The MPR Window

In PS version 6.8.6 and later you will want to create a folder named DCMTK which contains an HFS AXIAL orbital study series of 16-bit MONOCHROME DICOM files with little endian Transfer Syntax UID (tag 0002,0010 = 1.2.840.10008.1.2) that have been converted to .xml file format. PS is designed to use XML files. XML (Extensible Markup Language) is a modern, cross platform, file format that supports both text and embedded binary data (e.g. using base64 encoding) and hence is used extensively by many operating systems such as MacOS and forms the basis for all PS file operations. XML is a markup language similar to HTML, but without predefined tags. Instead, a user defines their own tags designed specifically for their needs. This is a powerful way to store data in a format that can be stored, searched, and easily shared over networks.

The DICOM toolkit DCMTK is a collection of libraries and applications implementing large parts the DICOM standard. To install DCMTK you must first install a package manager for MacOS such as Homebrew. Follow the instructions on the Homebrew web site. Once you have installed Homebrew, you can then install DCMTK from a MacOS terminal window using the command brew install dcmtk.

Be sure to make note of the Unix file path at which DCMTK was installed, it may differ slightly depending upon your version of Homebrew and MacOS. To determine where Homebrew installed the dcmtk package on your computer, in the Terminal application enter the command brew info dcmtk.
brewinfodcmtk

In my case, Homebrew installed the package at /usr/local/Cellar/dcmtk/3.6.6
dcmtcklocation
Add /bin to that path and enter the rsult in PS Folders Preferences as:
prefsdcmtkpath
The file path is typically some variant of usr/local/bin.

If you have successfully installed DCMTK and PS can find it, the DCMTK indicator on the right of the MPR window toolbar will be green. If the indicator is red you will need to customize the file path to DCMTK in PS Folders Preferences. Click the indicator to take you to the folder preferences window.

With the DCMTK toolkit installed and located:

  1. Create a folder named DICOM (note: additional special folders named CT, MRI, DJPEG and DRLE are also allowed) somewhere other than in your patient folder's first hierarchical level and place within it your HFS AXIAL series of DICOM files (e.g. xxx.dcm). These .dcm files should use little endian DICOM Transfer Syntax UID (the default is tag 0002,0010 = 1.2.840.10008.1.2). Ideally, this folder should contain only the images that comprise a single imaging series. The MacOS Finder provides thumbnails of .dcm files which may help to quickly eliminate unnecessary files.
  2. Note: PS does NOT support pixel data that uses a compressed DICOM Transfer Syntax UID, but does provide a method to convert JPEG and RLE compressed pixel data to the expected default Transfer Syntax UID. If the pixel data in the DICOM files is JPEG compressed, launch PS and drag the DICOM folder onto the MPR window while holding down the option key. If the pixel data is RLE compressed, follow the same procedure except press the command key. PS will create a new folder in the same location as the original folder named DJPEG or DRLE that contains uncompressed versions of all the DICOM files that were found in the DICOM folder. This conversion is performed by the dcmdjpeg and dcmdrle functions that are part of the DCMTK toolkit.
  3. Launch PS and drag the DICOM folder (or intermediate DJPEG or DRLE folder if you created one to deal with compressed pixel data) onto the MPR window of PS6. PS6 will create a new folder (in the same location as the original folder) named DCMTK that contains .xml versions of all the DICOM files that were found in the DICOM (or DJPEG or DRLE) folder. This is done using the dcm2xml function that is part of the DCMTK toolkit.
  4. Drag the resulting DCMTK folder to the first hierarchical level your patient folder along with your other imaging files such as US1, US2, optomap, misc# and so on... If the DCMTK folder is available, there is no longer any need to manually create and export .jpg planar reconstructions such as Axial, Sagittal, Equator, t-Coronal and t-Meridan using OsiriX or Horus.
  5. You can either manually drag a DCMTK folder onto the MPR window to load its images, or if the DCMTK folder is located in the first hierarchical level of the patient folder along with the ophthalmology images you can simply drag the patient folder itself onto the Image window as usually done when intializing a new patient plan.

