Error when running sample Slicer Jupyter Notebooks from local linux machine

Andrius · June 10, 2020, 7:29am

Dear Slicers,

I am just getting started with Python and slicer. My goal is to use slicer to combine ITK, VTK and VMTK capabilities for vascular segmentation and geometric data extraction. I love the idea that all this can be combined with the rest of python packages.

I installed into my vmtk python environment as per instructions here:

github.com

Slicer/SlicerJupyter/blob/master/README.md#setup

# SlicerJupyter
Extension for 3D Slicer that allows the application to be used from Jupyter notebook

Demo video: https://youtu.be/oZ3_cRXX2QM

[![](https://img.youtube.com/vi/oZ3_cRXX2QM/0.jpg)](https://www.youtube.com/watch?v=oZ3_cRXX2QM "Slicer Jupyter kernel demo")

# Usage

## Option 1. Run using Binder

You can use this option for a quick start. No installation or setup is needed, just click the link below and start using Slicer via Jupyter notebook in your web browser.

[![Binder](https://mybinder.org/badge.svg)](https://mybinder.org/v2/gh/Slicer/SlicerNotebooks/master)

When you click on the link, Binder launches 3D Slicer with SlicerJupyter extension on their cloud servers. Binder is a free service and server resources are quite limited. Also, there is no interactive access to the graphical user interface. Therefore, this option is only recommended for testing, demos, or simple computations or visualizations.

## Option 2. Run Slicer and Jupyter on your own computer

### Setup

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For the most part all the sample notebooks are running well from my local linux.
However, this particular bit of code gives me an error. The manual segmentation part:

github.com

Slicer/SlicerNotebooks/blob/master/04_Segmentation.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Segmentation"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "import JupyterNotebooksLib as slicernb\n",
    "\n",
    "# Set image viewer size to 50% (fill half of a cell)\n",
    "slicernb.AppWindow.setWindowSize(scale=0.5)\n",
    "# Hide patient information from slice view\n",

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The error I get:

TypeError Traceback (most recent call last)
In [8]:
Line 4:

TypeError: ‘MRMLCorePython.vtkMRMLScalarVolumeNode’ object is not subscriptable

Hope somebody can help to troubleshoot

Cheers,
Andrius

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Error when running sample Slicer Jupyter Notebooks from local linux machine

The error I get:

TypeError: ‘MRMLCorePython.vtkMRMLScalarVolumeNode’ object is not subscriptable

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