Differences

This shows you the differences between two versions of the page.

--- neuroelf_gui_-_rendering_ui [2010/08/10 01:08] – created jochen
+++ neuroelf_gui_-_rendering_ui [2011/05/07 23:59] (current) – updated to v0.9c jochen
@@ Line 2: / Line 2: @@
 ===== Motivation =====
-Whereas slice-displays can give a very "close-to-the-data" look at results of a whole-brain mapping, it sometimes is more desirable to visualize an entire 3D space with one image. One way to do this is by using mesh-based surfaces containing a projection of statistical information. However, the extent in the third dimension (orthogonal to the surface) is not easy to visualize in (and grasp from) such images. Another look at the data is to render the entire dataset slice by slice in a semi-transparent fashion. Here are three examples (click to zoom):
+Whereas slice-displays can give a very "close-to-the-data" look at results of a whole-brain mapping, it sometimes is more desirable to visualize an entire 3D space with one image. One way to do this is by using mesh-based surfaces containing a projection of statistical information. However, the extent in the third dimension (orthogonal to the surface) is not easy to visualize in (and grasp from) such images. Another look at the data is to render the entire dataset slice by slice in a semi-transparent fashion. Here are four examples (click to zoom):
 {{:render_brain_activation.jpg?320|Activation with brain}}
 {{:render_brain_activation_hemisphere.jpg?320|}}
 {{:render_brain_transparentskull_activation.jpg?320|Activation volume map together with opaque brain and transparently rendered skull}}
+{{:lh_backtovmr_rendered.jpg?320|Back-projected left hemisphere surface with activation map}}
 ===== Layout =====
 The Rendering UI is available via the Visualization -> Render menu item as well as the rendering button (below the surface pane button), and it looks like this:
-{{:render_ui_v09b.png|NeuroElf Rendering UI}}
+{{:neuroelf_gui:render_ui_v09c.png|NeuroElf Rendering UI (v0.9c)}}
 The dialog has the following controls and properties:
   * read-only edit box showing the anatomical dataset used for rendering (whatever object is selected while the dialog is invoked)
-  * drop-down box to chose an additional (secondary) anatomical dataset used for alpha (transparency) information (e.g. to make certain parts of the volume semi-transparent)
+  * colored buttons for the background as well as the lower and upper boundary values for the anatomical dataset, followed by a dropdown box defining the color-blending mechanism
-  * alpha-level factor for this secondary dataset
+  * drop-down box to chose an additional (secondary) anatomical dataset used for alpha (transparency) information (e.g. to make certain parts of the volume semi-transparent), followed by the alpha-level factor for this secondary dataset (edit box)
   * slice stepping controls (from, to, step size) which determine which planes in the 3D space will be sampled (smaller step sizes increase quality for high-res images)
   * planar bounding box controls (Y/Z from and to) which determine the coordinate space per sampled slice
@@ Line 26: / Line 27: @@
   * statistical alpha-level (negative values produce soft edges, as lower thresholds will be scaled between 0 and 1 internally already)
   * join maps, controls whether for multiple selected maps the colors are to represent a mixed color (joined) or the "top-most" color (in order of VMP container)
+  * statistics visibility restriction settings (multiplication with anatomical alpha checkbox and minimum anatomical alpha requirement)
   * statistics smoothing, this controls whether, regardless of edge smoothing, the **sampled slices** will be smoothed (does not affect actual map)
   * minimal visibility (through how much space of brain/skull should activations be visible at least?)
+  * interpolation method choice dropdowns (separately for anatomical and statistical datasets)
   * show continuously updated version of rendering
-  * target filename
+  * target filename and saving checkbox
   * UI close button
   * Render button
@@ Line 48: / Line 51: @@
 The full head dataset (colin_ICBMnorm.vmr) was selected in the main UI before invoking the rendering UI, and the background of the brain VMR was filled with a low value (30), and then selected as the secondary alpha channel, which makes all non-brain voxels appear with a very high transparency.
+==== Back-projected surface ====
+The left-hemisphere (160k vertices version) was back-projected to a 0.5mm VMR resolution VMR, border-smoothed, then filled up with a gray intensity value, and then rendered with an activation map overlaid.