Computes volumes, means, sums, and similar values across a segmented atlas
anatGetAll(filenames, atlas = NULL, defs = getOption("RMINC_LABEL_DEFINITIONS"), method = c("jacobians", "labels", "sums", "means"), side = c("both", "left", "right"), parallel = NULL, strict = TRUE, conf_file = getOption("RMINC_BATCH_CONF"))
| filenames | A vector of filenames (strings) which contain the information to be extracted at every structure in the atlas. |
|---|---|
| atlas | One of: NULL if the method is labels, a single atlas file for all subjects, or a vector of one atlas file per subject. |
| 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. |
| method | A string specifying the way information is to be computed at every voxel (default is "jacobians"). See the details section for the possible options and what they mean. |
| side | One of three choices, "right", "left", or "both" (the default) which specify what labels to obtain. |
| parallel | how many processors to run on (default=single processor). Specified as a two element vector, with the first element corresponding to the type of parallelization, and the second to the number of processors to use. For local running set the first element to "local" or "snowfall" for back-compatibility, anything else will be run with batchtools see pMincApply Leaving this argument NULL runs sequentially. |
| strict | check if any files differ in step sizes |
| conf_file | A batchtools configuration file defaulting to |
A matrix with ncols equal to the number of labels in the atlas and nrows equal to the number of files.
anatGetAll needs a set of files, an atlas (unless method=="labels"), 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.
If multiple atlases are passed in each subject will have the summary computed with respect to their atlas.