How to run a python file on 3D slicer and generate output

ashuashu · July 18, 2022, 9:53am

Operating system: macOS M1
Slicer version: 5.0.2
Expected behavior:
Actual behavior:

Hello,

I am completely new to the 3D slicer.

I have my deep learning model coded in python and my dataset ready. I want to deploy it in 3D Slicer and generate outputs.

What is the process or commands? Any links to follow the procedure are appreciated.

Thank you.

pieper · July 18, 2022, 6:31pm

You can start by watching this recent webinar and reading up on the topics discussed. You can follow up with specific questions here:

lassoan · July 18, 2022, 11:00pm

If you don’t use MONAI then you can find a complete example that brings a Pytorch-based model into Slicer:

github.com

lassoan/SlicerHDBrainExtraction/blob/main/HDBrainExtractionTool/HDBrainExtractionTool.py

import logging
import os

import vtk

import slicer
from slicer.ScriptedLoadableModule import *
from slicer.util import VTKObservationMixin


#
# HDBrainExtractionTool
#

class HDBrainExtractionTool(ScriptedLoadableModule):
  """Uses ScriptedLoadableModule base class, available at:
  https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py
  """

  def __init__(self, parent):

This file has been truncated. show original

The module installs pytorch, installs the deep learning based segmentation tool, downloads the model, and displays GUI for specifying inputs and outputs for the model.

Topic		Replies	Views
Running python file in Slicer on Mac Support	11	436	November 13, 2023
Guidance on Creating a Simplified Python-Based Version of 3D Slicer with Custom Modules Development	2	42	October 25, 2024
Scripted Module: How to install and import tensorflow-cpu on M2 Mac Support	2	537	July 25, 2023
Machine Learning Model Importing Development	9	2241	February 27, 2020
Running slicer from mac terminal Support python , macos	4	963	February 23, 2022

How to run a python file on 3D slicer and generate output

Related topics