Alternatively, if you dont want to install DCMTK, you can create a folder named "RAW" into which 16-bit signed image data in .raw file format and a single DICOM meta-data file in .xml format have been exported from OsiriX. PS7 is expected to further streamline the import of most DICOM files but will still require installing the DCMTK toolkit.

The Multi-Planar Reconstruction (MPR) window is used to manage the loading, display, and reconstructions derived from a 3D CT (or MRI) study series. The 3D study series is expected to consist of a head-first, supine (HFS) sequence of thin axial slices covering the orbits and including both eyes plus a few cm superior and inferior to the orbits. It is important that both eyes are included because ocular symmetry will be leveraged to help compensate for head rotations in the scanner. Slice spacing must be consistent and slice thickness as thin as possible (e.g. < 1mm). Image data must be 16-bit monochrome. Image dimensions should be 512x512 pixels.

The status line just below the toolbar provides information about the currently selected layout pane.

In addition to the buttons in this window, other reconstruction parameters and access to DICOM meta-data are adjustable from the MPR menu which is added to the menu bar any time this window is frontmost.

The MPR window defaults to single pane layout mode. In this layout you can load a study series by dragging and dropping a folder of DICOM images that have been converted to .xml file format. The folder must be named DCMTK. In version 6.8.6 a study series may optionally be exported from OsiriX as raw pixel data but this is far more involved than using the DCMTK folder approach. Using OsiriX, export the study series to a folder named RAW which contains all of the pixel data data in .raw file format using OsiriX's Export->Raw... menu. In this RAW folder there must also be a single file containing representative DICOM metadata, exported from OsiriX's Meta-Data window in .xml file format (e.g. PatientName.xml).

MPR window

Planar reconstructions are created by switching to 4 or 6 pane layout using the Layout control in the toolbar.

In 4 pane layout the planar reconstructions are:

  • Upper left pane (Sa): Sagittal reconstruction.
  • Lower left pane (Ax): Axial reconstruction.
  • Upper right pane (Eq): Equator reconstruction.
  • Lower right pane (Ne): Nerve-coronal reconstruction.

QuadLayout

In six pane layout the planar reconstructions are:

  • Upper left pane (Sa): Sagittal reconstruction.
  • Lower left pane (Ax): Axial reconstruction.
  • Upper middle pane (Eq): Equator reconstruction.
  • Lower middle pane (TM): Tumor-meridian reconstruction.
  • Upper right pane (Ne): Nerve-coronal reconstruction.
  • Lower right pane (TC): Tumor-coronal reconstruction.

HexLayout
The meridian angle and coronal planar offsets from the equator automatically track those planes as they are defined and set in the Planar Dosimetry window. The crosshair displayed in the axial, sagittal and equator is used to find the geometric center (as defined by Plaque Simulator) of the eye. Fine tuning of the eye model will be accomplished by capturing these MPR window reconstructions (using the Auto. Capture control) to Plaque Simulator's Image window and proceeding as usual in that window.

The orthogonal MPR crosshairs includes 1 mm tick marks and an optional histogram of the gray levels of the pixels beneath the histogram axes. The outer sclera is designated by a dashed green oval. The surface for oblate-spheroid reconstructions (e.g. the inner surface of the sclera to map the tumor base) is designated by a dashed red oval. The basic dimensions of the eye and spherical reconstruction surface can be adjusted using the control handles found on the crosshair axes. In the example below you can see in the nerve-coronal reconstruction (upper-right pane) that the center of the optic nerve connects to the eye about 1 mm superior to the geometric axial bisecting plane.


