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Next: 6. Advanced Image Visualization Up: 1 A. Overview Previous: 4. Application Structure   Contents

Subsections


5. Looking At Images

5.1 Image Formats

BioImage Suite uses as its default file format the Mayo/Analyze 7.5 (and since 2.5 the NIFTI) file format. BioImage Suite supports more or less the complete specification of the NIFTI format. We recommend using this in preference to the Analyze format if possible.

5.1.0.0.1 Analyze 7.5 format:

In this format images are stored as a pair of files .hdr/.img, for example brain.hdr and brain.img. The header file (.hdr) is 348 bytes long and stores information about the image dimensions (e.g. width x height x depth), voxel dimensions (how large the voxels are), and the orientation (e.g. coronal, axial, sagittal). (In the cases of images with gaps between slices, the voxel dimension is really the voxel to voxel spacing, including the gap!)

Analyze 7.5 is a ``non-standard'' standard. There are some extensions to it implemented by SPM (e.g. origin and axis direction) which BioImage Suite does not support. Also most implementations of this format do not correctly use the orientation field (e.g. some versions of AFNI).

The assumption made in BioImage Suite for the purpose of displaying the images is that images in Analyze format are stored as follows:

5.1.0.0.2 NIFTI Format:

This is a modernized version of the Analyze format. It has the advantage that the axis orientation is explicitly specified in the image header (unlike the old Analyze standard in which this was implicit). NIFTI images are either stored as single .nii (or .nii.gz compressed) files or as pairs of (.hdr/.img) files as in the Analyze format.

BioImage Suite supports almost the entire NIFTI standard with the exception of images with non-orthogonal axis. When an image is loaded into BioImage Suite it may be flipped to conform to our internal convention (which is implicitly assumed in the case of Analyze images - see above). For example, if an image comes in left to right, it will be flipped to be right-to-left. The header is also changed to reflect this - the image is still a valid, appropriately labeled NIFTI image!

Figure 5.1: The BioImage Suite Image Header Editor. This is accessible under File/Image Header Editor.
Image header_control

5.1.0.0.3 Other Formats:

Most scanners produce DICOM images, you will need to use external software to convert these to NIFTI or Analyze. The .mnc format is also popular - it was developed at the Montreal Neurological Institute. For arcane reasons, BioImage Suite supports v2 of the .mnc format, unfortunately v1 is more commonly used. Support for .mnc v1 will come with BioImage Suite 3 later this year.

5.1.0.0.4 Image Header Editor:

The image header can be examined and modified (i.e. corrected) using the Image Header Editor (shown in Figure 5.1.)

5.2 The Viewers

Figure 5.2: The BioImage Suite Orthogonal Viewers.
Image ortho


A: The Mode Selector - sets the viewer in 2D, 3D or combination modes. B,C: The 3D Mode Selectors - select which of many combinations of elements will appear in 3D. D,E: Buttons to access the Volume and Oblique sub-Controls. F: ``x-hairs'' - disables the viewer changing positions when the left mouse button is clicked in the viewer. This essentially locks/unlocks the viewer. ``Lb'' - this turns on/off the label/axis display in the viewer. ``Interp'' - this turns on/off Open GL blending interpolation of the image. If this is off and the image is zoomed sufficiently then individual voxels can be seen! G: The Talairach control - see later for more on this. H,N: These two controls interface with objectmap display and editing (not always present). I1,I2,I3: The navigation controls to select the slice display. J: Colormap Controls. The ``Cmap'' button brings up the colormap control, whereas the others set preset colormaps (see below). K: - the zoom control which allows the user to zoom in or/out. L: - the reset control which restores the view to a good default. M: - the save button which can be use to save screenshots of the viewer display as .jpeg or .tif images.

Figure 5.3: The BioImage Suite Mosaic Viewer.
Image mosaic


We will only describe here functionality that is different from the Orthogonal Viewer. A: The Mode Selector - selects the orientation of the displayed slices. B: The Talairach control - see later for more on this. C,D: Controls how many slices to display in Rows $\times$ Columns. E: Selects the slice for the top left view. F: Selects the increment, if this is greater than 1, then the viewer skips slices. G: Additional controls to reverse the order of the slices and to transpose the order in which they are displayed.

