames.csv")
volumes <- anatGetAll(filenames=filenames$absolute_jacobian, 
                      atlas="/tmp/rminctestdata/test_segmentation.mnc", 
                      method="jacobians",
                      defs="/tmp/rminctestdata/test_defs.csv")

## End(Not run)

Mouse-Imaging-Centre/RMINC documentation built on Nov. 12, 2022, 1:50 p.m.