When you run the help flag of the cli, atlasreader gives the following output:
usage: atlasreader [-h] [-a atlas [atlas ...]] [-t threshold] [-c extent]
[-p threshold] [-o outdir] [-d distance]
file
positional arguments:
file The full or relative path to the statistical mapfrom
which cluster information should be extracted.
optional arguments:
-h, --help show this help message and exit
-a atlas [atlas ...], --atlas atlas [atlas ...]
Atlas(es) to use for examining anatomical delineation
of clusters in provided statistical map. Default: all
available atlases.
-t threshold, --threshold threshold
Value threshold that voxels in provided file must
surpass in order to be considered in cluster
extraction.
-c extent, --cluster extent
Required number of contiguous voxels for a cluster to
be retained for analysis.
-p threshold, --probability threshold
Threshold to consider when using a probabilistic atlas
for extracting anatomical cluster locations. Value
will apply to all request probabilistic atlases, and
should range between 0 and 100.
-o outdir, --outdir outdir
Output directory for created files. If it is not
specified, then output files are created in the same
directory as the statistical map that is provided.
-d distance, --mindist distance
If specified, the program will attempt to find
subpeaks within detected clusters, rather than a
single peak per cluster. The specified value will
determine the minimum distance required between
subpeaks.
As you can see, only the atlas flag has information about default parameters.
It's a quick fix, but we should add the default parameters to the help text here.
When you run the help flag of the cli, atlasreader gives the following output:
As you can see, only the atlas flag has information about default parameters.
It's a quick fix, but we should add the default parameters to the help text here.