5.2.1 The Orthogonal Viewer

The orthogonal viewer is probably the most commonly used viewer in BioImage Suite. It is shown in Figure 5.2. The images are displayed in the black area on the left side of the viewer window. This viewer can display either (i) single 2D slices, (ii) linked cursor orthogonal slices, (iii) 3D renderings and (iv) combinations of (ii) and (iii). There are a variety of ways to manipulate the views and move through them. For the most efficient control, the use of a three-button mouse is recommended.

5.2.1.0.1 Mouse Control in the viewing area

Button 1 (left) Click the left mouse button (button 1) anywhere on any of the 2-D slice views to set the cross-hairs to this point. Click and hold button 1 as you drag through the view space to move the cross-hairs cursor when it is active, and to rotate the 3-D display, when it is shown. (Unchecking the ``x-hairs'' box in the viewer control panel disables mouse-in-viewer movement of the cross-hairs. In this case, use the slider bars as described below.)

Button 2 (middle/wheel) Click and drag with button 2 to scale the display. Drag down to zoom in, and drag up to zoom out.

Button 3 (right) Clicking and dragging with mouse button 3 translates the display. Use it to slide the display up, down, and side to side. Pressing the shift key and the right mouse button brings up the Renderer Control.

5.2.2 The Mosaic Viewer

The mosaic or ``simple'' viewer can be used to display sequences of slices in the same orientation. It is shown in Figure 5.3, where the functionality different to that of the orthogonal viewer is highlighted.

5.2.3 Colormaps

Figure 5.4: Left: The BioImage Suite Colormap Control. This is accessed using the ``Cmap'' button on the viewers. Right: The Window/Level Colormap.
Image colormap_editor Image session12_1

Colormaps (or lookup tables) are essentially functions that map image intensity to display color. The most common colormap (which is often implicitly used) simply maps the lowest intensity value in the image to black and the highest intensity value to white. For example, in the case of an image with range 0:255, 0 is mapped to black, 255 to white and everything in between to progressively lighter shades of gray. The most common medical image colormap is the so called Level/Window colormap, illustrated in Figure5.4(right). This colormap is defined by the variables, the level $l$ and the window size $w$. The mapping $x\mapsto y$, where $x$ is the input intensity and $y$ the output color (from $black=0$ to $white=1$) is then specified as:

\begin{displaymath} y = \left\{ \begin{array}{ll} 0 & if x \leq l - \frac{w}{2} ... ...{x-(l-\frac{w}{2})}{w} & \mbox{otherwise} \end{array} \right . \end{displaymath}

More complex colormaps can be defined by using the full spectrum of RGBA (Red, Green, Blue, Alpha=Opacity). This allow us to map different values to different colors to highlight certain effects, e.g. functional activations overlaid on anatomical data. Colormaps become a lot more interesting when volume rendering is involved.

BioImage Suite has a colormap editor (Section 5.3) for manipulating the colormap, as five preset maps labeled St, Nr, F1, F2, F4 - the later being directly accessible from the viewer controls. F1, F2 and F4 are overlay maps used for displaying functional overlay activations. St is the standard map where the darkest voxel is mapped to black and the brightest to white. Nr is a normalized colormap, where the window and level are set automatically to map the color spectrum from 1% to 99% of the cumulative histogram. This usually saturates the brightest voxels and results in better contrast in anatomical MRI scans.


5.3 The Colormap Editor

Figure 5.5: The colormap editor.
Image colormap1

The Colormap editor consists of a menu bar that allows the selection of Presets (for fMRI) as well as controlling the maximum number of colors in the colormap, by clicking on 'Levels'. The 'RGBA' button in the menubar allows for specifically editing one of the curves that represent Red, Green, Blue, Alpha (Opacity) and RGB (All three colors at the same time).

In the editor, the points of the curve can be edited with the mouse, which in turn ends up editing the colormap. At a time, only a single curve can be edited. The curve to be edited is picked by using the menu button, as described above, or the right mouse button cycles through all the possible choices of curves that can be edited.

