1.1.12. macOS, 12+ (Intel chip)¶
The essential system setup
What to do?¶
These setup instructions are for macOS 12.3.1 or greater with Intel CPUs (not Apple Silicon).
Each step involves either copy+pasting text into a terminal, which is in a green field like:
... or a rebooting/clicking on link.
The user must have admin privileges (able to run
sudo ls, for example). These steps have “(admin)” in their title. Do not include
sudoin a command unless it is already written.
If you need to know your shell type, copy+paste
This has been tested on macOS 12.3.1 and 12.4. It may work on macOS 11, but the python installation may not be necessary.
Install Homebrew and packages (admin)¶
Do not use
sudo explicitly with any of these commands. However,
some will prompt you for your admin password).
cd /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"
Privacy Setting (opt):
brew analytics off
brew install python netpbm cmake
brew install --cask xquartz
Reboot/restart your computer (for changes to take effect).
After you restart, open XQuartz and change a preference. Go to the XQuartz menu near the upper left corner of the desktop. Then go to Preferences… -> Windows -> “Click-through Inactive Windows”. Also “Focus On New Windows” may be useful.
Purpose: Homebrew will install the Xcode command line tools first.
macOS 12.3.1 removed
python, so we are installing it here.
netpbm is needed for some image outputs.
cmake is needed for
compiling some R libraries. Xquartz is the main desktop manager for
X11 programs like
Install R (admin)¶
Get R v3.6.3 gfortran v6.1:
cd curl -s -L -o R-3.6.3.nn.pkg "https://cran.r-project.org/bin/macosx/el-capitan/base/R-3.6.3.nn.pkg" curl -s -L -o gfortran-6.1.pkg "https://cloud.r-project.org/bin/macosx/tools/gfortran-6.1.pkg"
sudo installer -pkg R-3.6.3.nn.pkg -target /
sudo installer -pkg gfortran-6.1.pkg -target /
\rm gfortran-6.1.pkg \rm R-3.6.3.nn.pkg
Purpose: This downloads the installer packages and runs the
install from the command line (then removes the downloaded
installers). This slightly older R version is needed (at present)
to match the AFNI build.
gfortran is is used to compile some R
Add to path (zsh):
touch ~/.zshrc echo 'export PATH=$PATH:/usr/local/opt/python/libexec/bin' >> ~/.zshrc echo 'export PATH=$PATH:/Library/Frameworks/R.framework/Resources' >> ~/.zshrc echo 'export PATH=$PATH:/usr/local/gfortran/bin' >> ~/.zshrc source ~/.zshrc
Purpose: This adds
gfortran to your path
so the command line can use them. Assumes
zsh is your login shell
(the Mac default).
Install main R libraries:
Rscript -e "install.packages(c('afex','phia','snow','nlme','lmerTest'), repos='https://cloud.r-project.org')"
Purpose: Installs the R libraries needed for primary AFNI stats
(R-based) programs. Note that some newer Bayesian stats programs
require other libraries. Some libraries other libraries are not
available on macOS for R 3.6.3. (We are working on updating this)
afni_system_check.py -check_all will show some missing libraries.
Get+unpack AFNI binaries:
curl -O https://firstname.lastname@example.org tcsh @update.afni.binaries -package macos_10.12_local -do_extras
Open a new terminal (or source current shell’s “rc” file, as suggested in finishing text).
Purpose: Install AFNI binaries (in default
suma launch, the terminal will
pop up messages to ask for permissions to access various
data on your system, such as: Photos, Desktop, Contacts,
Calendar, Reminders, Documents, Downloads. I would
recommend not allowing Photos, Contacts, Calendars, and
Reminders. But the others will be useful.
And if you launch
afni from your home folder, you will
get a lot of “Operation not permitted” errors/warnings from
afni trying to find datasets in restricted folders under
your home directory, like
~/Library etc. You can safely
ignore those errors.
Evaluate setup/system (important!)¶
Open a new terminal, and then copy+paste:
- Read the “Please Fix” section at the end. If there are no suggestions, then rejoice! Otherwise, try the suggestion(s) there.
Open up the AFNI and SUMA GUIs, juuuust to make sure all is well:
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”.
Setup Python (a method)¶
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:
... 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 (install demo data)¶
curl -O https://afni.nimh.nih.gov/pub/dist/edu/data/CD.tgz tar xvzf CD.tgz cd CD tcsh s2.cp.files . ~ cd ..
Purpose: Download the Bootcamp class data; untar+unzip it (= open it up); move into the newly opened directory; execute a script to copy the files to
$HOME/..If no errors occur in the above, and your
afni_system_check.pysays things are OK, you can delete/remove the tarred/zipped package, using “
rm CD.tgz”. If you are really confident, you can also deleted the CD/ directory in the present location.
- !Pro tip!: Bring a computer mouse to use at the Bootcamp. It is muuuuch easier to follow the demos that way.
Read+practice with the handy Unix documentation/tutorial.
Purpose: 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!
Setup terminal (opt)¶
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.
Niceify terminal (add convenience!)¶
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
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,
Install extras (recommended for Bootcamp prep)¶
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!)¶
To update your AFNI sometime, copy+paste:
Purpose: This will automatically download the correct, latest AFNI version to your computer, replacing your old binaries. It will also update the
apearchhelp information. Update often!
To check your AFNI version, copy+paste:
Purpose: Report this useful info whenever asking a question on the Message Board!
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.
Enable more SUMA keypresses (recommended)¶
opt (or alt)
option (or alt)
left, up, down, right
left arrow, up arrow, down arrow, right arrow
Some of Mac’s default keyboard shortcuts hijack basic SUMA GUI keypresses. You can unset those from the Mac list, and therefore use them in SUMA.
Click your way to “System Preferences” -> “Keyboard” -> “Shortcuts”.
In the “Mission Control” tab, change or deselect:
Other key combinations to leave free include:
shiftplus any arrows
ctrl+shiftplus any arrows