Erodespare¶
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:
- Read in the image specified by the
-i
flag- 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.- Compute a fractional depth map such that, for instance, a voxel in the 33rd percentile of deepest voxels is assigned a value of 33
- Threshold the depth map according to the criterion set by the
-r
flag. (This is the erosion step.)- Binarise the map and write the eroded mask to the path specified by
-o
Output¶
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.