Assuming the nifti toolbox is in Matlab path, we can get the 91x109x91 mask to have the same dimensions as the normalized images generated with bounding boxes.
If we are making a mask for hippocampus, first we save that mask from WFU Pickatlas. Then to make it 79x95x68 voxels, run the following small script.
x=x.img;xdim=[1:6 86:91]; ydim=[1:6 102:109]; zdim=[1:11 80:91];
origin=[40 57 26]; datatype=16;
x(xdim,:,:)=; x(:,ydim,:)=; x(:,:,zdim)=;
nii=make_nii(x, [2 2 2], origin, datatype);
We can then use these masks for signal extraction or any further processing.