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ogles
control window
viewing
control window
localizer
ac-pc
trajectory
measurement
drawing
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The Main Ogles Control Window (OCW) has a file panel and buttons which invoke other control windows and all data views. The Ogles Control Window provides access to all graphical controls and windows:
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The 'File Panel' of the 'Ogles Control Window' allows for selection of the current data file. When clicked, a menu of data set files appears. Select the desired data file to have Ogles read the corresponding data set. This list reflects the entries in the 'xx.ogle' script file. When the data set has changed, data in the 'Ogle Render Window' are not re-rendered in real time since re-rendering is computationally intensive. In such cases, the status window will indicate that the view is not current. The view is made current when the orientation of the dataview is changed.
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| Parameters like transformation, windowing and slice positions are controlled in the Ogles Viewing Control (OVC) Window. The OVC offers two rollout panels: |
| The 'Options' panel: |
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Slicer Windowing: Please select the windowing carefully. Since the current slicer volume is recalculated entirely this procedure is time consuming. |
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Reference Volume Options: Select a reference volume that then can be superimposed onto other volumes. The reference volume is visible in Slicer Windows only. Reference slices are displayed by means of alpha blending (from Kevin Harris kevin@codesampler.com). |
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| The 'Geometry' panel: |
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Ogles provides routines to read and write 3d contours in a simple, unified, inter-subject coordinate system. The coordinate system is established by the anterior commissure (AC), the posterior commissure (PC) of the III. ventricle, and the mid line plane of the brain. An intersubject approximation is achieved by aligning these contours to the AC-PC coordinate system and transforming them according the width and length of the III. ventricle. AC-PC alignment is performed automatically, the selection of -or transformation to- the appropriate ventricle dimensions have to be done manually. The contours are generated by drawing voxels in Ogles and computing their 3d surface. The surface is saved as a triangle mesh in the Open Inventor (.iv) data format (see http://oss.sgi.com/projects/inventor/ and http://www.coin3d.org/). Ogles is by no means an Open Inventor file reader, it rather puts its mesh data into a very restricted iv syntax and can read only this syntax. Ogles iv files though are readable by real iv viewers (http://coindesigner.sourceforge.net/, http://www.sgi.com/products/software/performer/).
The 'Repository' subpanel allows for loading iv triangle
mesh files. The location of these files is hard coded to '../Ogles/ogles-0.7.0/data/repository'. When running ogles from inside M$ Visual C++, ogles won't find anything. You might want to either copy ogles.exe to \ogles-0.7.0\ win-bin, or copy \ogles-0.7.0\data\repository to ogles-0.7.0\src\data\repository. The width and length of the third ventricle in the original volume are displayed.
If the anterior commissure (AC) and posterior commissure (PC) are set in the current volume before(!) loading these contours, they will be aligned to the current AC-PC coordinate system. Otherwise these contours will be shown in arbitrary orientation. After selecting 'Act on Repository' in the Options Panel, contours can be transformed with the graphical controls of the Ogles Viewing Control Window.
3d contours are calculated from voxel drawings in the Measurements Control Windows. These contours then can be saved in the `Current voxel drawing` subpanel. The scale from millimeters to the OpenGL coordinate space is either known from pixel dimensions in the Analyze header file or from stereotactic localization.
If
1. the mm scale is known,
2. AC-PC are set, and
3. the width of the III. ventricle at mid-AC-PC
is set,
then a contour can be saved in AC-PC coordinate system.
Otherwise a contour can be saved "as is" only.
"As is" contours are saved in Open Inventor data format to
`../Ogles/data/arbitrary`, and can't be reloaded.
When large contours are viewed, the redisplay of data slows down significantly.
It is advisable to switch off viewing of large contours before transforming or
scrolling through slices, and switch on viewing again.
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The stereotactic localizer is selected and registered in Ogles Localizer Control (OLC) Window.
Currently only two localizers are implemented.
The semi-auto detection mode needs
really nice contrasts between rods and plates.
Out of many stereotactic systems, only two are implemented partially:
The Zamorano-Dujovny- and the Riechert-(Mundinger)-System.
(Which happen to be used in our department.)
Both Systems have to be mounted in positive z direction. The stereotactic
probe has point into negative direction. Settings for the Riechert
System are calculated for the anterior fixation.
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| Rods
can be selected in the axial view window only. |
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| Rods
clicked |
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In functional neurosurgery the anterior (AC) and posterior (PC) commissures of the third ventricle serve as a reference system to determine statistical target points. As the patients head is not always positioned symmetrically in the head ring a third point perpendicular to the ac-pc axis is needed to define the ac-pc coordinate system. AC-, PC, and the midline points are set in the Ogles AC-PC Control (OAP) Window. In order to transform ac-pc coordinates to image coordinates the localizer needs to be registered.
Three
standard targets for deep brain stimulation are provided. |
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AC-PC, and a "midline point" |
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Trajectories are set in the Ogles Trajectories Control (OTC) Window.
Target and entry points can be selected in the perpendicular slicer windows.
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Results:
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Basic Measurement is accessible via the Ogle Measurement Control (OMC) Window. |
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The Ogle Measurement Control Window also provides means for simple voxel based volume drawing.
Voxel drawing is very tedious and results in ugly square-edged shapes. (When the mouse cursor is moved in Glut, it tells the pixel position only, and i couldn't find a better solution than using the pixel position).
When an other data file is selected, the drawing will be lost.
When the 'Select' button is pressed, all pixels +/- range are selected under a left mouse click in the slicer windows.
The 'Grow Region' button selects all 3D adjacent pixels with the clicked color/gray value +/- range.
Usually either a minor part of the desired pixels is selected,
or the selection floods far beyond the boarders of the intended structure.
The 'Make geometry' button initiates a marching cube algorithm
from Thomas Lewiner (
jgt.akpeters.com/papers/LewinerEtAl03/),
followed by surface smoothing (Improved Laplacian Smoothing of Noisy Surface Meshes,
J. Vollmer, R. Mencl, and H. Mueller in
EUROGRAPHICS Volume 18, 1999, Number 3).
Because surface smoothing is extremely time consuming, the number of smoothing iterations is reduced for large datasets or skipped entirely. The calculated surface can be saved as triangle mesh in the 'Ogles Viewing Control Window'. If the AC-PC coordinate system is established, these mesh data can be reloaded in Ogles. All saved mesh files can be loaded Open Inventor viewers.
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Sample of Ogles mesh file, ventricles.iv, [12.4 MB].
One possible direction of this project is a public repository of AC-PC aligned brain structures.
Please don't hesitate to contact me. |
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Script file basics
