Hi, 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 Segment Comparison module in the SlicerRT extension allows you to compute Dice and Hausdorff on segmentations containing multiple labels. You’ll need to first convert the labelmap volumes to segmentation nodes (in Segmentations module Import/Export section, or in the Data module by right-clickin…

@cpinter Thanks a lot! It worked. I love Slicer! Btw, some features can be improved and can be made more interactive by incorporating some sort of automation. For example, the “Segment Comparison” tool should have the Box/tick option for all segments rather than the drop-down menu.

@cpinter Could you please point out where can I find the source code for Segment Comparison module (Version 5.2.2). I’m getting different values of dice score for 3D binary nifti masks when using 3D Slicer and Monai framework. This is the monai function I’m using: def calculate_dice_score(predicted…

Please create a new topic for this and I’ll answer there. If we keep reusing year-old topic nobidy will be able to find anything here. Thanks!

Noted. Thank you! Created a new topic: Dice score calculation of 3D binary masks using Segment Comparison module

@cpinter thank you. However I have trouble locating Dice and Hausdorff from SlicerRT extension. I’m using Slicer 5.6. Could you please point me where they are.

It’s in the Segment Comparison module. What operating system do you use? There have been issues on Mac lately with some extensions.

@cpinter , thanks for getting back to me. I use 14.2 (23C64) on an Apple M1 Pro. I couldn’t find this Segment Comparison module on Slicer 5.6 and Slicer 5.6.1. But I was able to find it on Slicer 5.2 after I revert it back.

Compute Dice score, Hausdorff distance for Multi-Region segmentation

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Topic		Replies	Views
Segmentation Comparsion Support slicerrt	2	1632	December 11, 2019
Hausdorff and Dice calculation principle Support segmentation	2	817	February 8, 2024
DiceComputation module does not calculate Support	15	1393	September 21, 2020
Segment comparison returns 0 for all metrics Development slicerrt	15	790	July 5, 2019
Repeated Segment Comparison Metric Calculations Support segmentation , slicerrt , python	0	40	July 8, 2025

Compute Dice score, Hausdorff distance for Multi-Region segmentation

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