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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."

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.

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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 (as of October 2013), the password is "data" (there is only one user, which you click). In the old Centos 5 version, the usual username/password is Paul/kokako  
You'll usually need to start a terminal (see black rectangle icon on top toolbar).
Type FSL fsl to get FSL (Linux is case sensitive, unlike Windows)

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sharedfolder sharedfolder

Shared folder

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

Updating

To update:

1. Change the VM's network settings to bridged
2. Start/restart the VM
3. Under System, Administration, Network, "Edit" the eth0 device and set to DHCP instead of static address
4. Under System, Administration, Server Settings, Services, go to Network and restart
5. To Add or Remove, go to Applications, Add/Remove Software
6. To Update, go to Applications, System Tools, Software Updater
7. Change back to static IP (System, Administration, Network, "Edit" the eth0 device)
8. Change the VM settings back to Host-Only, restart