The following steps are required to install the Linux VM, and optionally link with CSPM.
Get LinuxVM and copy to fast drive
The LinuxVM is a folder (~400GB) file created by Paul. Copy this to a local drive. Ideally use an SSD drive, or alternatively an SSD USB 3.0 external drive (500GB works as of 2015-11-23).
Configure VM settings
Install VMWare Player
VMware Workstation Player is the free software than runs the virtual machine (VM). You don't need the paid VMware Workstation software to run LinuxVM. You will need to enter an email address the first time you run the newly-installed software.
Configure memory, processors
Open VMware Player, select "Open a virtual machine," and select the file in LinuxVM. After a few seconds (up to 30 if it's on a hard drive), you will see settings. Go to "Edit virtual machine settings". Set the memory to be something less than your physical computer's memory. For example, if your computer has 32GB of RAM, set the memory to 20-25GB.
Set the processors to the maximum available on your computer (up to 16).
Choose and set a "LinuxShare" folder
Select a folder swapping between Windows and Linux; this should have a lot of space (at least 1TB, preferably more). Most of what is stored here can be re-calculated, so the backup is not as critical as for raw study data.
Upder the Options tab, select shared folders, and select the "LinuxShare". Choose Properties to set the path to a suitable location; you can choose any path, such as Q:\OddPathName. Whatever the path, the LinuxVM will always see it as "LinuxShare".
Start LinuxVM
"Play" the LinuxVM (VMware uses "play" to mean turn on). The first time you run it, you'll get a message about ownership; click "I copied it". Once it has booted, you will have a screen with a user "LinuxVM"; click on that. The password is "data".
Configure FSL and FreeSurfer subject folders
LinuxVM has set up FSL and FreeSurfer to look for subject folders "subjects4FSL" and "subjects4freesurfer" in LinuxShare, so create those.
From within Linux, open a file browser (1), and go to LinuxShare (2). Copy all the subfolders from the Desktop folder "subjects for FreeSurfer (must be in SUBJECTS_DIR)" to "subjects4freesurfer". (FreeSurfer expects these files to be in the subjects folder, similar to the way SPM needs MNI templates).
You can now use FreeSurfer and FSL in this LinuxVM.
Set up network connection between CSPM and LinuxVM
This step is to set up connections between CSPM and FSL & FreeSurfer, so CSPM can run commands automatically. The steps involve giving LinuxVM a network IP address, telling CSPM what that address is and logon details, and setting up the software for trusted communication.
Install PuTTy
Google "putty download" and select and run the installer. This link may work.)
