Process Guides

AFNI Processing Stream

**NEW October 10, 2016

CABI now offers a complete instruction manual, the AFNI Processing Manual, to introduce users to fMRI analysis in AFNI. This manual contains a tutorial that takes you from the intial fMRI preprocessing steps to group-level analysis using a sample dataset. The manual also includes instructions for quality assurance, creating stimulus timing files, and performing bash scripting in Linux.

To use this tutorial, follow these instructions:

  1. Navigate to /cgodwin9/AFNI_Analysis_Scripts/for_users and copy the three files a) afni_processing_manual.pdf, b) MNI152_T1_1mm.nii.gz, and c) into your tutorial folder

CABI also offers a separate functional connectivity demo. Click here for the guide (will open a Google Drive file).


Interested in running an independent component analysis (ICA)? In April 2017, CABI hosted an ICA workshop lead by Dr. Vince Calhoun from the University of New Mexico. This workshop focused on using the GIFT (Group ICA of fMRI Toolbox) software to run resting state and task ICA. Follow the link here to obtain the documentation to help you with your own ICA analysis: GIFT documentation

Information for PsychoPy Users

The CABI facilities are set up to support PsychoPy experiments. Depending on the demands of a given experiment, users may need to create their experiments in one of two possible versions of PsychoPy. These versions piggyback on the restart system that CABI employs to allow for switching between E*Prime versions 2.0.8 and 2.0.10. Note: if none of the following descriptions applies to your experiment, CABI recommends developing your experiments in the most recent version of PsychoPy (1.0.83) by default. To run this version of PsychoPy, start the computer system on the E*Prime 2.0.10 version.

Video Experiments – PsychoPy

Users who wish to present any kind of video stimuli in PsychoPy must currently build their experiment(s) in PsychoPy version This is due to a known problem in the more recent version that causes video stimuli to break when running the experiment. To run this version of PsychoPy, start the computer system on the E*Prime 2.0.8 version.

Stimulus Resizing – PsychoPy 1.0.83

Users who are dynamically resizing their stimulus images using the “WIDTH” and “HEIGHT” attributes may find that a warning is produced upon all or most stimulus presentations notifying the user that the stimulus may not be in the expected aspect ratio. In version, this warning message itself is broken, which will result in experiments breaking any time a stimulus must be resized. Version 1.0.83 has fixed this warning; it will still show, but will not break the experiment. To run this version of PsychoPy, start the computer system on the E*Prime 2.0.10 version.

Eyetracking in the MRI Scanner

We have an MRI-safe SR Research EyeLink 1000 Plus eyetracker for simultaneous MRI data collection and eyetracking. If you are interested in using the eyetracker in your MRI study, please contact Nytavia Wallace to get started. See the CABI user instructions for an overview of how to use the eyetracker in your experiment. See the EyeLink user manual for in-depth information about the eyetracker. Click here for the user manual (will open a Google Drive file).

Having Trouble?

If you have feedback on or problems with any of the guides listed here, please send an email to Christine including the following information:

– The process you are working on
– A brief description of what happened/what you were trying to do
– The part of the process that is unclear OR
– A copy of the output (if it exists) you are getting when the error occurs
– Any specific error messages that may occur

Any feedback you can give us on these resources will allow us to fix and improve them!