The following steps are required to install the Linux VM, and optionally link with CSPM.
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Get LinuxVM and copy to fast drive
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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 Linux VMWorkstation 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".
If get "VT..." error
You may get a message followed by an error screen like this:
In this case, you need to restart the computer and enter the BIOS on reboot. Usually this is the "F2" key (you might see a message like "F2 to enter setup"). In setup, look for something to do with virtualization (or "VT") and turn it on. There might be a couple of VT settings. Save and restart, and LinuxVM should turn on without error.
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.)
Identify VM network
Open CSPM, go to Options, Local settings. Click on the Linux subnet button; this will suggest an IP address. The logon details should be username "user", password "data", host "localhost", and IP as above.
Define an IP address
IP Address in Linux
Define the address within Linux; right-click over the network icon in the top-right, and "Edit connections".
Select "Wired connection 1, click Edit.
Got to IPv4 settings, and chance the third numbers in the address and gateway. Click Apply. Enter the root password ("data") and click "Authenticate".
IP address on network
"Run As Administrator" the "Virtual Network Editor"; get from Paul if you don't have it. (To run as administrator, right-click over the application file and select "Run as administrator".)
Select "VNet1"; at the bottom, deselect DHCP option, then save.
You can test the connection by clicking "Ping" in CSPM. It may take a few seconds for the IP address to register.
Note: it can take a few minutes for these changes to register. If things do not work right away, it may be simplest to shutdown the VM and restart the computer. Remember to restart LinuxVM before testing the connection.
Initialize trusted connection with Windows
Click "1st time..." and go to the MATLAB command window, and enter "y"; you can then quit.
Test CSPM connection
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Now in CSPM click "Send Test Command".