Once we've created the basic template of our experiment we then turn our attention to flow control, or how to guide the subject to different parts of the experiment. In the previous video we created a basic Stroop experiment that went in a predetermined direction: The subject would encounter one Stroop trial, and then another, exactly in the order that we had laid out. This was enough to qualify as an experiment, but most studies require more elements than that - randomization and counterbalancing, for example.
Read moreE-Prime Tutorial #3: Duration, Termination, and Pre-Release
This tutorial shows how to make a basic Stroop experiment. A new tool we will learn about is the Slide object - a versatile object that can contain several sub-objects, such as images and text boxes. The Slide object's properties are controlled by the property pages tab, while the sub-objects are controlled by the sub-object property pages tab.
Read moreCreating Masks from the Juelich Atlas
The atlases in FSL can be divided into two classes: probabilistic and non-probabilistic. In a probabilistic atlas, the number in each voxel represents the probability that the voxel belongs to a structure. Take the Harvard-Oxford atlas, for example. A voxel at the MNI coordinates 18, -102, 6 has a value of 76. This number means the odds are 76% that the voxel coordinates will be part of the occipital cortex, for a subject taken at random.
Read moreE-Prime Tutorial #2: Objects and Properties
This tutorial is about objects - the building blocks of an experiment. E-Prime uses object-oriented programming, which means that the user selects pre-designed objects from the E-Prime toolbox, and then arranges and modifies them to suit his experiment.
Read moreIntroduction to E-Prime
Over the next two weeks I'll be posting a series of videos on how to use E-Prime, by creating a Stroop experiment using building blocks known as objects. These objects have attributes, or properties, that determine object characteristics such as shape, duration, and color. Through arranging objects a certain way and modifying their properties, you can create a wide variety of experiments.
Read moreReverse Normalization of fMRI Data
Normalization - the transforming of data to a standardized space - is a common preprocessing step, and for good reason: it allows us to perform group analysis; it reduces variability in the size and shape of the brain images; and it allows for comparisons across studies by putting the data into a standardized space. Five millimeters to the left and ten millimeters to the rear of the anterior commissure then becomes same location from one study to the next.
Read moreExtracting Timecourses with 3dmaskdump
ROI analysis often means averaging over all the voxels within a mask - either the average parameter, or the average timeseries. For most researchers this is all they need.
Whether or not that applies to you as well, I would like to talk about one more type of ROI analysis: extracting data from each voxel. Most researchers use this analysis to extract the timeseries for each voxel in the brain, although you can extract whatever data you like - parameter estimates, timeseries, and anything else contained in your voxels.
Read morefMRI Lab: ROI Analysis in FSL
By now you should begin to see common themes in each of the videos: We create masks using either spheres or an atlas; we extract data from those masks using whichever tool is most appropriate for the software that you're using; and you can analyze the extracted numbers with whatever statistical software you like.
Read moreABB Podcast #3: Ken Pugh (President, Haskins Laboratories)
This week we talk to Ken Pugh, president of Haskins Laboratories, about reading disorders, the brain, and whether neuroimaging can treat and diagnose dyslexia.
fMRI Lab: ROI Analysis with AFNI
I'm updating some of the old videos I had on ROI analysis, this time with AFNI. I'm trying a new format, in which I have a separate video introducing the topic (in this case, ROI analysis), and then a "lab" video or two showing how to do it in different software packages. I'm trying to have the intro videos be on the shorter side, around 5 minutes, while the lab videos are a little longer and more in-depth, around the 10-minute mark. I hope the figures and animations make this technique more understandable.
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