Download Mac version, Windows version, and Linux version (.zip format, 1.7GB).
The LONI Pipeline Neuroimaging Virtual Environment (PNVE), is a self-contained virtual machine that can be executed on a common laptop or desktop, enabling the Pipeline to run virtually anywhere. Neophytes to the Pipeline can have their own private server running in minutes, software engineers and workflow designers can use the PNVE as a sandbox, and those without access to grid computing facilities can now take full advantage of the Pipeline processing environment.
PNVE version 1.0 is based is based on current Ubuntu, VMWare Player/Workstation/Fusion, and VirtualBox software technologies and ships with all major neuroimaging tools we are licensed to redistribute.
Requirements
- A CPU capable of 64-bit emulation (any Intel chip with VT-x or EPT technologies; or any AMD chip with AMD-V or RVI technologies–this feature may need to be enabled in BIOS, as system manufactures may choose to disable this feature by default).
- 1024MB of RAM or higher
- VMWare Fusion 3.x or VMWare Player 2.5.x
Installation
- Download VMWare Fusion for Mac.
- Download VMWare Player for Windows and Linux:
- Download the correct image for your host OS: for Mac, and for Windows or Linux.
- Unarchive to the directory of your choice, and:
. on a Mac, double click the extracted “PNVE-sparse-public-v1.0-rc1″ to invoke the VM.
. on Windows or Linux, double click the extracted PNVE-sparse-public-v1.0-rc1.vmx to invoke the VM.
- If asked if you moved or copied the VM, reply that you copied it.
Running
- To invoke Pipeline, simply double click the launcher on the desktop once boot-up has completed.
- Using the Library browser on the left, double click one of the localhost->Workflows->Training workflows to open. Typically you’ll need to provide your own data, but for the purposes of these workflows, the appropriate inputs have been provided for you, so simply press the Play button and the workflow will begin local execution.
- If the execution seems sluggish or too serialized, go to Preferences (command + comma keys on a Mac; or Edit->Preferences on Windows or Linux) and select the local execution tab. Set “Maximum Simultaneous Jobs” to the number of CPUs in your machine, and close the Preferences dialogue. Proceed to shutdown the VM using the icon in the upper-right hand corner, then adjust the VM image’s settings to use the same number of core, (and a higher amount of RAM if you have it to spare). Start the VM again, run the same workflow, and note the difference in execution time/parallelism.
- To share files between the virtual environment and your native operating system, you need to make the directories where the files reside shared. This is accomplished by opening VMWare and going to Settings -> Options -> Shared Folders, where you can drag and drop folders in your native OS shared in the virtual environment. After this is done, these folders will be accessible on your VM environment.
Installing Additional Tools
- Due to sizing constraints, certain tools are not shipped with the image to avoid unnecessary bloat. These tools, however, have been precompiled for your machine, and can be installed with little effort, provided that you have an internet connection. Open the Terminal application (Applications -> Accessories -> Terminal) and
* To install FSL, type (or copy and paste) “/opt/pnve/bin/installFSL” and hit enter. (If you receive an error at this stage, run “sudo apt-get -y –force-yes install fsl fsl-doc fslview fslview-doc” and then rerun the “/opt/pnve/bin/installFSL” command.) To add the FSL modules to your client, right click the Library and “Update library,” or simply relaunch Pipeline.
* To install the Insight Toolkit, type (or copy and paste) “/opt/pnve/bin/installInsightToolkit” and hit enter.
* Certain tools do not allow us to redistribute precompiled binaries. Please reference the “*.txt” files in the “Installers” folder on your desktop for instructions on how to proceed.
Questions and Help
For general help with the Pipeline client, double-click the “Pipeline Handbook” on the desktop, and you’ll be guided to the Pipeline website. If you experience any issues or bugs, please contact the Pipeline team, or post it on our forum. All issues will be resolved in a prompt manner. For updates on the Virtual Image and the expanded handbook, please check this page.
