1.5. Prep for Bootcamp

  1. Get the most uptodate AFNI on your computer.


    • IF you do not have AFNI installed on your computer system, then please see the step-by-step instructions (which optionally include installing the Bootcamp data, so then you will be all set) here for operating systems like macOS, Windows (via WSL) and a myriad of Linux flavors like Ubuntu, Fedora, Red Hat, CentOS and Rocky: Operating system selection page.

      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.


    • IF you already have AFNI installed on your computer, but you are not certain that it is the most up-to-date version, please do the following:

      1. Check your AFNI version number:

        afni -ver

        The major number is the year, and you can also compare this with the current release version that sits in the upper-left corner of this HTML documentation.


      2. In most cases, you can run the following command to update your local AFNI version:

        @update.afni.binaries -d

      3. If that doesn’t work, you might need to use build_afni.py to compile locally on your computer. Please see the Installation instructions for your OS.


  2. Boot up.

    Each page of installation page for AFNI includes instructions on downloading+unpacking the AFNI Bootcamp data. In case you did not follow those there, then we repeat them here.

    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!

    Each page of installation page for AFNI includes instructions on running a script to evaluate the setup and comment on any necessary fixes. In case you did not follow those there, then we repeat them here.

    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”.