The current curve that is being edited obtains the spherical handles that the user can move around. The other curves are shown in the background for reference.

Based on the changes made to the colormap, a scalar bar gets updated automatically and is shown at the bottom. Figure 5.5 shows a greyscale color bar. More complex color bars are discussed later.

The user is also able to manually specify the minimum and maximum intensity using the slider bars. The colormap gets rescaled accordingly and is reflected in the color bar immediately.

In our colormap editor, we provide a number of preset controls. The default colormap is set to 'Step' which is a greyscale colormap that varies from black to white. Greyscale colormaps are proven to be more accurately perceivable than rainbow colormaps. Rainbow colormaps, though widely used, are considered to lead to misinterpretation of data values in an image [13].

In BioImageSuite, we allow the user to select one of

Figure 5.6: Preset colormaps built into BioimageSuite.
Image colormap_options

Figure 5.6 shows a screenshot of the preset colormaps in BioImageSuite. The drop down menu is invoked by clicking on 'Step' in Figure 5.5.

Figure 5.7: These images show preset colormaps that are built into BioImageSuite. The top image shows the temperature colormap and the bottom image shows the rainbow colormap.
Image temperature


Image rainbow

5.3.1 User-controlled colormaps

The user can define their own colormap as needed. To facilitate interaction with the colormap, we allow the user to modify the colormap using the mouse. At a time only one of curves for Red, Green, Blue, Alpha or RGB can be edited. The curve that is being edited is highlighted by a thicker line and control points in the form of spheres that allow manipulation of the curve. In the user defined colormap shown in Figure 5.8, the red curve is being edited and is therefore shown by a thicker linewidth. The spherical control points for the red curve too can be seen. The other curves can be seen behind it. The left image in Figure 5.8 shows a volume rendering of CT data using the colormap on the right. The bottom image shows another example resulting image of a user-defined colormap that highlights the vessels in a CT scan of a patient.

Figure 5.8: A user defined colormap highlighting the skull in the CT data. At the same time the skin around the skull is shown in red. The bottom image shows a volume rendered image generated by a different user defined colormap. The vessels are clearly highlighted here and can be easily seen.
Image user_colormap


Image screen

The colormap can also be controlled by using the 'Complex Controls' which can be accessed by clicking on 'RGBA' in the menubar and then clicking on 'Complex Controls'. The Complex controls allow the user to fine tune the controls as per the needs. Based on the changes made to the controls using the slider bars, the curves are updated in the main colormap editor. Figure 5.9 shows an example where the red value of the colormap has been modified and the changes can be seen in the images as well as the colormap editor.

Figure 5.9: This image shows a screenshot of the Complex Controls being used to edit the colormap. The changes in the red value made using the slider bar are updated in the color bar as well the curves in the colormap editor. Accordingly, the three images on the left too have been updated.
Image complex_controls

5.4 Coordinates for NeuroImaging

The most popular Neuroimaging coordinate sets are (i) the Talairach coordinates - as defined by the Talairach atlas and (ii) the MNI coordinates as defined on the MNI template. In both cases the origin (0,0,0) is the AC (Anterior Commissure) and the axis are oriented as:

This is also known as RAS (Right, Anterior, Superior) setup. Both of these systems use millimeters as units, so a coordinate of (1,0,0) implies that the point is located 1mm to the right of the AC. For comparison, BioImage Suite internally and the DICOM standard tend to use an LPS coordinate system (i.e. X: Right to Left etc.)

The MNI coordinate system is relatively straightforward to use as there is an actual MRI image of the ``MNI template'' that defines the space. The Talairach system is based on a paper atlas and is harder to map to an actual MRI image. BioImage Suite uses a custom nonlinear mapping [56] to map MNI coordinates to Talairach space.

Figure 5.10: Talairach Coordinate facilities in BioImage Suite.
Image coordinates

5.4.0.0.1 Obtaining Coordinates

Once a brain image is registered to the MNI Template brain, and resliced to have the same voxel dimensions (Axial 1x1x1 mm resolution, 181x217x181) as this, it is trivial to obtain Talairach/MNI coordinates.

