1.1.7. Linux, Red Hat and CentOS¶

These setup instructions are for modern Linux versions of Red Hat (RHEL) 7, along with the corresponding CentOS 7.

Things to note before starting ¶

Each step involves either copy+pasting a command, or clicking on a download link.
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.
Note your terminal shell type (bash, zsh, tcsh, csh, etc.), by copy+pasting:
```
echo $0
```
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 AFNI Message Board.

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.)
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 &
```

Install prerequisite packages ¶

To be able to install latest packages, copy+paste:
```
sudo yum update
```

Copy+paste:

sudo yum install -y epel-release

Copy+paste:

sudo yum install -y tcsh libXp openmotif gsl xorg-x11-fonts-misc        \
                      PyQt4 R-devel netpbm-progs gnome-tweak-tool ed    \
                      libpng12 xorg-x11-server-Xvfb firefox             \
                      python3-matplotlib python3-numpy                  \
                      python3-flask python3-flask-cors

Copy+paste:

sudo yum update -y

Purpose: Installs a lot of packages that AFNI depends on (so we don’t have to reinvent the wheel!).

Install AFNI binaries ¶

Choose one of the following approaches:
- (default) To install 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 linux_centos_7_64 -do_extras
```
- (alternative) To install already-downloaded binaries, use -local_package .. (replacing 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/linux_centos_7_64.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.

Install R ¶

For …

… a tcsh terminal, copy+paste:

setenv R_LIBS $HOME/R
mkdir  $R_LIBS
echo  'export R_LIBS=$HOME/R' >> ~/.bashrc
echo  'setenv R_LIBS ~/R'     >> ~/.cshrc
. ~/.cshrc

… a bash terminal, copy+paste:

export R_LIBS=$HOME/R
mkdir  $R_LIBS
echo  'setenv R_LIBS ~/R'     >> ~/.cshrc
echo  'export R_LIBS=$HOME/R' >> ~/.bashrc
. ~/.bashrc

(To check your shell type, copy+paste: echo $0)

Purpose: Set the environment variable $R_LIBS to specify where to install+find the R packages.

Copy+paste:
```
rPkgsInstall -pkgs ALL
```
Purpose: Get specific R packages needed for AFNI programs. This step might take a while (of order an hour) to complete as R compiles packages. Sigh.

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.

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 ..

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

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

Open a new terminal, and then copy+paste:
```
afni_system_check.py -check_all
```
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:
```
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:
```
echo 'set filec'    >> ~/.cshrc
echo 'set autolist' >> ~/.cshrc
echo 'set nobeep'   >> ~/.cshrc

echo 'alias ls ls --color=auto' >> ~/.cshrc
echo 'alias ll ls --color -l'   >> ~/.cshrc
echo 'alias ltr ls --color -ltr'   >> ~/.cshrc
echo 'alias ls="ls --color"'    >> ~/.bashrc
echo 'alias ll="ls --color -l"' >> ~/.bashrc
echo 'alias ltr="ls --color -ltr"' >> ~/.bashrc
```
Purpose: The first commands set up tab autocompletion for tcsh (which should already be enabled for bash, by default). The second set of commands make aliases 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.

Install extras (optional, but 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:
```
@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!
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.

1.1.7. Linux, Red Hat and CentOS¶

Things to note before starting ¶

Install prerequisite packages ¶

Install AFNI binaries ¶

Install R ¶

Setup Python (opt)¶

Prepare for Bootcamp ¶

Evaluate setup/system (important!)¶

Niceify terminal (optional, but goood)¶

Install extras (optional, but recommended for Bootcamp prep)¶

Keep up-to-date (remember!)¶

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