is helpful to use this tutorial in conjunction with the
video on the first page.
preset configuration makes it easy to load datasets. To access the preset click
on "Presets" on the top-left.
Choose the "Brain Sectional" preset and set the "Folder" property to the
"./data/brain/" directory in the distribution folder. This dataset will load in
about one minute and requires approximately 1GB of free working memory. More
information on how to start from a raw data file can be
found at the end of the tutorial.
Once the preset loads, activate the "Viewers" tab on the top left and select
"Brain Viewer" in the list below. This will bring up the toolbox for the 3D
model. Activate the "Selections" group.
Adjust the size of each viewing pane by dragging on the dividing lines.
Position the mouse over the 3D model. To move the model in the xy plane, press
the right mouse button and drag. To move the model along the z axes, rotate the
mouse wheel (not holding any mouse button down). To rotate the model press the
'R' key; this will generate a rotation sphere which you can grab by pressing
down a mouse button and rotate.
model can also be positioned in the three orthogonal poses by pressing 'O' while
the mouse is positioned over the brain model.
select a bundle in the 2D representations, move the mouse over the axial plane.
Identify the cingulum bundle, press the left mouse button and drag a line
perpendicular to it. Any new selection will cancel the previous one except if
the "control" key is pressed (allowing multiple selections). You will notice
that a selection performed in one view is mirrored in all other views.
can orient a brain in a position that matches one of the 2D projections by
positioning the mouse over the 2D projection and pressing 'O'.
Move the mouse over the 3D model. Press 'H' a number of times. This will toggle
between two viewing modes: one that shows the entire brain and one that only
shows the current selection.
can refine a selection in the 3D space. Ensure that the "2D Brush" checkbox is
activated on the left menu. Change the "Selection Mode" to "Remove". Move the
mouse over the 3D model, hide
unselected tubes ('H'), and
drag (mouse-press+mouse-move) a line intersecting unwanted tubes. They
will change color to orange meaning they will be removed once the mouse button
can also experiment with the "Add" and "Intersect" selection modes. The "Add"
mode will add unselected tubes to the current selection and will only work when
unselected tubes are visible (since they are target of this operation).
"Intersect" will keep in the selection only tubes that are both in the current
selection and currently brushed over.
can save a selection for future use by entering a name in the "StoreSelection"
field and pressing "Set". Once several selections have been saved they can be
toggled between or used in common selection operations. To toggle between them
ensure that the selection mode is set to "Single Shot" (this will not aggregate
selections). Otherwise, clicking on a saved selection will aggregate it to the
current selection based on the selection mode (Add,Remove or Intersect). A list
of selections can also be saved to a file and then used with the same dataset
Selections on the 3D models can also be performed with a selection spehere.
Uncheck the "2DBrush" checkbox on the left. Move the mouse over the 3D model and
press the left mouse button down. This will bring about a selection sphere. You
can move the sphere, as you hold the mouse button down, by dragging the mouse
around the screen and by using the mouse wheel or up/down keys for the Z
direction. Tubes that intersect the sphere will highlighted as you keep the
mouse button pressed and selected once you release the button. You can change
the size of the sphere by pressing the "," and "." keys which should be placed
below the "<" and ">" keys.
"Clear" button clears the current selection while "Undo" discards the last
Email email@example.com with
any questions, comments requests for new presets etc.
Starting from scratch:
data files that our application files describe the white matter tracts as
collections of polylines. An example can be found in ./data/brain/tubes.data.
The first line contains the number of tracts in the model. The rest of the file
describes each individual fiber starting with the number of points describing
the tract and continuing with the coordinates of those points (only the first
three numbers are considered).
interact with a brain model in the way described in this tutorial a few
computations have to be performed and stored beforehand. You can use the "New
Brain" preset to this purpose. It requires two parameters: the model file in the
format describe in the previous paragraph and an output, cache directory. It
should be noted that this computation is not optimized in our prototype
application and takes
a long time for large datasets of around or over
5000 tubes (3-4 hours). Once the "New Brain" presets load the application should
be restarted and used as described in this tutorial. To become familiarized with
this process we provide a small model ./data/tubes_raw_small.txt.