3D Slicer Work Sample Portfolio

3D Slicer is a free, open-source platform for medical image informatics, visualization, and image-guided intervention research.
It supports DICOM and many imaging workflows, including segmentation and 3D model generation.

Quick project plan (dataset + approach)

For a reliable, no-download demo, I used 3D Slicer Sample Data -> MRHead and built a simple threshold-based segmentation workflow.
The script creates one segment from intensity thresholding, then exports a 3D model and saves both the segmentation and model files locally.
This keeps the sample beginner-friendly while showing practical Slicer automation.

What I did

• Loaded MRHead from Sample Data (public, de-identified sample bundled via Slicer).
• Created a new segmentation node linked to the loaded volume.
• Applied a simple threshold effect to generate a segment.
• Converted/exported segmentation content to a 3D model.
• Saved outputs to a local folder for reproducibility.
• Documented manual steps, script execution, and troubleshooting.

Datasets used

• Primary (scripted): Slicer Sample Data -> MRHead (required).
• Optional manual walkthrough: Slicer Sample Data -> CTChest (optional, not required for script).

No PHI/PII is included in this repository. Use only public/de-identified sample data.

Folder structure

.
├── README.md
├── notes/
│   └── worklog.md
├── screenshots/
│   ├── 01-sample-data-mrhead.png
│   ├── 02-threshold-segmentation.png
│   ├── 03-3d-model-view.png
│   └── 04-saved-files.png
└── scripts/
    ├── mrhead_threshold_to_model.py
    └── RUN.md

Reproduce the sample (manual click-by-click)

1. Open 3D Slicer.
2. Go to Sample Data module.
3. Click MRHead to load the sample volume.
4. Open Segment Editor.
5. Click Add to create a new segment.
6. Select Threshold effect.
7. Adjust threshold range so major head structures are selected (example start: lower 500, upper 2000; tune visually).
8. Click Apply.
9. Click Show 3D to generate/display the 3D surface.
10. (Optional) Open Segmentations module and export segment(s) to model(s).
11. Save scene/data via File -> Save.

Reproduce the sample (script)

1. Start 3D Slicer.
2. Open View -> Python Interactor.
3. Run:

   exec(open(r"/absolute/path/to/scripts/mrhead_threshold_to_model.py", encoding="utf-8").read())

4. Check generated files in outputs/mrhead_threshold_demo/.

See scripts/RUN.md for details.

Screenshots checklist

Place screenshots in /screenshots using these filenames:

• 01-sample-data-mrhead.png — MRHead loaded in slice viewers.
• 02-threshold-segmentation.png — Segment Editor threshold settings and result.
• 03-3d-model-view.png — 3D view with segmentation/model visible.
• 04-saved-files.png — File browser showing saved .seg.nrrd and .stl outputs.

What I learned

• How to move from sample volume loading -> segmentation -> 3D model export in Slicer.
• Basic Slicer Python automation patterns (SampleData, SegmentEditor, save/export logic).

Next steps

• Add multi-segment workflow (e.g., bone + soft tissue labels).
• Add quantitative metrics (segment volume/surface area).
• Expand optional CTChest manual walkthrough with comparison notes.