[Neurodebian-users] Problem's Opening AFNI 3dClustSim

[Alex Waite]

Hey Harry,

> I've recently started using Neurodebian and have hit a bit of a brick wall.
> I want to run the Afni subprogram 3dClustSim to do a Monte Carlo Simulation
> but am unable to get it to work. When I've used it previously on a
> non-Neurodebian system all I had to do was type in 3dClustSim along with
> the correct syntax to specify the mask, FWHM etc.  However now if I do this
> I simply get the message that the command is not found. AFNI itself seems
> to work fine, typing in afni leads to the GUI opening without any issues.

3dClustSim is available, but first you need to source the AFNI setup 
script (/etc/afni/afni.sh) to setup the environment.

Assuming you're using bash, simply type the following in your shell 
(including the preceding dot):

. /etc/afni/afni.sh

Then you should be able to run any and all AFNI programs.

Though, for convenience, you'll probably want to add the above command 
to your .bashrc file. (echo '. /etc/afni/afni.sh' >> ~/.bashrc).

So, the fair question is why do we require a setup script? This is 
because AFNI ships with many, many commands, and some of their command 
names conflict with commands in other packages that also exist in 
Debian. Hence why this hoop needs to be jumped through.

---Alex