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Tina Memo No. 2005-002
Internal

Tina 5.0 User's Guide

Edited by N.A. Thacker and P.A. Bromiley

Last updated
7 / 12 / 2005
Neuro-Imaging Analysis Centre
Medical School
University of Manchester
Manchester M13 9PL
England

©University of Manchester, England.
Software contributors: Steve Pollard, John Porrill,
Neil Thacker, Stuart Cornell, Julian Briggs, Dave Prendergast,
Richard Lane, Anthony Ashbrook, Beth Vokurka, Tony Lacey,
Paul Bromiley, Marietta Scott, Gio Buonaccorsi, Maja Pokric.

Contents
Introduction
- The Main Tool
- Infrastructure Sub-Tools
- Machine Vision Research Sub-Tools
- Medical Image Analysis Sub-Tools
- File Handling
- Display Selection
- Standard File Names
Tv Tool
- Introduction
- The Logical Tv and the Tv Tool
- Interaction
  - Mouse Interaction
  - ROI Interaction
View Tool
- Introduction
- Graphics Options
- Colour Maps
- Graphic Hard Copy Output
- Making Movies
Macro Tool
- Introduction
- Button Functionality
Histogram Tool
- Introduction
Terrain Tool
- Introduction
- Display Options
- User Interaction
- Functionality
Mono, Stereo and Sequence Tools
- Introduction
- File handling
- Display
- Mouse Activity
- Sequences
- Push and Pop
Imcalc Tool
- Introduction
- Mouse Interaction
- Stack manipulation.
- Basic Image Manipulation.
- Basic Algebra
- Transendental Algebra.
- Standard Noise and Texture Filters.
- Numerical differential functions.
- Complex Image manipulation
- Fourier and related Functions.
- Misc.
- IP defaults:
- Create Tool
- CP defaults:
- Standard Usage
- Non-Parametric Image Subtraction
Edge Geom Tool
- Introduction
- Standard Usage
- Edge Geom Tool Buttons
- Pick and Mouse Menus
Corner Tool
- Introduction
- Standard Useage
- Processing Functions
- Pick and Mouse Facilities
Calib Tool
- Introduction
- The Camera Model
- Tina Interaction
- Input/Output
- Pre-Processing
- Calibration Methods
- Covariance Computation
- Calibration Errors
- Grid Calibration
- Calibrating Arbitrary Stereo Images
- Model Based calibration
  - Model Parameters
  - Recommended settings
PMF Stereo Tool
- Introduction
- Initial Matching
- Cost Options
- Match Support
- Choosing Matches
- Mouse Activity
- Default stereo matching
Correlation Stereo Tool
- Introduction
- Standard Usage
- Stereo Correlation Matching
- Default stereo matching
Matching Tool
- Introduction
- Standard Usage
- Matcher File/View
- Geometry
- Initialisation
- Interactive Matching
- Automatic Matching
- PWR Params
- Match Parameters
Pairs Tool
- Introduction
- Standard Usage
- Scene and Model Data
- Single Line Functions
- Complete Scene Functions
- Matched Model Functions.
- Dialog Boxes
Colour Image Tool
- Introduction
- Colour Theory 101
  - Colour spaces
- The Tina Colour Tool
- Quick Reference
SmartROI Tool
- Introduction
- Graphical Display and Data Selection
- Profile Input/Output
- Mark-up
- Training
- Search
  - SmartROI Parameters
- Typical Use
NMR-Segment Tool
- Introduction
- Tool Description
- Image segmentation example
NMR-Analysis Tool
- Introduction
- Tool Description
- Sequence images segmentation examples
  - FMRI example
  - Perfusion segmentation example
Coreg Tool
- Introduction
- The Simple Coreg Tool
- Simple Coreg Tool Quick Reference
- The AIR Parameters Dialog Box
- AIR Parameters Dialog Box Quick Reference
- The Advanced Coreg Tool
SeqROI Tool
- Introduction
- Graphics and Splines
- The VOL: Buttons
The DODECANTS Tool
- Introduction
- Installation
- Use of the DODECANTS Tool
- Quick Reference
Bibliography
Talairach Tool
- Introduction
- Tool Description and Use
Flow Tool
- Introduction
- Pre-requisites for Use
- Using the Tool
Cortical Thickness Tool
- Introduction
- Tool Description
  - Cortical Thickness Tool
  - Cortical Thickness Parameters
- Standard Usage
- Histogram Numbers and Labels
File Formats
- AIFF Images
- Edge Files
- Geometry File formats
- Calibration Data
- Matcher Files
- OLD format
- NEW format
- Multi-Dimensional MR model
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