Simple answer: Read the doc for anova2. There are examples which you can use to understand "how" to use anova2. Also, the doc can be also helpful.
So, what are SumAbsJtCbnMeanAST, SumAbsJtMtpMeanAST, SumAbsJtAnkMeanAST, SumAbsJtKneMeanAST, SumAbsJtHipMeanAST?
Without background information, no one can understand what you need but can only assume. With random values with random size, the code runs. What's your question?
SumAbsJtCbnMeanAST = rand(33,5,5);
SumAbsJtMtpMeanAST = rand(33,5,5);
SumAbsJtAnkMeanAST = rand(33,5,5);
SumAbsJtKneMeanAST = rand(33,5,5);
SumAbsJtHipMeanAST = rand(33,5,5);
% anova2
[pJtASTAnova2(1,:), ~] = anova2(...
[SumAbsJtCbnMeanAST(:,2:5,5)-SumAbsJtCbnMeanAST(:,1,5); ...
SumAbsJtCbnMeanAST(:,2:5,1)-SumAbsJtCbnMeanAST(:,1,1)], 11, "off" );
[pJtASTAnova2(2,:), ~] = anova2(...
[SumAbsJtMtpMeanAST(:,2:5,5)-SumAbsJtMtpMeanAST(:,1,5); ...
SumAbsJtMtpMeanAST(:,2:5,1)-SumAbsJtMtpMeanAST(:,1,1)], 11, "off" );
[pJtASTAnova2(3,:), ~] = anova2(...
[SumAbsJtAnkMeanAST(:,2:5,5)-SumAbsJtAnkMeanAST(:,1,5); ...
SumAbsJtAnkMeanAST(:,2:5,1)-SumAbsJtAnkMeanAST(:,1,1)], 11, "off" );
[pJtASTAnova2(4,:), ~] = anova2(...
[SumAbsJtKneMeanAST(:,2:5,5)-SumAbsJtKneMeanAST(:,1,5); ...
SumAbsJtKneMeanAST(:,2:5,1)-SumAbsJtKneMeanAST(:,1,1)], 11, "off" );
[pJtASTAnova2(5,:), ~] = anova2(...
[SumAbsJtHipMeanAST(:,2:5,5)-SumAbsJtHipMeanAST(:,1,5); ...
SumAbsJtHipMeanAST(:,2:5,1)-SumAbsJtHipMeanAST(:,1,1)], 11, "off" );
display(pJtASTAnova2)
