Traveling Wave Tutorial


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[edit] Overview

[edit] Traveling wave model

The first step in using mrVista to analyze traveling-wave data is to find the best-fitting harmonic to the time series at each cortical location. We store the information about the best-fitting harmonic in a structure we call the corAnal, which is short for "correlation analysis".

To compute the corAnal information from traveling wave data, you need to have the proper analysis parameters set. These are usually set in mrInitRet, but can be edited later in mrVista using the menu option 'Edit' | 'Data Type' | 'Edit Data Type'. The parameters for the corAnal are listed under the 'blocked analysis parameters' section. (Note that for block-design experiments in which the block order does not cycle through continuously -- e.g. ABCABC -- the 'event-related' analyses are actually more applicable; this nomenclature is intended to distinguish analyses where you have to specify the onset of each event type versus the corAnal, where you only need to know the total number of cycles). The key parameter to set is the number of cycles per scan: the sinsuoid predictor will have this frequency.

A traveling wave analysis is most effective when the time series contains an integer number of cycles. It is common practice to acquire data from an extra half cycle or so, and trim the extra frames at the beginning of the scan when initializing. (The reason for discarding the initial frames is that magnetic gradients are not typically uniform at the start of a scan.) There are options to trim frames during the initialization step in mrInitRet, as well as afterwards using the menu Analysis | tSeries | Clip Frames from tSeries.

The corAnal is computed by selecting 'Analysis' | 'Traveling wave analyses' | 'Compute corAnal' for the current scan, all scans, or a user-selected set of scans. The computation is fairly fast, taking approximately 5 minutes for 10 scans on a 2Ghz Pentium machine. This calculation produces the coherence, phase and amplitude of the response to the traveling wave. These values are computed at every voxel location.

Also, it is possible to examine a mixed-frequency traveling wave. In this application a stimulus may map a parameter at one frequency (e.g., sweeping across visual eccentricity 8 times a scan), but may also include a blank stimulus at a separate, nonharmonic frequency (e.g., switching on and off 10 times a scan). Running two corAnals at these two principal frequencies can identify both the representation of polar angle and the response contrast of stimulus vs. no stimulus. To do this, you can run 'Analysis' | 'Traveling wave analyses' | 'Compute corAnal 2 Freq.'. This runs the correlation analysis for each frequency.

[edit] Viewing the results of a traveling wave analysis

After a corAnal is computed, a file 'corAnal.mat' is saved in the view's data directory (e.g., 'Inplane/Original/corAnal.mat'). This saved file contains three fields which describe the results of the analysis: The signal coherence for each voxel ('') which measures the goodness-of-fit of the sinusoid model; the amplitude of the best-fitting sinusoid ('view.amp'), and the phase of the best-fitting sinusoid (''). The phase data are what is usually viewed during retinotopy experiments. The phase reflects the zero-crossing of the best fitting sinusoid within one stimulus cycle. A voxel with a phase of 0 radians has a BOLD response which is rising at the beginning of the cycle, and therefore whose most effective neural stimulation occurs approximately at the beginning of the cycle. Variations in the hemodynamic impulse response function between subjects may affect the relation between the phase and the actual best time within the cycle.

The different data fields in a corAnal can be toggled by using the View menu; further details are in the Inplane page.

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