1.5. Prep for Bootcamp

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 Linux:

       1. versions 15.10 and earlier, or

       2. versions 16.04 through 17.10

     • for other Linux:

       1. Fedora

       2. RedHat/CentOS

     • for Mac OS X:

       1. old-school instructions, or

       2. App-ified version

     • for Windows 10:

       1. the modern “Fall Creators Update” version, or

       2. older (and now out of date) “Creators Update” version

     • for other 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.afni.binaries -d
       

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

2. Boot up.

   The AFNI Bootcamp involves hands-on learning with processing and looking at data. The packages installed here include the data, handouts and useful “cheat sheets” of commands. The full download size is several GB, and you should leave at least 10 GB free on your computer after downloading+unpacking the data, to be able to run various examples.

   1. Copy+paste (to download+upack Bootcamp data to your home directory):

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

      
      

   2. Copy+paste (to download+upack data for investigating QC in FMRI):

      cd
      curl -O https://afni.nimh.nih.gov/pub/dist/edu/data/boot_qc/bootcamp_qc_sub_rest_A.tgz
      curl -O https://afni.nimh.nih.gov/pub/dist/edu/data/boot_qc/bootcamp_qc_sub_rest_B.tgz
      curl -O https://afni.nimh.nih.gov/pub/dist/edu/data/boot_qc/bootcamp_qc_sub_task_A.tgz
      tar -xf bootcamp_qc_sub_task_A.tgz
      tar -xf bootcamp_qc_sub_rest_A.tgz
      tar -xf bootcamp_qc_sub_rest_B.tgz
      

   3. If no errors occur in the above, and your afni_system_check.py says things are OK, you can delete/remove the tarred/zipped package, using:

      cd
      rm CD.tgz
      rm bootcamp_qc_sub_task_A.tgz
      rm bootcamp_qc_sub_rest_A.tgz
      rm bootcamp_qc_sub_rest_B.tgz
      

      If you are confident in the downloads+unpacking, you can also deleted the CD/ directory in the present location.

      
      
   4. !Pro tip!: Bring a computer mouse to use at the Bootcamp. It is muuuuch easier to follow the demos that way.

      
      

   5. Read+practice the handy Unix documentation/tutorial. This will give you a quick lesson/refresher on using basic Linux shell commands (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. Open a new terminal, and then copy+paste:

      afni_system_check.py -check_all
      

   2. Read the “Please Fix” section at the end. If there are no suggestions, then rejoice! Otherwise, try the suggestion(s) there.

      
      

   3. Open up the AFNI and SUMA GUIs, juuuust to make sure all is well:

      afni
      suma
      

   Report any crashes or problems!

   If stuck, then …

   • try searching online with the error message, and/or ask on the Message Board

   • send the system check to an AFNI guru for advice—copy+paste:

     afni_system_check.py -check_all > out.ASC.txt
     

     ... and email the file “out.ASC.txt”.