# Quick start — opening a patient CT / MRI

Patient scans are opened **in the desktop app on your own machine**. They are
processed locally and **never uploaded** (the website has no patient upload by
design — that would put PHI on a server). The public website is only a demo.

## 1. Install (once)
```
python -m venv .venv && source .venv/bin/activate     # Windows: .venv\Scripts\activate
pip install -e ".[gui,sample]"
```

## 2. Launch the app
```
sulcora            # or:  python -m sulcora.app
```
(You can also open a scan directly: `sulcora /path/to/scan.nii.gz`)

## 3. Import the patient scan
In the app window:

- **CT or MRI from PACS (a folder of DICOM files):**
  `File ▸ Open patient CT / MRI — DICOM series…` → choose the folder
  (or the toolbar button **📂 Open patient CT / MRI (DICOM)…**).
- **A single NIfTI file (`.nii` / `.nii.gz`):** `File ▸ Open NIfTI…`

CT is auto-detected in Hounsfield units (for haemorrhage/ICH); MRI is used for
DBS / biopsy / tumour. Stuck? `Help ▸ How do I import a patient scan?`

## 4. Plan
1. Pick the **Procedure** (right-hand panel) — the **Targets** list fills in
   automatically (detected clots for ICH, nuclei for DBS, …).
2. Pick a target (or **① Set Target** by clicking in a view).
3. **Load Atlas** / **Load Vessels…** to score eloquent-structure and vessel
   clearance.
4. **③ Plan** or **④ Optimize**, then **Export Report (PDF)**.

*Research software — not a medical device.*
