1.1.7. macOS: The App-based system setup

Welcome to the Jungle [1]

The following is a set of scripts packaged as an app. It is designed to automate the AFNI installation steps. You should launch the script by double clicking the icon like a regular program.

This app will download and install the recommended versions of the following:
  1. Xcode Command Line Tools
  2. Xquartz
  3. Homebrew
  4. R
  5. AFNI

It can also run the afni_system_check, download class / bootcamp data, and install shiny packages.

If a package is already installed, you may be asked if you want to reinstall it. But you can skip it if you like. This script will also setup your ~/.cshrc, ~/.bashrc, and ~/.bash_profile. It will add the appropriate entries to your paths specified there. After completion, you should restart your computer just in case.

This is a BETA script, so your feedback is welcome. We have tested the app on 10.10 to 10.14 with various hardware.

If you are seeking the non-App version of install instructions, please see HERE.

Take the File and Run [2]

Note

This script will has been tested on various systems from to macOS 10.11 to 10.14. It should work down to 10.7, but it has not been tested.

Start Your Engines [3]

  • Download the file and extract the zip if it did not extract automatically in your Downloads folder.

  • If you double click the “afni_macOS_install_BETA_V2” icon, you may get a popup notification about an “unidentified developer” similar to this:

    ../../_images/mac_app_V2_first_dev_warning.png
  • If so, you can continue by:
    ../../_images/mac_app_V2_right_click_open.png
    • Now you will be able to open it.
../../_images/mac_app_V2_second_dev_warning.png



  • You may also get warnings for “System Events” or “Finder” access.
warning1 warning2
  • These will grant access for the app to use apple script and automator for opening dialogs and using the Finder to choose folders.
  • If you click “Don’t Allow”, this installer quit with an error similar to this:
../../_images/mac_app_V2_event_error.png
  • If you see this error, you can allow access by going to:
    • “System Preferences” -> “Security & Privacy” -> “Privacy” -> “Automation”
    • Click the lock to make changes and check the box(es) under the “afni_macOS_install_BETA_V2” entry.
    • Then run the installer again.
    ../../_images/mac_app_V2_settings_privacy.png

Note

This is NOT an unattended install! The dialogs WILL time out after ~10 hours.

Use your M-O-U-S-E!

  • The first dialog box is an introduction and brief explanation

    ../../_images/mac_app_V2_intro.png
  • You will see a text box that will show you the output from the terminal progress. (it may pop up behind your current window)

    ../../_images/mac_app_V2_starting_text_box.png

Note

Everything you see in the text box will be saved to a log file on your desktop with a name similar to “afni_install_log.20190223-055115.txt”

  • The next dialog presents you with choices of what to install.

    The recommended choices are automatically selected by default, but you can pick and choose what you want. You can multi select items using ⌘+click

    ../../_images/mac_app_V2_selections.png
  • Do you have the POWER?

    For some packages, you may need to enter your password in the dialog box.

    ../../_images/mac_app_V2_password_dialog.png

Note

Notice that a temporary folder “afni_install_temp_delete_me” is created in your home directory. It will be deleted when you quit. If not, it is safe to delete.

Don’t let the fear install [4]

Here are a few details of the choices that presented for installation.

Command Line Tools for Xcode

The command line tools are mostly necessary for compiling some R packages from source (gcc etc.). But that mostly happens behind the scenes so you won’t have to deal directly with any of that.

The usual way of installing this is typing this in the terminal:

xcode-select --install

XQuartz

This is desktop manager needed to run X11 programs, such as afni.

  • During the install you may notice the xquartz installer drive briefly mount and unmount.

    ../../_images/mac_app_V2_xquartz_dmg.png
  • See XQuartz main page.


Homebrew 🍺

No. Not beer, but a package manager for macOS. It is used to 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. Also installs openmpi for multiprocessor support in R.


R ☠️

This is what is usual the catch phrase of pirates on the high seas. But here we are talking about the free software environment for statistical computing and graphics. afni needs this for several of the group analysis programs.


AFNI

AFNI is a set of C programs for processing, analyzing, and displaying functional MRI (FMRI) data. (taken from the about page…)

A few thing are happening here.

  • Basically running @update.afni.binaries. It will default to installing in ~/abin, but you can choose your own favorite folder.

  • Updates your ~/.cshrc, ~/.bashrc, ~/.bash_profile, and other environments.

  • Installs the R packages necessary for afni. First it checks to make sure you have R and Homebrew’s openmpi installed. rPkgsInstall -pkgs ALL will fail without those…


afni_system_check

Runs afni_system_check.py -check_all.

If you selected afni_system_check (which you should do…), you will be presented with a dialog to let you view it before you procede.

../../_images/mac_app_V2_afni_system_check.png

The afni_system_check output will have been saved to your desktop. It is named something obvious like “afni_system_check.20190208-145815.txt”. Clicking “View” will open the file in your default text editor. This file may be useful for figuring out problems with the install, especially when posting to the message board.

Note

When you are finished with installation, you may want to open up the AFNI and SUMA GUIs, juuuust to make sure all is well:

afni
suma

Class / Bootcamp data download

Download class data and prep it for bootcamps or your own practice.

You may want to do the following later:

  1. 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!

  2. Pro tip: If you will be attending a Bootcamp, you might want to bring a mouse to use with your laptop. It will be easier to follow the demos using a mouse than a trackpad. (eh…)


Shiny packages

Install optional packages for some of afni’s shiny integrations. You can learn more about shiny apps here.

This is needed if you want to run any of these programs:

All Done

Upon completion of all installations, and barring any error, you should see a completion dialog.

../../_images/mac_app_V2_complete.png

Then you can review the text or quit the app.

../../_images/mac_app_V2_quit.png

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.


Older Version BETA V1

The following is a set of scripts packaged as an app. It is designed to automate the AFNI installation steps. You should launch the script by double clicking the icon like a regular program.

This app will download and install the recommended versions of the following:
  1. Xcode command line tools
  2. Xquartz
  3. R
  4. AFNI

If a package is already installed, you may be asked if you want to reinstall it. But you can skip it if you like. This script will also setup your ~/.cshrc, ~/.bashrc, and ~/.bash_profile. It will add the appropriate entries to your paths specified there. After completion, you should restart your computer just in case.

This is a BETA script, so your feedback is welcome. We have tested the app on 10.10 to 10.13 with various hardware.

If you are seeking the non-App version of install instructions, please see HERE.



  • Download the file and open it to extract the contents.

  • Read the README!!

  • Double click the “afni_macOS_install_10.7_BETA” or “afni_macOS_install_10.12_BETA” icon.

  • You may get a popup notification about an “unidentified developer”.

    ../../_images/unknown_dev_warning.png
    If so, you can continue by:
  • This will launch your terminal.

    Most of the rest of the interactions are in the terminal. If needed, the Xcode command line tools will popup an installation window. Once complete, return to the terminal to continue.

  • To accept the default options (shown in [ ]), just press Enter.

    For some sections, you may need to type in your password. If you are not an administrator on your computer, this installation may fail. Make sure you have permissions for the folder you choose for AFNI! The sudo prompt will time out after awhile, so this is not an unattended install.

  • This script does not install fink. Nor does it download the class data.

../../_images/apple_brain_color_flipped.png

The icon is a work in progress. If you have some design skills, please send me alternatives.

Footnotes

[1]Guns N’ Roses
[2]Steve Miller Band
[3]Tears for Fears
[4]Birds by Coldplay