Label statistics

Given an input volume and a label mask, generate a table of statistics for each label in the label mask.

CLI

To get more information about the workflow and its required arguments use the following command on the CLI:

$ miracl stats lbls_stats -h

Main Inputs

Input volume and registered Allen labels.

Arguments

lbls_stats requires at least two input arguments:

Flags	Type	Description	Default
-i, --invol	str	Input volume	Required
-l, --lbls	str	Registered Allen lbls	Required

The rest of the arguments are optional:

Flags	Type	Description	Default
-o, --outfile	str	Output file name	clarity_label_statistics.csv
-s, --sort	str	Sort values by, options are: Mean StdD Max Min Count Vol(mm^3) Mean -> mean intensity values Count -> number of voxels	Mean
-m, --hemi	str	Labels hemi, options are: combined split	combined
-d, --depth	int	Labels depth	None i.e. not used
-r, --ratio	str	Tractography (.trk) file used to generate tract ratio	None i.e. not used

Main Outpus

csv file containing the label statistics per brain region (default: clarity_label_statistics.csv).