genVSM - generate Visual Sign Map
Creates a visual sign map using the azimuth and elevation maps.
Description
This function uses the azimuth and elevation phase maps created in the function genRetinotopyMaps to create the Visual Sign Map (VSM). Optionally, this function can segment the VSM to create ROIs compatible with the ROImanager app.
Input
Azimuth and Elevation maps stored in the AzimuthMap and ElevationMap .dat files.
The algorithm
In brief, the visual sign map is calculated as the sine of the difference between the gradients of the azimuth and elevation phase maps. This function uses the algorithm described by Sereno et al. [1,2] and Garret et al. [3].
Output
The output of this function is a numerical matrix with dimensions Y,X containing the visual sign map and its associated meta data structure.
Parameters
The parameters of this function are the following:
Standard deviation of the gaussian spatial filter (in pixels) to be applied to the visual sign map. Set to skip spatial filter.
Set to true to export a labeled matrix containing masks based on the visual sign map.
Name of the .mat file with the labeled matrix with the ROIs extracted from the visual sign map. This file will be stored in the same folder as the input files to this function.
Set to true to use a logical mask stored in a variable named logical_mask in a .mat file. This mask is used to exclude non-pertinent areas of the visual sign map before the ROI creation.
Name of the file containing the logical mask.
References
- Sereno, M. I., A. M. Dale, J. B. Reppas, K. K. Kwong, J. W. Belliveau, T. J. Brady, B. R. Rosen, and R. B. Tootell. 1995. ‘Borders of Multiple Visual Areas in Humans Revealed by Functional Magnetic Resonance Imaging’. Science (New York, N.Y.) 268 (5212): 889–93.https://doi.org/10.1126/science.7754376.
- Sereno, Martin I., Colin T. McDonald, and John M. Allman. 1994. ‘Analysis of Retinotopic Maps in Extrastriate Cortex’. Cerebral Cortex 4 (6): 601–20. https://doi.org/10.1093/cercor/4.6.601.
- Garrett, Marina E., Ian Nauhaus, James H. Marshel, and Edward M. Callaway. 2014. ‘Topography and Areal Organization of Mouse Visual Cortex’. The Journal of Neuroscience 34 (37): 12587–600. https://doi.org/10.1523/JNEUROSCI.1124-14.2014.