Toolbar controls

The toolbar buttons near the top of the window include controls for 8-bit and 16-bit enhancement of reconstruction images, select mouse cursor function, window layout and which eye is being modeled. The screens used with personal computers may be able to display millions of colors, but are limited to only 256 levels of gray because each pixel is represented using a 32-bit format which is composed of an 8-bit value for each color component (red, green, blue) and an 8-bit value for opacity (alpha). To display 16-bit monochome CT (and MRI) data on a screen capable of only 8-bits of monochome brightness, the 16-bit data is initally passed through window level and width functions (WL and WW) which are adjusted using the mouse cursor and/or WL and WW sliders. Once the 8-bit representation of the image is created, the image may be further enhanced in the same manner as found in the Image window. Plaque Simulator supports two methods of 8-bit image tonal adjustment: (1) Brightness & Contrast (BC), and (2) Gamma, which has controls for Bias, Gain and Level. In Gamma mode, slightly decreasing Gain and shifting Level is often very effective for enhancing scleral contrast in a CT image.

MPRToolbar
  • Gamma (vs Brightness & Contrast) - Toggles between the BC and Gamma methods of tonal adjustment.
  • Bias/Brightness - Turn knob CW to increase the Bias or Brightness, CCW to decrease.
  • Gain/Contrast - Turn knob CW to increase the Gain or Contrast, CCW to decrease.
  • Level - Turn knob CW to shift the Gamma Level setting to the right towards white, CCW to shift left towards black.
  • Reset - Resets the image tonal controls to their default settings.
  • Mouse Cursor - Sets the mouse cursor function.
    • Information - In this mode, clicking the mouse button will display a crosshair cursor with information about the crosshair coordinate and the voxel at that coordinate.
    • Drag image - In this mode, click the mouse button to drag the image set with respect to the crosshair.
    • Zoom - Magnify the image. Zoom is automatically synchronized for all panes. The information displayed in a pane varies automatically depending upon the current zoom control magnification. For example, you may need to "zoom-in" to reveal the image histogram.
    • Rotate crosshair - In this mode, position the cursor over a crosshair axis and click the mouse button to drag the crosshair around its center. If you position the cursor over the crosshair center you can click the mouse button to drag the crosshair center on the image plane. When you release the mouse button, the cursor will return to image center and the image set will shift to remain centered on the crosshair.
    • 16-bit window & level - In this mode, click and drag to adjust the window center (WC) and window width (WW) parameters which are used to rescale the raw 16-bit data for display on an 8-bit gray level screen.
  • Previous - displays the previous (lesser z coordinate) slice when in single pane layout.
  • Slider - Slide to display the image series axial slices. In the example above, the image set consists of 196 slices, numbered 0..195. Slice 0 will be the slice with the lowest z coordinate, slice 195 will have the greatest z coordinate.
  • Next - displays the next (greater z coordinate) slice when in single pane layout.
  • Center - Locks the eye center (0,0,0) in the 3D image voxel set. Lock to prevent accidentally translating the image or crosshair center by dragging.
  • Eye - Select left or right eye for treatment and 3D modeling. The eye laterality context will change automatically as you drag the image set or crosshair depending upon the eye center coordinate in the data set assuming the patient was scanned HFS with the head centered in the scanner. To prevent automatic eye laterality, manually select left or right eye and then lock the Eye laterality by clicking the lock at the center of this control.
  • Layout - Switches between single pane (raw image set functions), 4-pane and 6-pane (planar reconstruction functions) modes.
  • Auto. Capture - Click to toggle the state of Image Auto. Capture. Auto. Capture will remain in effect until you toggle the control off by clicking the button again. When Auto. Capture is enabled, PS will continuously capture planar reconstructions to the Image window in response to changes in plaque or eye position. This might tend to make some aspects of the interactive user interface sluggish on older and/or underpowered computer systems. If you experience sluggish behavior, disable Auto. Capture and manually update the Image window only when you think it is necessary. You can customize the appearance of image captures in Images Preferences.
  • Reset rotations - Resets all crosshair rotations to zero.
  • WL slider - Adjust 16-bit window level.
  • WW slider - Adjust 16-bit window width.
  • Magnification slider - Adjust image magnification, range 0.5 to 5.0.
  • DCMTK drop zones - Toggles display of the DICOM toolkit drop zones. These drop zones operate on drag & dropped folders containing DICOM files. The zones provide easy access to dcmtk functions that decompress DICOM files containing compressed (e.g. JPEG) pixel data and/or convert noncompliant DICOM files (e.g. files that may be missing a preamble or group 2 meta header). The drop zones are hidden by default to save screen space because these functions are not usually needed. It is more common for modern DICOM study series to meet the current DICOM file specifications and not employ pixel data compression.
  • DCMTK indicator - Green if dcmtk toolkit functions (e.g. dcm2xml) are available, red if not. If red, follow the installation instructions for Homebrew and DCMTK and check that the PS Folders Preferences file path (e.g. usr/local/bin) to the dcmtk folder is correct.

