A Slicer module for Evaluate segmentation/labelmap you can download the module and add it to 3D Slicer-->Edit-->Application Settings-->Modules, then add the path of the module to "Additional module paths" and restart. It will appear somewhere in module lists in Example. The module needs tensorflow, scikit,.... that automatically installs them. if you receive an error, push apply again might solve it.
if you need a fast processing, you should increase the voxel size using "resample scaler volume" tool.
if you received an error about permission to run:
$ chmod +x EvaluationSegmentation_linux/EvaluateSegmentation/Resources/EvaluateSegmentation
if you want to run on folders, I suggest to use shell script as:
touch temp.txt
touch temp2.txt
touch temp3.txt
touch results.txt
for l in {1,2,3,4,...}; do
pred='labels'$l1'.nii.gz'
orig='orig'$l2'.nii.gz'
/path to/EvaluateSegmentation $orig $pred |sed -n 2,32p | awk '{print $3}'> temp.txt
cp -v 'results.txt' 'temp2.txt'
awk '{getline l <"temp2.txt"; print $0"\t"l} ' temp.txt > temp3.txt
cp -v 'temp3.txt' 'results.txt'
done
Help:
If you used this module in your research or need more details about the metrics please cite these papers: