SlicerCART: Configurable Annotation and Review Tool.
- 3D Slicer extension
- Adapted from code of Dr. Laurent Létourneau-Guillon and his team in ICH_SEGMENTER_V2, SlicerCART, and Brain_Extraction. This is an effort to create a unified code for a configurable 3D Slicer extension.
- Inspired from Neuropoly's workflow.
- This tool is made to improve manual segmentation and classification workflows across different teams.
Keywords: medical imaging, manual segmentation, manual correction, workflow, ground-truth segmentation, quality control
Abbreviations:
- MRI - Magnetic Resonance Imaging
- CT - Computed Tomography
- BIDS - Brain Imaging Data Structure
- GUI - Graphical User Interface
- QC - Quality Control
Rationale:
- Manual segmentation and classification tasks are required in the research setting related to medical imaging artificial intelligence tool development
- An open-source solution for such tasks would better benefit the research setting
- Actual open-source solutions that enable imaging viewing and annotation are not optimal from an end-user standpoint (especially from various background), increasing the already high burden of manual segmentation and classification tasks
- A workflow aimed to efficiently navigate through a dataset while performing manual segmentation / correction, including revision steps and robust annotation consistency assessment is crucial for handling large amount of data and provide the best ground-truth references segmentation as possible.
Module specific functions (in details)
This module has been adapted to perform several tasks. Among other things, it allows the user to:
- Customize configuration preferences (see below for details)
- Customize keyboard shortcuts
- Identify the name, degree and revision step related to the human annotator
- Select folder of interest where volumes are saved (and possibly impose BIDS)
- Select the output folder where processing and work is preferred to be saved
- Select a ground-truth folder where references studies can be used for iterative self-assessment
- Display in the GUI a case list of all the studies of interests for the segmentation task (*from a site directory or a customized list)
- Select from the GUI case list any volume of interest to display
- Navigate through case list from next and previous buttons
- Load automatically the first remaining case for segmentation in a customized list
- Create automatically all required segments that may be used according to the project configuration each time a volume is displayed
- Toggle interpolation of the volume loaded
- Execute multiple automated functions when saving segmentation masks for a given volume. Indeed, the automated functions:
- Save segmentation masks in the selected output folder with volume file hierarchy
- Track the different versions (save the following version if previous version(s) already exist(s)) *N.B. limitation to 99 versions for a single volume
- Save a .csv file with segmentation statistics (e.g. subject, annotator's name and degree, revision step, date and time, total duration, duration of each label annotation)
- Save a .csv file with classification statistics (e.g. subject, annotator's name and degree, revision step, date and time, checkboxes / dropdown / free text fields)
- Go to the next remaining case and make it ready to segment without any further action
- Load a pre-existing segmentation for further modification (will be saved as a new version of the segmentation)
- MacOS Sonoma or Sequoia is recommended
- A working version of 3D Slicer.
- N.B. The version currently used to develop this module is the version 5.6.2 (most stable release as of 2024-10-22). The version 5.2.2 has also been used.
This module has been developed on:
- MacOS Sonoma version 14.1.1 and Sequoia 15.0.1
- 3D Slicer version 5.6.2
Although it may work on other versions and/or operating system, please note that it has not been tested.
If previous version of Slicer ---» delete the app. If on MacOS, you can do it by doing right lick on the app in the application folder --- move to trash --- go to trash --- empty the trash --- restart your computer.
- Install 3D Slicer.
- Clone this repository in the location of your choice.
- Then, go in the finder --- find the file SlicerCART.py file, and copy the pathname.
- Open 3D Slicer.
- Activate the checkbox
Enable developer modeinEdit -> Application Settings -> Developer -> Enable developer mode. - Add the path of the
SlicerCART.pyfile inEdit -> Application Settings -> Modules -> Additional module paths.(N.B. 1) You must have the file: if it is the folder path, then the module will not work; 2) in the Additional modul path section, the path copied might be shown to the folder: this is a Slicer thing, and should not affect working property of the module if it was the file that you copied). - The module can be found under
Examples -> SlicerCART: the module should now be opened (N.B. 1) If first use, you may have additional requirements to install. A pop-up window from Slicer advertising you should pop-up if so: just click ok). - (Optional) Set the SlicerCART module to launch at 3DSlicer startup. To do so, go to
Edit -> Application Settings -> Modules -> Default startup module - There might be errors. These would be seen in the Python Console: if any errors, we highly recommend you to fix them before any further use!
- Qt might need to be installed. The first five steps of the following procedure might be useful for this: procedure.
SlicerJupyterto be able to use Jupyter Notebooks connected to 3D Slicer.
TODO (after sufficient development has been made)
TODO (after sufficient development has been made)
- Laurent Létourneau-Guillon
- Emmanuel Montagnon
- An Ni Wu
- Maxime Bouthillier
- Delphine Pilon
- Neuropoly Team