Meta-data sheet

This modal sheet displays meta-data extracted from DICOM file meta-data tags. If using a series of image files exported from OsiriX in Raw.nnn file format you may need to manually override the 16-bit pixel representation to the Signed setting. PS uses the value stored in the hexadecimal slice thickness tag (0x0018,0x0050) and the decimal filename tag (.nnn) to calculate the z coordinate of Raw.nnn files. For some image series, you might also need to manually set the slice thickness to instead use the value found in the DICOM slice spacing tag in order to create properly scaled 3D reconstructions.

MetaDataSheet

Dosimetry window reconstructions

In the Planar Dosimetry window, set the dosimetry plane to overlay the appropriate image (e.g. T-Mer) as usual. If a tumor-meridan image has been loaded or captured, it will be used. To "live" recalculate the planar reconstruction every time the image window is updated, such as when rotating or translating the dosimetry plane, enable the Use MPR control. Live recalculation of the dosimetry plane reconstruction adds about 3 msec per pane (e.g. when in 2-pane layout mode, both meridian and coronal reconstructions will need to be recalculated) to the window update time.

PlanarReconstructions

Retinal diagram spheroidal reconstruction

In the Retinal Diagram window you may optionally map a reconstruction of the oblate-spheroidal surface to the retinal diagram which is an azimuthal equidistant projection. The reconstructed surface should be slightly inset from the inner scleral surface in order to best visualize the tumor base. Insets in the range 0.5 to 1.5 mm work well. The inset can be adjusted either in the Retinal Diagram window or in the MPR window by dragging the red control handle in one of the orthogonal reconstruction panes. Below is a comparison of spheroidal surface reconstruction (inset = 1 mm) and fundus imaging. The reconstruction is displayed using custom spheroidal pseudo coloring to highlight the tumor base. Spheroidal surface reconstructions can be very useful when portions of the tumor base are located too anterior to photograph using optical technologies such as fundus photography.

SpheroidalReconstruction
SpheroidalReconstructionFundus

Footer controls
Footer

WindowSize
Opens the Window Size Dialog dialog.

ZoomOut
Zoom out
Halves the screen size of an image pixel.

ZoomIn
Zoom in
Doubles the screen size of an image pixel.

Home
Home
Displays the image as 1 screen pixel per image pixel.

Ruler
Ruler crosshair
Enables full time display of the ruler crosshair in single pane layout.

Crosshair
Centering crosshair
Displays crosshair used for centering on the orthogonal reconstructions.

color
Crosshair Histogram
Toggles display of the crosshair histogram of 8-bit monochrome gray levels.

Centering
Centering circles
Toggles display of the crosshair centering circles.

EyeModel
Eye model
Toggles display of the cursor full eye model.

Preferences
Preferences
Opens the Preferences Images window.

AutoFont
Auto (font)
Enables automatic font size.

FontSlider
Font Slider
Manually set font size (when auto is disabled).