Introduction

Version 6 of Plaque Simulator (PS6) is designed for recent (2009 models or later) Apple Macintosh computers with Intel Xeon, Core i5, i7 or i9 multicore processors that can install OSX version 10.11 or greater. As of August 2018, Eye Physics recommends running PS6 on the fastest computer you can afford (e.g. ≥3.46 GHz) with at least 4 processor cores, at least 16 GB of RAM and OSX 10.13.6 (Sierra). Support for MacOS 10.13 (High Sierra) requires PS6 version 6.6.1 or later.

Intel Xeon and Core i7 processors are hyper-threaded which means that for each processor core that is physically present, the operating system addresses two virtual or logical cores, and shares the workload between them when possible. The Intel Core i5 processor found in many off-the-shelf iMacs and Mac laptops has less cache and the 4 core variant is not hyper-threaded. These computers may, however, be ordered with an upgrade to the Core i7 or i9 processor at the time of purchase at a slightly higher price. PS6 will run on the Core i5 processor but dosimetry performance will be slower than on an i7 or i9 6 core processor.

Plaque Simulator version 6.2 and later leverages multicore processors when performing all 2D, 3D and histogram dosimetry calculations. For instance, when running on the hyper-threaded 4 core Xeon processor, PS6 distributes its dosimetry calculations uniformly and concurrently amongst 8 logical cores, resulting in a 5X acceleration compared to running on a single logical core. The acceleration factor is about 7X on a 6 core processor and at ≥12X on a 12 core processor.

Eye Physics recommends running PS6 on the fastest hyper-threaded multicore processor (e.g. 12 core Xeon, 4 or 6 Core i7, or 6 core i9) that your institution can afford in order to achieve the best overall user experience possible. For any given processor speed, increasing the number of cores will proportionally increase the speed of multidimensional dosimetry calculations, resulting in more rapid isodose line, isodose surface and dose histogram comparisons of alternative plan options. OSX leverages the GPUs on the video card to accelerate some graphics and many features of the operating system, so choosing the most powerful video capability offered at the time of purchase (or as an after-market upgrade for 2009-2012 Mac Pros) is also desireable.

The software development system as of February 2018 is a 2009 Mac Pro desktop (aluminum tower case) which has been upgraded from its stock configuration to firmware MacPro5,1 and a pair of 3.46 GHz 6-Core Intel Xeon processors (total 12 physical cores, 24 logical cores), an 802.11ac+Bluetooth_4 mini PCIe card, an AMD Radeon R9 280X 3072 MB graphics card reflashed for OSX (Note: if you are runing MacOS 10.13.6 (High Sierra) the Sapphire Radeon Nitro+ RX 580 8GB GDDR5 Dual HDMI / DVI-D / Dual DP w/ Backplate Special Edition (UEFI) PCI-E Graphic Card 11265-21-20G works nicely except you wont see the initial MacOS boot screen and you will need an inexpensive dual 6-pin to single 8-pin power adapter), a 4 port USB3 PCI card, a 2TB Samsung SSD boot drive mounted on a PCI SATA3 adapter card and 4 WD Black series 6TB hard disks, a DVD-RW optical drive, and 64 GB RAM running under MacOSX 10.13.6 (High Sierra). Peripherals include a pair of Dell 24" ultrasharp display monitors, Epson 4870 and 4990 Photo flatbed scanners with VueScan software and either an HP Color LaserJet Pro M254dw or a Dell C1760nw LED printer. All of the 2009 Mac Pro upgrade components are available on ebay and/or from various other internet vendors.


