Warning

This is as a Lab Notebook which describes how to solve a specific problem at a specific time. Please keep this in mind as you read and use the content. Please pay close attention to the date, version information and other details.

Using AFNI Graphical User Interfaces

The version of AFNI installed on the HPCC does not support graphical interfaces (or "GUIs") by default. This is because AFNI relies on old dependencies that are not easily compatible with the operating system of the HPCC.

Instead, you need to run AFNI through a container. ICER has uploaded a Singularity container image to the HPCC at /mnt/research/common-data/Container_images/afni.sif that has the necessary libraries installed.

Running AFNI GUIs from a container

To run a GUI from the container, you first need to start an Interactive Desktop through ICER's web portal OnDemand. Be sure to request enough memory for the analyses you plan to run.

Once you have connected to the Interactive Desktop, open a terminal by going to the menu in the top left corner, and searching for "MATE Terminal". Hitting Enter or selecting the application entry will start a terminal in your Interactive Desktop.

To start an AFNI GUI, e.g., uber_subject.py, run the command:

singularity exec -B /run /mnt/research/common-data/Container_images/afni.sif uber_subject.py

Copy/pasting in an Interactive Desktop

You cannot directly paste something you copy from your computer into the Interactive Desktop. To copy/paste, you first need to open the popout menu signified by a tab on the left-hand side of the Interactive Desktop. Click the clipboard, then paste into the large text box. Close the menu, and select the location you would like to paste your text. You can then paste as normal. If you are pasting into a terminal, use Ctrl+Shift+V instead of just Ctrl+V.

If you need to copy/paste from the Interactive Desktop to your computer, it works the same way, just backwards. First copy from the interactive desktop. Then open the popout menu, and click the clipboard. You can copy the text in that clipboard and then paste on your computer as normal.

Running AFNI from a container

The steps above work outside of an interactive desktop for non-GUI applications as well. If you want to run any AFNI program from the command line, you can use the command

singularity exec /mnt/research/common-data/Container_images/afni.sif <insert-afni-command>