README.md

SegmentationReview

The SegmentationReview extension is a powerful tool for clinicians who need to quickly and efficiently review deep-learning generated segmentations. With this extension, you can use a Likert-type rating system that scores segmentations on a four-point scale, ranging from "Acceptable with no changes" to "Unacceptable, not visible/wrong location".

One of the key benefits of SegmentationReview is the ability to load the entire dataset with all masks and volumes in one batch. This simplifies the workflow and eliminates the need to load masks and volumes separately. Additionally, the results of the review are saved as a csv file, which can be easily used for further analysis.

NOTE: If you have not finished the review of all the masks in one go, feel free to close and resume the extension later on. The last annotated file would be restored from the annotations.csv file saved in the path. (That being said, this won't work if you annotated cases and then added new ones to the same folder. Keep new cases in the separate folder once you already started annotations to avoid conflicts)

Overall, SegmentationReview provides a streamlined solution for clinicians who want to speed up the validation process of deep-learning generated segmentations. It is a valuable tool that can help to improve workflow efficiency and reduce the burden associated with segmentation validation.

Installing the extension

You can install SegmentationReview from the 3D Slicer extensions manager.

To open the extension manager, go to View -> Extensions Manager in the main menu. In the extensions manager, search for SegmentationReview and click Install to install the extension. Once the extension is installed, switch to the SegmentationReview module by clicking Modules -> SegmentationReview in the main menu.

Interface

Panel Overview:

The interface displays three main panels:

• Likert-type segmentation assessment: Ratings are provided on a scale of 1 to 4, representing levels of (1) Acceptable with no changes, (2) Acceptable with minor changes, (3) Unacceptable with major changes, and (4) Unacceptable and not visible. A 5th option for bad images is also available.
• Segmentation Editor: The editor panel allows for fine-tuning of the segmentation.
• 2D/3D Segmentation View: The 2D/3D view allows for visualization and comparison of the original image and the segmentation.

Results:

AI-generated segmentation ratings are automatically saved as a .csv file, which can be further analyzed using any tool of choice. The example above presents a dummy dataset using MS Office, but any other analysis tool can be used.

The annotation.csv has a following structure (with no header):

Filename	Rating	Comments
image1.nii.gz	1
image2.nii.gz	5	wrong sequence
...	...	...

"Rating" (2nd column) has the following encoding: (1) Acceptable with no changes, (2) Acceptable with minor changes, (3) Unacceptable with major changes, (4) Unacceptable and not visible, and (5) Bad images.

Tutorial

1. Prepare the dataset:

   • Option 1 - Provide a mappings.csv file

     Create a mappings.csv file in the inputs folder specifying the img_path and the respective mask_path. Se bellow an example of the content of this file:

     img_path,mask_path
     data/1.nrrd,/path/to/respective/1_mask.nii.gz
     data/2.nii.gz,/path/to/respective/2_mask.nii.gz
     ...
     

     ⚠️ The name of the file must be mappings.csv and the first line must contain the column names img_path and mask_path.

   • Option 2 - Structure the input data folder (only works for nifti)

     To get started, create a folder with the following file structure:

     - image1.nii.gz
     - image1_mask.nii.gz
     - image2.nii.gz
     - image2_mask.nii.gz
     ...
     

     The images should be in NIfTI format (.nii.gz), with corresponding segmentation masks labeled _mask.nii.gz.

   An example dataset of T1w brain scans and their corresponding brain segmentations is provided in the example_data folder with already reviewed images. You can use this dataset to test the extension. If you want to review the images yourself, you can delete the annotations.csv file and start the review process from scratch.

2. Load the dataset into 3D Slicer: After starting 3D Slicer, open File -> Add Data from the main menu, then select the folder containing the images and masks and press OK. After loading, you will see how many images are loaded under the Checked status. If the path is opened for the first time, an annotations.csv file will be created in the same folder. This file will contain the results of the rating and will be automatically updated after each rating. Additionally, the annotations.csv file allows you to restore the annotation process in case of a crash or if there are too many images to rate in one session.

3. Assign a Likert score to each image: In the "SegmentationReview" module, click on the Likert rating tab, select the image, and then select a rating from the drop-down menu (ranging from Acceptable with no changes to Unacceptable and not visible). When you're done, click Save and Next to move to the next image. The results will be automatically saved in the annotations.csv file.

4. Optional: Edit the mask of an image: If you want to change the segmentation mask of any image, you can use the "Segment Editor" module that is added to the extension. Select the Segment editor tab, edit the mask using the brushes or eraser, and then click Overwrite edited mask to save the new mask. The new mask will be saved in the same folder as the original mask, with _upd added to the end of the name.

Installation

This extension is available from the extensions marketplace starting v.5.3.0 (currently a preview version). Here are the steps to install the extension from the source and develop the extension locally. This is useful for testing and contributing changes leveraging the GitHub pull request contribution workflow.

1. Download the source code using git / OR download the .zip and unpack it

git clone [email protected]:zapaishchykova/SegmentationReview.git

(Optional) Enable the developer mode will allow to reload the module from source without having to restart the application.

3. After starting 3D Slicer:

• install the module by drag&drop the extension source directory (works only in Preview Release) OR
• Navigate to "Developer tools"-> "Extension wizard" -> "Select extension" and point to the root of the cloned repo.

The extension will pop up under the Modules:"Examples" section.

Example Dataset

The example data was obtained from the OpenfMRI databaset. Its accession number is ds000228. Brains were segmented using HD Brain Extraction tool.

Citation

If you found it useful in your work please cite the paper: Anna Zapaishchykova, Divyanshu Tak, Aidan Boyd, Zezhong Ye, Hugo J.W.L. Aerts, Benjamin H. Kann "SegmentationReview: A Slicer3D extension for fast review of AI-generated segmentations" https://doi.org/10.1016/j.simpa.2023.100536

Current development branches

If you want to check scans only without masks, clone and install no-masks-dev branch. If you want automated centering on the masks (for example, useful when the segmentations are super small) clone [dev-centroid](https://github.com/zapaishchykova/SegmentationReview/tree/no-masks-dev.

PRs are welcome!

License

This extension is distributed under the terms of the MIT license.