Basic AFNI Setup

1. Get the most uptodate AFNI on your computer.

   • IF you do not have AFNI set up on your computer system at all, then please see the step-by-step instructions (which optionally include installing the Bootcamp data, so then you will be all set):

     • for Ubuntu
     • for Fedora, Redhat, etc 
     • for Mac OS
     • for Windows users... eek.

     Methods for checking/evaluating each setup are also described on those pages. PLEASE make sure you have verified that all is well with AFNI on your computer.

   • ELSE (you have AFNI set up on your computer, but you are not certain that it is the most up-to-date version), please do the following:

     • if you have installed pre-compiled binaries on your computer (the most common approach):

       @update.binaries.afni -d
       

     • if you compile AFNI from source, then go here and download the latest source.

2. Boot up.

   This step is required if you are about to attend a Bootcamp:

   curl -O https://afni.nimh.nih.gov/pub/dist/edu/data/CD.tgz
   tar xvzf CD.tgz
   cd CD
   tcsh s2.cp.files . ~
   cd ..
   

   In order, these commands: get the tarred+zipped directory that contains the class data (and is hence named “CD”), downloading it to the current location in the terminal; untar/unzip it (=opens it up); go into the newly opened directory; execute a script to copy the files to $HOME/CD/; and finally exit the directory.

   At this point, if there have been no errors, you can delete/remove the tarred/zipped package, using “rm CD.tgz”. If you are really confident, you can also deleted the CD tree in the present location (but leaving it in $HOME/CD/).

   Also don’t forget to give a quick glance at the handy Unix documentation/tutorial. And why not practice a few of the basic commands on your own system (e.g., ls, cd, less, etc.)? It will greatly enhance your bootcamp experience– we promise!

3. EVALUATE THE SETUP: an important and useful step in this process!

   1. There is a very useful script to check on your installed AFNI and lots of its dependencies, such as looking for the installed R libraries, profiles, Python stuff, etc. You can run it

      • outputting to the screen:

        afni_system_check.py -check_all
        

      • outputting to a text file:

        afni_system_check.py -check_all > out.afni_system_check.txt
        

      which might be useful to email to your local AFNI Guru if there are any problems.

   2. So, at this point, if your “system check” doesn’t really give any errors, you’re all set to go. If it did give some errors, please:

      • check the list of known setup issues;
      • search on the Message Board, and/or put the error into google;
      • post a question on the aforementioned Message Board.