CNL VirtualBox Setup

by Kyle on June 20, 2013

Ok so I have no, with Antoine’s excellent help, setup the virtual linux machine on Arch4.

Once you are setup, a shared folder will exist between /bi-cnl-arch4/data/freesurfer and /home/cnl/freesurfer

This is the freesurfer director in ubuntu, DONT CLUTTER IT UP WITH OTHER STUFF!!!!!

You should be able to log into Arch4 remotely or in person on your account.

At this time you should see an icon on the desktop

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This will pop up: You need to find and load the disk image that we all share by following these instructions:

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Click New: image

Now fill in the name for this disk, Ubuntu64_[your username], the rest should fill in automatically, press next

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Change the RAM amount to 2048 and press next

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Use an existing virtual hard drive file, click the folder, and go to Ubuntu64.vdi

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Now click settings, image

Shared Folders, Add new icon image

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Select the freesurfer C:/data/freesurfer folder and select automount, then press Ok> OK

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Now press start, it will open the virtual linux OS

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Login as CNL, no password

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Maximize the window to make it full screen if you like

***BEFORE YOU DO ANYTHING ELSE, setup the environment by running the terminal:

On the left side, open a terminal

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Type the CNL password XXXXXXXXX:

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Now you are ready to go..

type tksurfer 1501 lh inflated for example to see the inflated brain of subject 1501

You can also use AFNI from this terminal,

just type

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All of the AFNI, FSL, and freesurfer commands should work from the command line

You can use the FSL viewer here to see any of your .nii files

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