macOS 11 (via command line)

What to do?

These setup instructions are for macOS 11.

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

  2. The user must have admin privileges (can run sudo ...). Some steps require an internet connection.

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

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

Install Xcode and XQuartz (admin priviledges required)

  • Copy+paste:

    xcode-select --install

Note

You may want to check “Software Update” in “System Preferences” for an xcode update after this finishes installing.

  • For XQuartz, click on this link:
    http://www.xquartz.org
    Then click on the “Quick Download” DMG, and follow the instructions to install.

Note

The XQuartz installer may log you out after the installation completes.

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!).

All in One Block

  • 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=${DYLD_LIBRARY_PATH}:/opt/X11/lib/flat_namespace' >> ~/.bashrc
echo 'export PATH=$PATH:/Library/Frameworks/R.framework' >> ~/.bashrc

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

source ~/.bashrc
cp $HOME/abin/AFNI.afnirc $HOME/.afnirc
suma -update_env

Note

Upon first afni or suma launch, the terminal will pop up messages to ask for permissions to access various data on your system. Possibly including: Photos, Desktop, Contacts, Calendar, Reminders, Documents, Downloads. I would recommend NOT allowing Photos, Contacts, Calendars, and Reminders. But the others will be useful.

Note

And if you launch afni from your home folder, you will get a lot of “Operation not permitted” errors from afni trying to find datasets in restricted folders under your home directory. Like “~/Library” etc. You can safely ignore those errors.

Reboot

Please logout and log back into your system.

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

Install R (admin priviledges required)

Note

You will get an error that prevents you from launching the installer when you double click it. You will have to go to your “Downloads” folder, right click the R-3.6.3.nn.pkg file and select “Open”. Then you will get the same warning, but you can click “Open” to launch the installer.

  • Copy+paste:

    sudo rPkgsInstall -pkgs ALL

Purpose: Get specific R packages needed for AFNI programs.

Note

Note for afni staff.

Need path update in .zshrc etc to include /Library/Frameworks/R.framework/Resources

also may need gfortran https://cloud.r-project.org/bin/macosx/tools/gfortran-6.1.pkg

Install Netpbm (admin priviledges required)

  • Copy+paste:

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

  • Copy+paste:

    brew install netpbm

Extras

  1. Copy+paste the following:

    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

Setup Python (opt)

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.

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.