I have NIFTI files of sizes (512 x 512 x 150) of auto-segmentation and manual segmentation. Each file/slice contains the segmentation of multiple regions (seven regions). I want to compute the dice score, Hausdorff distance, Jaccard index, and average surface distance.
Could you please suggest the easiest method for that purpose? I don’t want to convert NIFTI to PNGs/JPEGs. I tried the plastimatch dice. It seems that it doesn’t work for multi-region segmentation. Please find the command and relevant output of plastimatch. Please suggest if I am missing anything or if there is a better approach.
plastimatch dice --all manual_GT.nii Auto_seg.nii
ref 15.9689 -56.3064 -32.7915
cmp 16.4171 -56.3639 -35.121
Hausdorff distance = 12.750913
Avg average Hausdorff distance = 0.131478
Max average Hausdorff distance = 0.160547
Percent (0.95) Hausdorff distance = 0.634766
Hausdorff distance (boundary) = 27.516542
Avg average Hausdorff distance (boundary) = 1.705389
Max average Hausdorff distance (boundary) = 1.814141
Percent (0.95) Hausdorff distance (boundary) = 5.156286