Teaching fMRI analysis is a formidable task; one has to know some basic facts about statistics, image analysis, physiology, psychology, WW2 history, movie trivia, and a few pick-up lines to even get started. (The well-known line that uses "regions of interest" as a euphemism for erogenous zones has been quoted threadbare, but is still surprisingly effective.)Read More
Note: See Wiktor's comment below for a comparison of frequency cutoffs across AFNI, FSL, and SPM.
Yesterday I had the following conversation on one of my YouTube videos:
J: Thanks for the video. My question pertains the cut-off filtering frequency: When you apply a HP [High-Pass] filter in fMRI (typically it's .008 Hz), is this at the Nyquist frequency? Meaning that .008/2 is the actual frequency we are removing? Thank you.Read More
This tutorial uses many of the concepts you've learned so far about E-Prime: Objects, attributes, E-Basic code, and more. It is a summary of everything we've done in the previous tutorials and also applies your learning to something you may do for your research: Creating a scanner-compatible E-Prime experiment.Read More
When an E-Prime experiment terminates without any errors, E-Prime generates data files called edat files. An edat file is created each time the experiment terminates, and each edat file is labeled with the experiment name, subject number, and session number. These files contain the value of each attribute for each trial and log them into a spreadsheet. Depending on how you set up your experiment there can be one or several edat files per subject.Read More
The following was a conversation on the message boards of my old blog, and I thought it might be interesting to those of you using AFNI tools on SPM data. As I mention below, I'm not sure whether the following approach works, but it seemed reasonable. If anyone else has any thoughts, I'd like to hear them in the comments section below!Read More
We've learned how to declared variables and how to change the properties of other objects using E-Basic code. But what if we want to use a variable or attribute not yet coded into our experiment? What if we want an attribute created by what the user at the beginning of the experiment?Read More
What if we want to have both practice trials and experimental trials in a single E-Prime experiment? What if we want to exit the practice trials when the subject's accuracy had reached a certain level? Both of these goals can be achieved with E-Basic, E-Prime's programming language. If you're new to programming, be prepared to spend some time learning the vocabulary and syntax - things like conditional statements, data types, and declarations. Yet remember that all we're doing is converting logical thoughts from English into computer code. If you keep that in mind, learning how to program becomes more comprehensible and less mysterious.Read More
Alert reader Surya recently pointed out how using different masks in the command fslstats led to the same result, leading him to question whether there was an error when creating the masks.
The actual cause of the error, however, was in how the command was constructed. Here was the initial syntax:
fslstats image.nii.gz -M -k mask.nii.gzRead More
SlideStates are different instances of the same Slide object. For example, you may want to present two types of conditions, one where the subject responds to the color of a word, and another condition where the subject responds to the color of a car. Instead of creating two separate Slide objects, you can put both conditions into a single Slide, making the experiment more compact and more flexible.Read More
The Feedback Display object displays different screens based on whether the response to a previous slide was correct or incorrect. This introduces the concept of SlideStates, which are different instances of a Slide that are activated based on the value stored in an attribute. The Feedback Display objects monitor the value of the Accuracy attribute from a previous Slide, determine whether it was correct or incorrect, and then display the corresponding SlideState.Read More