SegmentWithSAM module not working

Jessica_de_Kort · October 17, 2025, 6:00pm

Hello! I am trying to use SegmentWithSAM module. I downloaded it through Extension Wizard, restarted Slicer a few times, and the module has no prompts or buttons on the left hand side of the screen. I looked at the error code and it mentions something about a bad git. I am not quite sure what that means or if that is the problem. Does anyone have any ideas on what to do?

Here is a photo of the interface:

lassoan · October 17, 2025, 6:39pm

I haven’t seen any SAM variant outperforming classic interactive segmentation tools for medical image segmentation. Therefore, I would not spend time with trying to figure out why this this extension fails.

In contrast, NNInteractive model is an AI-based interactive segmentation tool that actually works, and it works really well. For many segmentation tasks it performs much better than classic tools. You can often get a perfect segmentation of a bone from a single click. I would recommend to use it instead of any SAM-based tools. It is available in the Extensions Manager.

Jessica_de_Kort · October 22, 2025, 3:49pm

The NNInteractive model needs a Nvidia GPU which we do not have yet. I will try NNInteractive once we have a Nvidia GPU. Thank you for your help.

muratmaga · October 22, 2025, 4:17pm

You can always give it a try on [MorphoCloud](https://morphocloud.org). Brief instructions are here:

github.com/SlicerMorph/Tutorials

MorphoCloud/NNInteractive.MD

MorphoCloud

# Setting & Using NNInteractive extension on the MorphoCloud instances
nnInteractive is a deep learning-based framework for interactive segmentation of 3D images, allowing for fast voxel-wise segmentation using prompts like points, scribbles, bounding boxes, and lasso. It is a very useful and effective tool for rapid 3D segmentation with few clicks. It is a little different from the typical Slicer extensions, because it is a client and server application. While Slicer installation on the MOrphoCloud instances come with SlicerNNInteractive, that's only the **client**; you still have to install and then run the server each time you are planning to use NNInteractive. 

The official repository and most up-to-date instructions on how to install NNInteractive can be found at https://github.com/coendevente/SlicerNNInteractive/blob/main/README.md. This guide covers specific steps specific known to work with on MorphoCloud.

## Installing the server and running it.
There are multiple ways of running the server. On MorphoCloud we suggest you use the [**pip install** option as documented in the official documentation](https://github.com/coendevente/SlicerNNInteractive?tab=readme-ov-file#option-2-using-pip). 

1. Open a terminal window 
2. To create a python virtual environment specific to NNinteractive copy and paste this command to the terminal window (one-time only)
```
python3 -m venv /media/volume/MyData/nninteractive
```
3. To activate this python virtual enviroment copy and paste this command to the terminal window (everytime you want to run the server)
```
source /media/volume/MyData/nninteractive/bin/activate
```
4. To install the NNinteractive server copy and paste this command to the terminal window (one-time only)
```
pip install nninteractive-slicer-server

This file has been truncated. show original

muratmaga · October 23, 2025, 2:30am

Actually this is the correct link for the short tutorial: Tutorials/MorphoCloud/NNInteractive.MD at main · SlicerMorph/Tutorials · GitHub

Topic		Replies	Views
Run SAMM (Segment Any Medical Model) in 3D Slicer Support segmentation , python	13	1013	October 24, 2023
Struggling to integrate SAM model to 3D slicer, need help Development	6	805	June 26, 2023
Integration of “Segment Anything Model”? Development	23	3871	June 17, 2023
Nvidia AI-assisted annotation (AIAA) for 3D Slicer for Windows Support segmentation	2	677	June 14, 2021
Slicer interact with external deep learning segmentation software Development python	6	389	June 16, 2021

SegmentWithSAM module not working

Related topics