Thanks for your input Francois I appreciate it!
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As per your suggestion I've included the block that loads all the input files into AllMat to the "SAVE THE RESULTS" section within the "for" loop for grouping. As I included the AllMat within the "for" loop for grouping I did NOT change AllMat(: , : , i) into AllMat(:, :, iGroups(i)).
I hope what I'm showing here is correct.
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As per your suggestion I've used GetOutputStudy and changed line 132 from:
OutputFiles{1} = bst_process('GetNewFilename', fileparts(sInputs(1).FileName), 'data_WAvg');
to
OutputFiles{1} = bst_process('GetOutputStudy', sProcess, sInputs(iGroups(i)), 'data_WAvg');
However, I then get an error message saying that "Index exceeds the number of array elements. Index must not exceed 4."
So I then went through "bst_process.m" and discovered that 'GetOutputStudy' only requires 3 inputs:
[sStudy, iStudy, Comment, uniqueDataFile] = GetOutputStudy(sProcess, [sInputA, sInputB], sOutput.Condition);
Is this why I am getting the error message? How do I solve this issue?