(old) Mac OS, 10.9-10.15: administered system

What to do?

Here we describe the two halves of installation AFNI on an administered computer specifically running Mac OS versions 10.9-10.15.

Note: This version of Mac computer (OS 10.9-10.15) is now quite old, so please make sure this actually corresponds to your system setup before starting.*

The instructions are split into 2 parts:


Part 1: for the administrator

Here we describe the administrator’s part of the AFNI installation, which must be performed prior to the user’s part.

Root privilege is required for the steps in this section.

Install Xcode and XQuartz

  1. Copy+paste:

    xcode-select --install

  2. For …

    • … OS X >= 10.11, click on this link:
      http://www.xquartz.org
      Then click on the “Quick Download” DMG, and follow the instructions to install.

    • … OS X 10.9 and 10.10, copy+paste:

      /Applications/Utilities/X11.app

    Purpose: These install Xcode command line tools (needed for the gcc compiler et al.) and XQuartz (the desktop manager needed to run X11 programs, such as afni!).

Install R

  1. Click on this link:
    https://cran-archive.r-project.org/bin/macosx/el-capitan/base/R-3.6.3.nn.pkg
    Purpose: Get R-3.6.3 (a recent, but not the most recent, version of R).

  2. Copy+paste:

    sudo rPkgsInstall -pkgs ALL

    Purpose: Get specific R packages needed for AFNI programs.

Install Netpbm

  1. Copy+paste:

    /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install.sh)"

  2. Copy+paste:

    brew install netpbm

Purpose: Install “netpbm”, which has functionality for converting image formats (such as to PNG) and is used in several programs like @snapshot_volreg, @chauffeur_afni and others. Uses the package manager homebrew to do the installation.

Part 2: for the regular user

Here we describe the regular (= administrator) user’s part of the AFNI installation, which must be performed after the administrator’s part.

Root privilege is not required for the steps in this section.

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

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

Check shell

To find out what shell you are using (e.g., bash or tcsh), type:

echo $0

Most AFNI scripts are written in tcsh, and most command line examples presented also use tcsh syntax. If you would like to change your default shell, please ask your administrator to do so (as it typically requires admin privileges on a Mac to do so).

Setup terminal

  1. Copy+paste:

    defaults write org.macosforge.xquartz.X11 wm_ffm -bool true
defaults write org.x.X11 wm_ffm -bool true
defaults write com.apple.Terminal FocusFollowsMouse -string YES

    Purpose: This sets the policy where “focus follows mouse” for relevant applications. After this, clicks on a new window are directly applied, without needing to “pre-click” it. You’re welcome.

Install AFNI binaries

  1. For …:

    • … (default) installing the binaries from online, copy+paste:

      cd
curl -O https://afni.nimh.nih.gov/pub/dist/bin/misc/@update.afni.binaries
tcsh @update.afni.binaries -package macos_10.12_local -do_extras

    • … (alternative) installing already-downloaded binaries, you can use -local_package .. (replace “PATH_TO_FILE” with the actual path; also, if @update.afni.binaries has also been downloaded, you can skip the curl .. command), copy+paste:

      cd
curl -O https://afni.nimh.nih.gov/pub/dist/bin/misc/@update.afni.binaries
tcsh @update.afni.binaries -local_package PATH_TO_FILE/macos_10.12_local.tgz -do_extras

    Purpose: Download and unpack the current binaries in your $HOME directory; set the AFNI binary directory name to $HOME/abin/; and add that location to the $PATH in both ~/.cshrc and ~/.bashrc. This command also sets up default ~/.afnirc and ~/.sumarc profiles and environment variables.

Setup Mac environment variables

  1. Copy+paste the following:

    touch ~/.cshrc
echo 'if ( $?DYLD_LIBRARY_PATH ) then' >> ~/.cshrc
echo '  setenv DYLD_LIBRARY_PATH ${DYLD_LIBRARY_PATH}:/opt/X11/lib/flat_namespace' >> ~/.cshrc
echo 'else' >> ~/.cshrc
echo '  setenv DYLD_LIBRARY_PATH /opt/X11/lib/flat_namespace' >> ~/.cshrc
echo 'endif' >> ~/.cshrc

touch ~/.bashrc
echo 'export DYLD_LIBRARY_PATH=${DYLD_LIBRARY_PATH}:/opt/X11/lib/flat_namespace' >> ~/.bashrc

    Purpose: This adjusts the library format variable for XQuartz in both tcsh and bash. Sigh.

Reboot

Please logout and log back into your system.

Purpose: This deals with system updates, any change in login shell, and path updates.

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+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!

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”.

Niceify terminal (optional, but goood)

To improve your life when using the terminal, copy+paste these:

echo 'set filec'    >> ~/.cshrc
echo 'set autolist' >> ~/.cshrc
echo 'set nobeep'   >> ~/.cshrc

echo 'alias ls ls -G'       >> ~/.cshrc
echo 'alias ll ls -lG'      >> ~/.cshrc
echo 'alias ltr ls -lGtr'   >> ~/.cshrc
echo 'alias ls="ls -G"'     >> ~/.bashrc
echo 'alias ll="ls -lG"'    >> ~/.bashrc
echo 'alias ltr="ls -lGtr"' >> ~/.bashrc
echo 'alias ls="ls -G"'     >> ~/.zshrc
echo 'alias ll="ls -lG"'    >> ~/.zshrc
echo 'alias ltr="ls -lGtr"' >> ~/.zshrc

Purpose: The first command block sets up tab autocompletion for tcsh (which should already be enabled for bash users by default). The second set of commands make aliases for the main shells so that different types of files (“normal” files, zipped files, executables, et al.) and directories are shown using different colors and boldness. It makes it much easier to navigate on a terminal, IMHO.

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.