Note that this sometimes works if the slab has the correct header/scanner information on image orientation and location relative to the anatomical images. The top row of images were made using a pretty standard call that works fine on whole-brain EPI images: align_epi_anat.py \Īnd the second row of images was made with a slight modification of adding “-partial_axial” flag, which sometimes works if you have sufficient coverage AND the images aren’t terribly far off. If you were to attempt to register this slab to the whole-brain anatomical using a standard process like align_epi_anat.py, you’d get something like this:ĭefault alignment that works fine on whole-brain images On the left I have just the axial slice, followed by the axial slice with the overlay showing significant mis-alignment – caused primarily from the slab being too low in the brain. Now we can clearly see that the default AFNI view with no transformations shows the slab in the wrong position.
Right out of the box your two images might look something like this: Default view of images off the scanner
#PSYCHOPY PICTURE SIZE SOFTWARE#
This is true of all software packages (FSL, AFNI, and yes even ANTs).
#PSYCHOPY PICTURE SIZE REGISTRATION#
Which means that you generally have something that looks like this: Our “Slab” Partial Volume EPIĪnd if you have’t already tried, that means that registration of these partial volumes is often more difficult than when your functional images (EPI, etc) cover the entire brain. One of the frustrating things about doing sub-1mm resolution is that you’re often constrained to partial volume coverage. 7T+) is the ability to see smaller structures and even discern layers of the human cortex (examples: motor cortex and DLPFC). One of the benefits of high-resolution fMRI (e.g. Hopefully putting it here makes it easier to find for everyone, and obviously for me! This content kindly provided on the PsychoPy message boards courtesy of Jonathan Peirce, the developer of PsychoPy. Also don’t forget to set the “Color” component to “set every repeat” otherwise PsychoPy will be angry with you and likely won’t run, definitely won’t change with each stimulus.Īnd there you have it, a PsychoPy experiment with a background that is dynamically set and does so at the start of a routine (unlike using the setColor() function, which would change it after the start of the routine. Under “Advanced” make sure you change the Texture to “None” and the mask to “None”. Now we define the grating object as follows, the duration, color, size (2,2), and units to “norm”. My understanding of PsychoPy is that it draws in order, so you want the background first and the video second, so that the video appears on top of the background – yes I tried it the other way and as expected the video was underneath.
#PSYCHOPY PICTURE SIZE MOVIE#
Turning our attention to the second “ShowVid1” object/routine, we have two components, the first is a grating object, and the second is our movie object. This loop has two components, the first is just a title of the video (Title from above) and the second is the actual video with the background color (green or red): Experiment Flow The next step is to construct a fairly simple PsychoPy experiment that has a loop that will contain the trials. Now with any well designed and modular PsychoPy experiment, we have a list that that conveys the stimuli and in that list we might want to specify titles for the videos and background colors: List file containing stimuli and related information (including color) An example stimulus might look like this ( borrowed from this amazing clip of Skye and Naomi dancing): Skye and Naomi Dancing Lindy Hop “Category 2” just to help participants keep track of the stimulus sets they’re seeing. You can think of this as “Category 1” vs. In this particular experiment I wanted to have a type of video stimulus that was surrounded by a background color representing additional information to the participant. Since every time I write a new experiment, I end up googling this and going through the usual steps to try and find a “good” solution – I figured it’s time to write it down. This is a fairly common thing to do, but it’s necessarily straightforward in PsychoPy. Say that you want to have an experiment where the background color changes based on a particular condition.
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