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. Download the AFNI Processing Stream backbone files.
  2. Unzip the folder in your home directory
  3. Navigate to /cgodwin9/AFNI_Analysis_Scripts/for_users and copy the two files a) afni_processing_manual.pdf and b) MNI152_T1_1mm.nii.gz into your tutorial folder

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

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 (10.1.83) by default. To run this version of PsychoPy, start the computer system on the E*Prime 2.0.10 version.

Video Experiments – PsychoPy 10.1.80

Users who wish to present any kind of video stimuli in PsychoPy must currently build their experiment(s) in PsychoPy version 10.1.80. 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 10.1.83

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 10.1.80, this warning message itself is broken, which will result in experiments breaking any time a stimulus must be resized. Version 10.1.83 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.

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!