Label erosion tool.

erodespare erodes a subset of labels (or range of values) in a provided image such that only the deepest k percent of voxels in the label set are retained. erodespare erodes an image while sparing the deepest voxels. This can be a useful tool for generating tissue maps for nuisance regression in a way that minimizes partial volume effects and decreases the correlation between tissue-based nuisance regressors and the global signal.

erodespare executes in the following order, using its inputs as follows:

  1. Read in the image specified by the -i flag
  2. Binarise the image such that voxels with the values specified by the -v flag are set to 1 while all other voxels are set to 0.
  3. Compute a fractional depth map such that, for instance, a voxel in the 33rd percentile of deepest voxels is assigned a value of 33
  4. Threshold the depth map according to the criterion set by the -r flag. (This is the erosion step.)
  5. Binarise the map and write the eroded mask to the path specified by -o


A binary-valued mask indicating whether each voxel belongs to a specified label set following erosion to the deepest k percent.

Input arguments

-i: Input mask

A mask, image, or label set that the user wishes to erode.

-o: Output path

A path in a valid directory, where the eroded map will be written once it is computed.

Optional input arguments

-r: Retention criterion

Default value: 5 percent

The percent of voxels that should be retained in the eroded mask. The argument should be a percent value, not a fractional value (e.g., 5 not 0.05 for 5 percent). For instance, a value of 5 will erode all but the deepest 5 percent of voxels. (At least 5 percent of voxels will be preserved.)

-v: Value set

If this variable is defined, then the specified range of labels will be extracted from the provided mask prior to erosion. For instance, -v 2,4 will extract cortical and deep grey matter from a standard 6-class segmentation. Syntax follows the -v specification in val2mask. If this option is not provided, then a mask comprising all nonzero values from the input will be generated and eroded.

-n: Intermediate output path

A path where erodespare stores temporary files. If your machine or file system has a designated space for temporary files (e.g., /tmp), then using this space can substantially improve I/O speed.