Hardware recommendations, in order of preference:
  • Computer:
    • Desktop: Current generation 27 inch iMacs or iMac Pros with 4, 6, 8 or more core i7 or Xeon W processors running at least 3 GHz are recommended for their power and cost effectiveness. All Mac Pro towers manufactured from 2009-2012 will work after upgraded cpus and video cards are installed. For example, a 2009-2012 Mac Pro (aluminum tower case) running OSX 10.13.6 (High Sierra) should be upgraded with a MacOS compatible Radeon 7950 class (or better) video card to leverage the GPUs and possibly an 802.11ac+Bluetooth 4 mini PCIe card in order to work with the new force-touch magic trackpads. 2013 and later Mac Pros (black cylinder cases) are fine in all stock configurations. iMacs with quad-core i5 processors are also acceptable.
    • Laptop: MacBook Pros with 4 and 6 core i7 or i9 processors are acceptable. PS6 has been tested on several 15" MacBook Pro laptops. All are equipped with 500 GB or 1 TB SSD drives. The first was manufactured in 2010 and has a 2.66 GHz dual-core i7 processor, 8 GB RAM and an HD display. The second is a mid 2015 model with a 2.8 GHz quad-core i7 processor (up to 4 GHz turbo boost speed), 16 GB RAM and Retina display. The 3rd is a 2018 model with touch bar keyboard, a 2.9 GHz hex-core i9 processor (up to 4.8 GHz turbo boost speed), 32 GB RAM and Retina display. Performance is adequate on the 2010 and mid 2015 laptops but is notably slower compared to my 6 and 12-core 2009 era Mac Pro desktops equipped with 3.46 GHz Xeon processors. The 2018 MacbookPro with 2.9 GHz 6-core i9 processor and 32 GB RAM matches the performance of my 2009 12-core desktop.
    • Other models: Avoid models with processors slower than 2 GHz and dual-core processors such as the Mac mini, MacBook, MacBook Air and any others that are only available with dual-core processors and of course avoid all older models that can't run OSX 10.11 or later.
  • Intel CPU:
    • Xeon: Single and multiple processor configurations with 4 or more cores per processor are recommended.
    • Core i9: Hex (or more) core versions of the i9 cpu are recommended.
    • Core i7: Quad (or more) core versions of the i7 cpu are recommended.
    • Core i5: The i5 processor has less on-board cache than the i7 and its 4-core version is not hyper-threaded, but it is adequate.
    • Other models: Dual-core processor variants work but are not recommended.
  • Speed: Fastest affordable (e.g. ≥3.46 GHz), 2.6 GHz minimum.
  • Cores: Six or more processor cores are recommended, 4 cores minimum.
  • RAM: ≥32 GB is recommended, 16 GB minimum.
  • OS: MacOSX 10.13.6 (High Sierra) is recommended and is what Eye Physics uses for routine treatment planning. MacOS 10.13 (High Sierra) is supported by PS6 versions >= 6.6.1. MacOSX 10.8 is the absolute minimum supported OS version.
  • Graphics: Any Apple supplied standard or upgraded graphics configuration that is compatible with your computer and OSX version is fine. Only the pre-2013 Mac Pro desktop computers accept graphics card upgrades. Several 3rd party flashed graphics card upgrades are available for the 2009-2012 Mac Pros running MacOS 10.11 or later. The best are the AMD Radeon R9 280X 3072 MB graphics card reflashed for OSX, and if you are runing MacOS 10.13.6 (High Sierra) the Sapphire Radeon Nitro+ RX 580 8GB GDDR5 Dual HDMI / DVI-D / Dual DP w/ Backplate Special Edition (UEFI) PCI-E Graphic Card 11265-21-20G works nicely except you wont see the initial MacOS boot screen and you will need an inexpensive dual 6-pin to single 8-pin power adapter.
  • Displays: Display monitors in the 24" and larger class greatly enhance the user experience when preparing CT and MRI multiplanar reconstructions with OsiriX, fundus photo collages and fusions using Photoshop, and for treatment planning in general. iMacs and laptops with Retina displays are fine.
    • Mac Pro: One or more 27" or 24" monitors strongly recommended.
    • iMac: Models with 27" screens, with or without Retina display panels, are highly recommended, smaller screen versions are okay but not recommended.
    • MacBook Pro: 15" or larger screen recommended, 13" screen is okay, an external 24" display monitor is recommended for use with all laptops.
    • Retina display: Plaque Simulator has been tested with the ultra high resolution retina display. It works best when the display resolution preference is set to "default". Image quality and performance degrade ever so slightly if any of the other scaled resolutions are selected in order to display more (or fewer) logical pixels. Retina display iMacs and laptops are highly recommended.
  • Flatbed Digitizer: A "high-quality" flatbed scanner with 8x10 inch transparency option and USB or firewire connection (e.g. Epson Perfection V700 Photo). Only the most recent Apple hardware supports USB3, and recent models no longer include firewire ports, so verify in advance that your computer is compatible with whichever scanner you select. These scanners usually cost less than $700.
  • Input devices: PS6 is designed to work best with a wired USB multi-button mouse with a scroll-ball such as Apple's "mighty" mouse. Apple's wireless bluetooth "magic" mouse and/or trackpad (version 2) with forceTouch are also higly recommended add-ons. These "magic" devices enable PS6 to respond to modern finger gestures such as pinches, swipes, and rotation gestures when running OSX 10.11 (El Capitan). Current Apple laptops come equipped with forceTouch trackpads.
  • Printer: Eye Physics uses an HP Color LaserJet Pro M254dw printer and a Dell model C1760nw LED printer (the Dell is now discontinued), but any MacOSX compatible printer, either networked or directly connected, will work. Dell released an updated 1760 series driver for OSX 10.11 (El Capitan) compatability in October 2015. MacOS 10.13 (High Sierra) compatible drivers for the HP M254dw are available online from HP.
  • Example: As of February 2018 this is one of the more powerful and cost effective hardware configurations.

    Hardware841x973

Additional software recommendations

To get the most from Plaque Simulator you will want to do image based planning. Eye Physics uses the following well known 3rd party software solutions to prepare CT, MR, ultrasound and fundus images for export to Plaque Simulator.

  • OsiriX: Please download the latest version of OsiriX that is compatible with your OSX version. OsiriX, a well established open source DICOM viwer and listener, is used by Eye Physics to create and export to Plaque Simulator several multiplanar reconstructions (MPR) of the eye from 3D CT and MR sources.
  • Photoshop: Adobe Photoshop for Mac, a component of Adobe Creative Suite for Mac is used by Eye Physics when creating fundus collages and fusions, editing CT, MR and ultrasound images, and cropping and otherwise preparing pictures of plaques and seed carriers for inclusion in plaque model files.
  • Vuescan: from Hamrick Software is a superior application for Windows, Mac OS X, and Linux that replaces the software that came with your flatbed scanner.
  • BBEdit: from Bare Bones Software is a great text file editor that can be used to view and edit the .xml files created by PS6.
  • Excel: Microsoft Excel:Mac, the spreadsheet component of Microsoft Office for Mac was used by Eye Physics to create and edit the tab delimited text physics files used by Plaque Simulator version 5 (PS5). PS6 can open and save PS5 (.iphys) physics files, but prefers the newer xml versions (.iphys6) of these files.