Functionalities

This section lists the functionalities of SlicerCART. If the function you are looking for is not found below, it is likely that SlicerCART does not have yet this feature: you are invited to open an issue on the Github Repository to request the functionality you are looking for.

Details:

This module has been adapted to perform several tasks. Among other things, it allows the user to:

  • Customize configuration preferences for project-specific segmentation or classification tasks, including:

    • Task Selection (Segmentation and/or Classification)

    • Modality to be viewed/process/annotated (CT or MRI) [Must be one or the other for now. Does not currently take DICOM images.]

    • Brain Imaging Data Structure (BIDS) format imposition (test quickly if a dataset respects the BIDS convention through a BIDS-validator script: makes unable to load a dataset if it does not respect BIDS format)

    • View to display by default in the viewer (e.g. axial, sagittal, etc.) [only one at the time]

    • Interpolation of images (by default, Slicer images that are displayed get “interpolated” (i.e. smoother): with SlicerCART, you can toggle through this option)

    • For CT-Scans:

      • Specify the range of Hounsfield units for which a segmentation mask will be feasible (e.g. 45 to 90): otherwise, segmentation mask will not be created.

    • Customize keyboard shortcuts

    • Customize mouse button functions

    • Configure from the user interface the segmentation labels, including:

      • Label name

      • Label value

      • Color

      • Adding/Removal of labels (at least one is required for proper use)

    • Select if timer should be displayed during segmentation task

    • Configure from the GUI the classification labels, including adding/Removal of:

      • Labels

      • Checkbox

      • DropDown Menu (options)

      • Text field

  • Identify the name, degree and revision step related to the human annotator

  • Select folder of interest where volumes are saved

    • Display automatically the PATH of the loaded volume

  • Select the output folder where processing and work is preferred to be saved

  • Display in the user interface a case list of all the studies of interests for the segmentation task (from a site directory or a customized list)

  • Select from the 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

  • From the Classification window:

    • Perform classification tasks e.g. checkbox, dropdown menu, textbox

    • Check and load a specific classification labels version for a given volume

    • 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 automatically to the next case in the UI

  • From the Segmentation window:

    • Open directly the Segment Editor

    • Select the active segment to edit

    • Start Painting

    • Erase any part of visible masks

    • Select Lasso Paint (fills the space of a contour-based geometrical annotation)

    • Place a measurement line

    • Load the latest available segmentation mask versions available

    • 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)

      • 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)

See Repository Organization for the repository files and folders tree structure.

See Class Organization for the class diagrams of the repository scripts.

This documentation was last updated on June 10, 2025.