- Date: 2018 April 30 - May 2.
- Time: 9:30 AM to 4:00 PM every day.
- Location: Goodwin Hall (25 Union Street, Kingston, ON K7L 3N6), room 524.
- Registration: please fill this registration form. Registration is free.
- You need to arrange travel and accommodation. Most affordable motel at walking distance is Howard Johnson Kingston or you may find a room near the campus on AirBnb.
- Lunch will be provided (pizza, sandwich, etc.).
- Any questions? Send an email to Andras Lasso.
Please fill out the feedback form!
- Prepare with a short introduction about yourself (2-3 minutes, supported by 1-2 slides): experience, research interests, something personal
- Bring your own laptop. Windows OS is strongly recommended.
- Install 3D Slicer latest stable version (4.8.1) -> nightly 64-bit installer. After you installed Slicer, start it, open the Extension manager, and install these extensions: SlicerIGT, Sequences, Debugging tools, SlicerElastix, SegmentRegistration, TCIABrowser, Perk Tutor, SlicerDMRI
- Install recent Slicer nightly version (Windows, MacOS), and install all extensions that you installed for 4.8.1.
- Install Git for Windows and TortoiseGit if you bring a Windows computer. On macOS and Linux, Git comes with the OS so all we need is a client. On macOS we recommend using GitHub Desktop. On Linux, terminal commands are best. See the "Git on macOS and Unix" pdf for a tutorial.
- PyCharm Professional Edition (you can activate it immediately with your university email address), Community version is not suitable (does not support remote debugging)
- Install latest version of PLUS from: http://perk-software.cs.queensu.ca/plus/packages/nightly/ -> PlusApp-...-Win32.exe package (the generic version, not Ultrasonix, Telemed, etc.). If you bring a non-Windows computer then you may not be able to follow certain hands-on exercises (less than 2 hours in total).
- Register a user at www.github.com
- Optionally, install Autodesk Fusion 360 CAD software. Register an account with a university email address to get access to Fusion 360 for free. You will be able to follow model design and 3D printing tutorial without Fusion 360, if you laptop does not meet minimum hardware requirements. If you would also print your designed models, download Makerbot Desktop
- 9:30 Lab policies, available services, and guides – required only for PerkLab members (Thomas/Tamas)
- 10:00 Introduction of participants and instructors – with tea and cookies.
- 11:00 Software platform, open-source, reproducible science (Andras)
- 11:30 Project management (Andras, Mark)
- 12:30 Lunch break (pizza)
- 13:00 3D Slicer basics (Csaba, Andras, Mark)
- Overview: core features, community, major extensions (30 min)
- Visualization: load/save, sample data, viewers, models, volume rendering (30 min)
- DICOM: tags, where to get them (web, TCIA browser), loading options, plugins, export (15 min)
- Segmentation: (45 min, Andras)
- Registration: BRAINS, Elastix, landmark registration, SegmentRegistration, transforms, transform visualization (45 min)
- Other: Sequences, MatlabBridge, Virtual reality (15 min)
- 16:00 Adjourn
Dinner 6pm at Brew Pub (optional, $)
- 9:30 Tracking basics, Coordinate systems and transforms (Tamas)
- 10:30 PLUS main features (Matthew, Kyle)
- 11:00 Writing Plus config files for tracking and image acquisition (Matthew, Kyle)
- 12:00 Lunch break (sandwich)
- 12:30 Design for 3D printing (Tamas)
- 13:30 SlicerIGT modules: neuronavigation - calibrations, visualization (Matthew, Tamas, Mark)
- 15:30 Perk Tutor (Matthew, Zsuzsanna)
- 16:30 Break
- 17:00 Social (Mario Kart, snacks)
- 9:30 Writing correct and understandable code (Andras)
- 10:30 3D Slicer module types and programming Slicer - part 1 (Csaba, Andras, Matthew): Python basics and developing simple example Python module Center of Masses
- 12:30 Lunch break (sushi)
- 13:00 3D Slicer module types and programming Slicer - part 2 (Csaba, Andras, Kyle): Individual work to develop a more advanced module
- 16:00 Adjourn
Presentation slides and additional files will be available in this repository.
- Top of the application window cut off, rest of the window is shifted up: known Intel graphics card driver issue. See details here
- DICOM browser window did not appear: last used window position is stored in settings and restored - the position was invalid (outside of screen). Fixed in latest nightly.
- Extension manager: double "Search" text appearance - pull request sent with a fix: commontk/CTK#801
- Extension manager: when typing quickly in search box some letters are removed. Fixed in latest nightly.https://github.com/Slicer/Slicer/commit/d80402c226ecc6b9813cf06226d4db7a23a22a2c
- Extension manager: window size too high (cannot click restart button)
- Nightly crashed on startup on Paola's computer
- SlicerRT installation was incomplete (on Mac) probably because slicer was restarted before installation was completed