First, examine whether the Y-coordinate in the image (i.e. the actual pixel ordering as represented by the Y-Coord in the viewer) is increasing from Anterior to Posterior (BioImage Suite default) or Posterior to Anterior.

Next, press either the ``Tal Rad'' button in the ``coordinate bar'' (see Figure 1) if the y-coordinate increase from anterior to posterior or the ``Tal Neuro'' button otherwise. Pressing either of these buttons for the first time may result in a slight delay (5-10 seconds) as the lookup table from MNI Template image coordinates to Talairach space is loaded.

Now, simply navigate with the left mouse button in the viewer. The coordinates in the black label box, displayed in red, inside the ``coordinate bar'' are the Talairach coordinates under the mouse. (There are four numbers in the text box: the first three are the coordinates, the fourth number is the image intensity at this point).

If the internal nonlinear map is used then the Talairach coordinates are printed in green with the prefix C_AP or C_PA (depending on whether is the brain y-axis is anterior-to-posterior - Rad, or posterior-to-anterior - Neuro). The box below this (with the prefix MNI) shows the MNI Coordinates. See Figure 5.10.

Note: BioImage Suite can not actually tell whether an image is in MNI space or not. However, if it has the right dimensions, it assumes that it is in MNI space and that the user ``knows what s/he is doing''.

5.5 Atlas Tools

5.5.1 Yale Broadmann Areas Atlas Tool

Figure 5.11: The Yale Broadmann Areas Atlas Tool
Image yale_atlas

BioImage Suite provides a recently generated atlas of Broadmann areas defined on the MNI T1 template (the ``Colin27'' brain) at 1mm resolution [56]. To use the Yale Atlas tool:

  1. Load an image into the viewer that is in MNI space (either 1mm, or 2mm resolution is fine).
  2. Select the ``Yale Broadmann Areas Atlas Tool'' from the Atlas Tools Menu.
  3. Load the atlas files using the Load Atlas Files button.
  4. Confirm that the image is an MNI space by clicking the Tal RAD button.
  5. You can now browse the image with your viewer, and read out your location in the brain and other atlas information from the Atlas Viewer's Identify tab - see Figure 5.12.

Figure 5.11 shows a screenshot of the Yale Atlas tool that shows the cross hairs identifying a 3D location in space. Based on the Yale Broadmann Areas Atlas, a region is identified on the right as shown in this case to be the ``PrimSensory'' which is the ``Primary Sensory Area'' of the brain. The 3D location of the point are shown for reference. The atlas file's location is also shown below for reference.

In User Preferences, the ``YaleAtlasAutoInitialize'' can be enabled /disabled to automatically initialize the Yale Atlas tool, see Section 3.4 for more details about the Preferences Editor.

5.5.2 WFU Atlas Tool

Figure 5.12: The WFU Pick::Atlas Tool.
Image atlas04

BioImage Suite can also interface to the WFU Pick Atlas [61] (which derives from the Talairach Daemon work [57]) to perform atlas lookups for specific brain locations. Note that these labels are at best approximate, but can be useful nonetheless. To use the WFU Pick atlas tool, you will need to first install the WFU pick atlas somewhere on your disk - see instructions below. To use the atlas do:

  1. Load an image into the viewer that is in MNI space (either 1mm, or 2mm resolution is fine).
  2. Select the WFU pick tool from the Atlas Tools Menu.
  3. Load the atlas files using the Load Atlas Files button.
  4. Confirm that the image is an MNI space by clicking the Tal RAD button.
  5. You can now browse the image with your viewer, and read out your location in the brain and other atlas information from the Atlas Viewer's Identify tab - see Figure 5.12.

In User Preferences, the ``WFUAtlasAutoInitialize'' can be enabled /disabled to automatically initialize the WFU Atlas tool, see Section 3.4 for more details about the Preferences Editor.

See Section A.2 for instructions as to how to obtain and install the WFU Pick Atlas.

next up previous contents
Next: 6. Advanced Image Visualization Up: 1 A. Overview Previous: 4. Application Structure   Contents