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
This will pop up: You need to find and load the disk image that we all share by following these instructions:
Now fill in the name for this disk, Ubuntu64_[your username], the rest should fill in automatically, press next
Change the RAM amount to 2048 and press next
Use an existing virtual hard drive file, click the folder, and go to Ubuntu64.vdi
Select the freesurfer C:/data/freesurfer folder and select automount, then press Ok> OK
Now press start, it will open the virtual linux OS
Login as CNL, no password
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
Type the CNL password XXXXXXXXX:
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,
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