usage: __main__.py [-h] (--metrics_dir dir | --metrics file [file ...])
[--bin] [--normalize_weights] [--indent INDENT]
[--sort_keys] [-v [{DEBUG,INFO,WARNING}]] [-f]
in_rois [in_rois ...]
Compute the statistics (mean, std) of scalar maps, which can represent
diffusion metrics, in ROIs. Prints the results.
The ROIs can either be binary masks, or weighting masks. If the ROIs are
weighting masks, they should either contain floats between 0 and 1 or should be
normalized with --normalize_weights. IMPORTANT: if the ROIs contain weights
(and not 0 and 1 exclusively), the standard deviation will also be weighted.
positional arguments:
in_rois ROIs volume filenames.
Can be binary masks or weighted masks.
options:
-h, --help show this help message and exit
--bin If set, will consider every value of the mask higherthan 0 to be
part of the mask (equivalent weighting for every voxel).
--normalize_weights If set, the weights will be normalized to the [0,1] range.
-v [{DEBUG,INFO,WARNING}]
Produces verbose output depending on the provided level.
Default level is warning, default when using -v is info.
-f Force overwriting of the output files.
Metrics input options:
--metrics_dir dir Name of the directory containing metrics files: we will
load all nifti files.
--metrics file [file ...]
Metrics nifti filename. List of the names of the metrics file,
in nifti format.
Json options:
--indent INDENT Indent for json pretty print.
--sort_keys Sort keys in output json.
Scilpy version: 2.0.2