ViewTool:
Orientation
and Location of Display Slices in 3D
Rview is capable of rendering slices or
planes through 3D image volumes at any orientation (using the current
interpolation mode ). This is controlled
using the Slice View tool (see the main Tool Menu).
As of rview version
8.134B
there are separate display angle controls (transformations) for
different types of
display. These have also been separated from the transformations
accounting for the actual acquisition angle of the data
(Historically rview
simply had one set
of rotations controlling all views and also used to account for the
data
orientation as well as the display). Things are
now sadly more complicated but also more flexible:
The user's overall view of the 3D data volume in
an rview display window is now determined by two main sets of 3D
rotations: the
overall 'Data Orientation', and
the either the slice
view
angles or the render view
angles which modify the view, depending on
the view type in the different windows.
Slice
View:
The control of the final slice view can be summarized by a set of
transformations, from the raw acquired data to each individual display
window:
The data orientation first accounts for
the slicing angle of the data, then the slice view modifies this for
the user preference. Finally each sub window of the rview display has a
separate fixed orientation with respect to this view, to provide for
example orthogonal slices (axial, sagittal and coronal) or multiple
parallel slices at different fixed offsets in the user space.
For the slice view rotations defining
the overall user view of the 3D data: Conventionally the 'X' rotation
corresponds to the nodding angle (dipping the head forwards or
backwards), the 'Y' rotation corresponds to dipping the head to the
left or right, and the 'Z' rotation corresponds to turning the head to
the left and the right. Note: Unlike the registration
parameters, altering these angles sets the
orientation of the reference co-ordinates and therefore applies to the
display of all the image data. Enter the new angle and press the
'Update Display' button to force rview to redraw the display.
The following displays illustrate the
effect of modifying the 'X' (nodding) angle by +10 deg and -10 deg:
'X' rotation set
to
-10 degrees
'X' rotation set
to
+10 degrees (note changes in each column from previous display)
Alternatively the display can be
interactively updated by holding down one of the up/down arrow buttons
next to the angle value. This has the effect of incrementing the angle
by 5 degrees and redrawing the display (Note: if you have a slow
machine
or are displaying a complex 3D volume rendered scene,
this may not be very quick: so do not click very quickly!!!!)
Render
View
This controls
the viewing direction for any 2D to 3D rendering (ray casting) display
(see render tool). This works in a
similar way to the slice views, but the mapping between the standard
and user view has an independent set of three rotations:
For
example, a change in one render view angle of 10 degrees (note slice
view rotations are
unchanged) changes the rendering:
Segmentation
display with surface and slice views: both slice and
render angles are set to zero.
Segmentation
display with surface and slice views: render X rotation angle set to 10
degrees (note slice views are unchanged).
Data
Orientation
This set of three angles describes
the
mapping between the acquired data orientation (for example
coronal) and the internal rview orientation (axial). These should
normally be read automatically from the data file: More information
about these is given in the data loading
explanation. You may modify these manually or by using the controls
in the Data
Orientation area of the slice
view tool. This allows
rview
to ensure that by convention in orthogonal displays the transaxial,
sagittal
and coronal slices are placed in a consistent location on the screen
e.g.:
Independent
of whether the data was originally acquired with transaxial, coronal or
sagittal slices. If the data slice orientation was not read
automatically then the data slicing angle can be set manually to
transaxial, coronal or sagittal using the 'Data Slices Are' options
(Note: this may still not work if there are data reading problems e.g.
with analyze formats).
Translations
As with the rotations: simply manually
enter the new location in mm and then press the update button.
Translations alter the centre or focus of ALL displays (both 2D to 3D
rendering and slice views)
History
Each time the slice location is modified rview records the points in a
history list (as with a browser)
The back button allows you to go back to a previous location.
Regrid Refim
The display controls in the view tool modify the way data slices cut
through the image volumes when displays are created. However, this does
not modify the image data directly and voxels of the data remain in the
acquired orientation (axial/sagittal etc)
For tracing it is often useful to trace the image data with the data in
a standard alignment so that tracing planes are orthogonal to specific
anatomical axes. To do this in rview you can use the display tools
above to setup
a view (e.g. AC-PC horizontal) of the data, and then apply
this transformation to reorient a dn resample the data. This is
done by simply pressing the 'Regrid Refim' button at the bottom of the
view tool. This will apply the current view transformation to the
reference image data and sets the view angles back to zero.
Notes:
This transformation uses higher accuracy (sinc) interpolation to
prevent blurring of the data (not good for tracing fine structures) and
so may take a minute or so even on a fast machine!
This does not transform the segmentation image or floating images! (so
it is best to regrid the reference image first before starting
segmentation or registration)
You must remember to SAVE the Reference image !!! (because it has now
been modified from the original data you loaded)
