I did my preprocessing in a third-party software (for resting fMRI) and have obtained an output size of (61, 73, 61; normalized to 3x3x3 vozel dim). Now I would like to know which brain mask (binary, with ones representing voxels falling within the brain and zeros otherwise) I can use to vectorize my data and work in Matlab/Python (to obtain only voxels that fall within the brain). This is, to convert my data from 4D (x space, y space, x, space, time) to 2D (x*y*z, time). Or else, what is the protocol at this stage of the data preprocessing prior analyzing (to which template size is it normally converted and how?).
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