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Program Functions
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the main source directory of mrFindBorders or, if a mrSESSION.mat file was used to load the
data, in the selected “Flat” directory. In this case, i.e., if data was loaded by specifying a
mr.SESSION.mat file, the ROIs are not stored in the mrFindBordersProgramData directory
but in the ROIs directory in the “Flat” directory. This directory is the one that mrLoadRet uses
to store ROIs by default. In addition to setting standard directory names and creating directo-
ries, standard file names, namely for the data and options, are also set.
6.9 Main
The Main directory currently contains only one file: vFbGuiCallbackFns.m. There are many
callback sub functions within this file. They are started by the user when he/she selects a menu
item or presses a button in the user interface of mrFindBorders. Due to the way in which the
name space is handled by MATLAB, one file with many callback sub functions was preferred
over many functions in one directory. In this way, the sub functions are hidden. They can only
be accessed by calling vFbGuiCallbackFns.m with the sub function’s name as the first argu-
ment. The following arguments that are given to vFbGuiCallbackFns.m are passed on as ar-
guments to the sub function. In the following, the sub functions of vFbGuiCallbackFns.m are
separately explained. Due to the number of sub functions, only short explanations can be
given here.
start
At first, vMkAtlasAtStart is called to create the atlases. Then, the phase offset for the ring-
stimulus phase image is automatically estimated by calling vFindPhaseShift. The phase offset
for the ring-stimulus phase image cannot be estimated while pre-processing the data (where
the phase offset for the wedge-stimulus phase image is estimated) since the corresponding at-
las has to be given for finding the phase offset here. This is because the phase offset for the
wedge-stimulus phase image can be determined in a different way than in this case because
that image theoretically contains only half of the phases. The other phases are found in the im-
age from the other hemisphere. The phase images from the ring stimulus have almost all
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