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Program Functions
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ence matrices for rotating wedge and expanding ring visual stimuli) are got in seven different
ways.
1. “currentDir”: The mrSESSION.mat file is in the current directory. The vLoadFromFlatDir
function is called directly. Please refer to this function’s explanation below for more in-
formation.
2. “browse”: Before the function vLoadFromFlatDir is called, the user can browse to the
mrSESSION.mat file by using a file browser window.
3. “browse_mrdata”: Similar to “browse” but the user can browse/search for flat data within
a data base. The selected data is automatically copied to a local temporary directory by
mrData from where it can then be loaded by vLoadFromFlatDir. This functionality has
not been completely implemented.
4. “empty”: Sets all matrices that are returned to empty matrices. Therefore, the initial win-
dow with the name definitions of the visual areas is displayed in mrFindBorders.
5. “huk”: The huk data set is an exemplary data set that is saved in the ProgramData direc-
tory of the mrFindBorders main directory. It is called huk data set because the data were
taken from Alex Huk, a graduate student at the Heeger lab.
6. “atlas1”: When choosing this option, no measured phase and coherence data for wedge
and ring visual stimuli is loaded. The program rather creates the phase and coherence
data. The phase data is created by using the same function (vMkAtlases) as for the atlas
creation. The initial coherence images are just matrices of ones. Then, the initial matrices
are rotated, noise is added to the phase matrices by calling vAddNoiseToPhIm. The func-
tion vWarpManually is called so that the user can manually distort the images. vWarp-
Manually returns the displacement fields for the control points (cu and cv), which are
used to deform the phase and coherence images. The gold standard ROIs can be calcu-
lated for this case since the displacement fields are known. Therefore, the quality of the
ROIs that the program found can be determined later by using the known gold standard
ROIs. At the end, a phase offset is added to the phase image from the wedge stimulus.
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