Vogt-Bailey index toolbox in Matlab
While we recommend that users use the Python version of the toolbox (https://github.com/VBIndex/py_vb_toolbox) which can be installed as a standalone command-line application this readme file will help users navigate through the MATLAB version of the code.
The two starting functions are vb_index.m and vb_cluster.m
The function vb_index.m is used to perform the searchlight VB Index.
RESULT = vb_index(GIFTI_SURF, DATA, NORM, CORT_INDEX, OUTPUT, nthreads)
The input variables should already be loaded into MATLAB.
GIFTI_SURF is a variable that contains the GIFTI structure of the surface file containing the faces and vertices of a surface
DATA is an array that contains the timeseries that are associated with the GIFTI surface (above)
CORT_INDEX is an array that contains a mask of all cortical vertices (excluding the midline vertices)
OUTPUT is a string for the basename of your output file
nthreads is an option to use more than one thread for parallelising parts of the process. The default is using a single thread.
This function is used to perform the full brain gradient analysis and the clustered gradient and VB Index. Note that the full brain gradient analysis is considered to be a special case of the clustered analysis.
[ RESULT_EigenValues , RESULT_EigenVectors ]= vb_cluster(DATA, NORM, CORT_INDEX, CLUST_INDEX, OUTPUT, nthreads)
Most variables from this function are identical to the one above. The principal difference is the addition of the CLUST_INDEX. This file defines the clusters / parcellation of the brain. Should one wish to carry out a whole brain gradient analysis, CLUST_INDEX should simply be the same variable as CORT_INDEX (the brain is considered to be one big parcel).