This page describes setting up a local connection to an already-created Linux VM.

A virtual machine ("VM") is software that runs an operating system within a computer. For MRI analyses, we run Linux software on a windows computer. We install the virtual machine software (VMware), and that software runs Linux. The shorthand is "LinuxVM."

These pages are principally designed for the system administrator who will be creating the LinuxVM. If you are a user, you would typically start off with a large set of files that compose the LinuxVM.

Technical Note: For text files to be used in Linux, open as "t" to avoid the DOS double-charater CR+LF at the end of each line (CR = carriage return /r, LF = line feed /n). (http://www.mathworks.com/support/solutions/en/data/1-15HVX/index.html?product=SL&solution=1-15HVX link]
e.g., id = fopen(newfile.bat,'wt+');
The Linux command dos2unix will remove CR characters.

See bottom of page for updating.

Setting up Windows with LinuxVM

VMware

#Get and install "VMware Player" (free)#Enable "Virtualization Technology"#In the BIOS, you must make sure the option to run "Intel Vistualization Technology" (or similar in AMD) is enabled; here are some instructions:www.microsoft.com/windows/virtual-pc/support/configure-bios.aspx Microsoft Virtual PC pageYou will also need a 64-bit machine running 64-bit Windows.

Virtual Machine

Get the copy of the virtual machine (VM) you will use (or create your own using "VMware Workstation"). You will need the MRI software (FSL and FreeSurfer), the account name and password, and sshd service. There is a copy ("clone") on the Share drive:
LinuxCloneVM

Copy this to a local folder; I suggest C:\LinuxVM. You will need ~300GB.

Download and install VMware Player (free).

Open VMware Player, and open the saved VM; select the copy option.

To test:
Start ("Play") the virtual machine
In the Centos 6+ version (since October 2013), the password is "data" (there is only one user, which you click).

Note: since the machine is host-only, having the password visible does not matter since the machine cannot "see" or be seen by the internet.

You'll usually need to start a terminal (see black rectangle icon on top toolbar).
Type fsl to get FSL (Linux is case sensitive, unlike Windows)

Shared folder

Choose a shared folder; I use one on the network, but something simple is good (e.g., "V:\LinuxShare\"). Avoid spaces in any Linux path.

Edit the VM settings, choose the Options tab, Shared Folders
Always enabled
"Add..." the folder

This will now show up in Linux (at least in CentOS) under /mnt/hgfs.

In Windows, change the folder permissions so that all users can modify, read and write.

Troubleshooting high disk usage

In 2015, the LinuxVM's started going crazy accessing the disk constantly, and killing the whole system. Here are some changes suggested:

Open the .vmx (configuration) file for the affected virtual machine while it is powered off. Add the following lines to the file using a text editor. For more information, see Editing the .vmx file of a VMware Workstation and VMware Player virtual machine (2057902)

MemTrimRate = "0"
mainMem.useNamedFile = "FALSE"
sched.mem.pshare.enable = "FALSE"
prefvmx.useRecommendedLockedMemSize = "TRUE"

These pages describe how to create a new Linux VM.
Creating a new Centos 6 VM
FreeSurfer Installation in VM
Creating a new Centos 7 VM
FSL Installation in VM
Increasing space
Network connections
Obsolete - Linux VM with Centos 5 (for freesurfer, FSL)
Obsolete - Network connections (Centos 5)
Creating a new Ubuntu 20 VM
fmriprep installation on Ubuntu (VM)
The key steps are:
Initiate instance in VMware Workstation
Install OS
Install FSL and FreeSurfer
Change shell to tsch
Create tsch profile that sets FSL and FreeSurfer environment variables
The VM parameters are:
Set shared folder
Memory to max
Network connection to host-only (for local installations)
After an instance is placed on a local computer or network:
Set the network IP and other entries (be careful with DNS if host-only)
Other tidying can be to install MRIcron, and remove programs or services that are unused. For example, updates will not work for host-only.