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Hi Sai,

The reference manual for braph2 is already included automatically in the software. If you want to know the properties (e.g., P for *CompareEnsemble* or P1, P2, DIFF for *ComparisonEnsemble*), you can simply type the following commands in the MATLAB command window:

`help CompareEnsemble`

and

`help ComparisonEnsemble`

These commands will show you the description of all the properties related to *CompareEnsemble* and *ComparisonEnsemble* as attached:

In the description, you will find the answers you wanted:

– P (parameter, scalar) is the permutation number.

– DIFF (result, cell) is the ensemble comparison value.

– P1 (result, cell) is the one-tailed p-value.

– P2 (result, cell) is the two-tailed p-value.

– CIL (result, cell) is the lower value of the 95%% confidence interval.

– CIU (result, cell) is the upper value of the 95%% confidence interval.

I also recommend checking our freely available tutorials online that explain how to perform graph and deep learning analysis using braph2. You can access them through this link: http://braph.org/tutorials/pipelines/pipeline-functional-comparison-bud/.

Let me know if you have any further questions.

Best,

Yu-Wei