1.1.2. Linux, Ubuntu 26.04

These setup instructions are for Ubuntu Linux version 26.04 (Resolute Raccoon).

Things to note before starting

  1. Each step involves either copy+pasting a command, or clicking on a download link.

  2. Admin privileges are needed for some steps: check if you can run sudo ls, entering the correct password. If you can’t, perhaps ask an administrator to do that step, and you can do the others that don’t require it.

  3. Note your terminal shell type (bash, zsh, tcsh, csh, etc.), by copy+pasting:

    echo $0

  4. Do the system check in the “Evaluate” stage. Try any recommendations in its “Please Fix” section.

  5. If you run into any problems, please just ask a clear question on the AFNI Message Board.

  1. To copy and paste in a Linux terminal, one can use Ctrl+Shift+c and Ctrl+Shift+v, respectively. (In WSL terminals, one might first enable this functionality: rightclick on the panel’s taskbar, select “Properties” and put a checkmark by this option.)

  2. To open a text file, use any text editor you like, and/or you can type gedit FILENAME, such as either:

    gedit ~/.bashrc

gedit ~/.bashrc &

Quick setup

This is the quick form of AFNI setup for Ubuntu 26.04. It includes downloading the Bootcamp data and running the system check (don’t forget to do that!).

  1. Download the command scripts.

    Copy+paste:

    cd
curl -O https://raw.githubusercontent.com/afni/afni/master/src/other_builds/OS_notes.linux_ubuntu_26_64_a_admin.txt
curl -O https://raw.githubusercontent.com/afni/afni/master/src/other_builds/OS_notes.linux_ubuntu_26_64_b_user.tcsh
curl -O https://raw.githubusercontent.com/afni/afni/master/src/other_builds/OS_notes.linux_ubuntu_26_64_c_nice.tcsh
    Feel free to read any of these, for educational purposes.

  2. Run command scripts.

    Check your shell (echo $0), and use the appropriate set of commands below. Running the commands this way creates a text file, o.ubuntu*.txt, which can be sent to an AFNI guru for troubleshooting, if necessary.

    For bash users:

    1. Copy+paste the following (requires sudo with password):

      sudo bash OS_notes.linux_ubuntu_26_64_a_admin.txt 2>&1 | tee o.ubuntu_26_a.txt

    2. Copy+paste the following (no sudo):

      tcsh OS_notes.linux_ubuntu_26_64_b_user.tcsh 2>&1 | tee o.ubuntu_26_b.txt

    3. (optional, but useful) To niceify your terminal, copy+paste the following (no sudo):

      tcsh OS_notes.linux_ubuntu_26_64_c_nice.tcsh 2>&1 | tee o.ubuntu_26_c.txt

    For tcsh or csh users:

    1. Copy+paste the following (requires sudo with password):

      sudo bash OS_notes.linux_ubuntu_26_64_a_admin.txt |& tee o.ubuntu_26_a.txt

    2. Copy+paste the following (no sudo):

      tcsh OS_notes.linux_ubuntu_26_64_b_user.tcsh |& tee o.ubuntu_26_b.txt

    3. (optional, but useful) To niceify your terminal, copy+paste the following (no sudo):

      tcsh OS_notes.linux_ubuntu_26_64_c_nice.tcsh |& tee o.ubuntu_26_c.txt

(optional) Prepare for Bootcamp

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+unpack Bootcamp data to your home directory; note that this will overwrite any pre-existing Bootcamp directories):

    cd
install_bootcamp_data.tcsh -do_install yes
    If you want to remove the compressed packages that were downloaded, you can also delete the afni_boot_packages/ directory.

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

  3. 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!

Evaluate setup/system (important!)

  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”.

(optional) Install extra R packages

  1. If you plan to use the FATCAT_matplot functionality in AFNI, then copy+paste the following:

    @afni_R_package_install -shiny -circos

    Purpose: This script will install the R packages for FATCAT_matplot and other ‘shiny’ tools (via bioconductor). And it might take a little while to complete…

Keep up-to-date (remember!)

  1. To update your AFNI sometime, copy+paste:

    @update.afni.binaries -d

    That’s it!!

    Purpose: This will automatically download the correct, latest AFNI version to your computer, replacing your old binaries. It will also update the apearch help information. Update often!

  2. To check your AFNI version, copy+paste:

    afni -ver

    Purpose: Report this useful info whenever asking a question on the Message Board!

Note

The record of all changes (new options, new programs, bug fixes, et al.) in AFNI programs is maintained for all to see in the online AFNI History.

A note on setting up Python/using Conda (opt)

For this OS, you should not need to do anything further to set up your Python.

AFNI has very minimal Python requirements—at present, matplotlib and numpy. For example, for the recommended automatic QC output from afni_proc.py, matplotlib is necessary.

You can use any method to install+manage Python and its dependencies. In fact, your OS might have all the Python+modules needed to run AFNI already. Check this by running:

afni_system_check.py -check_all

... and seeing there are no notes in the “Please fix” section at the end—if there are none about Python, then you are all set!

But if you do still need to setup Python with appropriate modules, or you want to manage different environments with different package needs (Python or otherwise), then we note that we have found Miniconda to be convenient. It is cross-platform (with occasional OS-specific quirks). If you are interested in either using it or reading more about it, you can check out this tutorial, which has both verbose and quick instructions.

But Miniconda is not required.