Here's one way
temp = vertcat(originalData{:});
D = repmat({zeros(3,27)},1,1000); % preallocate
for ii = 1:1000
D{ii} = reshape(temp(:,ii),3,27);
end
The approach takes the first column from each matrix in the 1x27 input cell array and concatenates the them making a 3x27 matrix for the first cell of the output; then continues to the second input columns for the second cell in the output, and so on and so forth.
EDIT
You could use splitapply as follows:
D = splitapply(@(x) {reshape(x,3,27)}, vertcat(originalData{:}), 1:1000);
Actually, much simpler is not orgainsing the data into cells in the first place - you can have a 3 by 27 by 1000 matrix and this is just easier to work on in the long run:
D = reshape(vertcat(originalData{:}),3,27,1000);
