dev_pipeline

Adapt a Pipeline Script

This is the developer tutorial for adapting a pipeline script. In this tutorial, you will learn how to edit a "*.braph2" file to change the steps of a pipeline. Here, you will use as an example the pipeline Pipeline Structural Multiplex Comparison BUD in the file "pipeline_structural_multiplex_comparison_bud.braph2" (the pipeline for comparing two groups of subjects using structural multiplex data and binary undirected graphs at fixed densities) and adapt it in order to add a third group for structural multiplex.

Table of Contents

Adaption of the pipeline

Adaption of the pipeline ⬆

You will adapt in Pipeline Structural Multiplex Comparison BUD in the file "pipeline_structural_multiplex_comparison_bud.braph2" as shown in Code 1. The changes are highlighted in the comments.

Code 1. Adapted pipeline to compare three groups of subjects using structural multiplex data and binary undirected graphs at fixed densities.

%% Pipeline Structural Multiplex Comparison BUD  ①

% This is the pipeline script to compare two groups of subjects using structural multiplex data and binary undirected graphs at fixed densities.  ②
% 1. It loads a brain atlas from an XLS file (e.g., desikan_atlas.xlsx).
% 2. It loads the data of two groups of subjects from two directories (e.g., ST_MP_group_1_XLS and ST_MP_group_2_XLS).
% 3. It analyzes the first group using structural multiplex analyses (ST_MP) based on binary unidrected graphs at fixed densities (BUD).
% 4. It analyzes the second group using the same parameters selected for the first group.
% 5. It compares the results of the two analyses.

% PDF: /tutorials/pipelines/tut_a_mp_st_bud/tut_a_mp_st_bud.pdf  ③
% README: /tutorials/pipelines/tut_a_mp_st_bud/readme.md

%% Brain Atlas
ba = ImporterBrainAtlasXLS('WAITBAR', true).get('GET_FILE').get('BA');  ④

%% Groups
gr1 = ImporterGroupSubjectST_MP_XLS('BA', ba, 'WAITBAR', true).get('GET_DIR').get('GR');  ⑤
gr2 = ImporterGroupSubjectST_MP_XLS('BA', ba, 'WAITBAR', true).get('GET_DIR').get('GR');  ⑥
gr3 = ImporterGroupSubjectST_MP_XLS('BA', ba, 'WAITBAR', true).get('GET_DIR').get('GR');  ⑦

%% Analysis 1
a_BUD1 = AnalyzeGroup_ST_MP_BUD('GR', gr1, 'DENSITIES', [10 20 30 40 50]);  ⑧

%% Analysis 2
a_BUD2 = AnalyzeGroup_ST_MP_BUD('GR', gr2, 'TEMPLATE', a_BUD1);  ⑨

%% Analysis 3
a_BUD3 = AnalyzeGroup_ST_MP_BUD('GR', gr3, 'TEMPLATE', a_BUD1);  ⑩

%% Comparison
c_BUD1 = CompareGroup('P', 1000, 'A1', a_BUD1, 'A2', a_BUD2, 'MEMORIZE', true);  ⑩
c_BUD2 = CompareGroup('P', 1000, 'A1', a_BUD1, 'A3', a_BUD3, 'MEMORIZE', true);  ⑫
c_BUD3 = CompareGroup('P', 1000, 'A2', a_BUD2, 'A3', a_BUD3, 'MEMORIZE', true);  ⑬

① specifies the name of the pipeline. The name is changed to avoid conflicts.

② provides descriptions for the overall pipeline as well as for each step. This is updated to reflect the updated pipeline.

③ provides the relative file paths for this pipeline’s tutorial, including both the PDF and README versions

④ loads the brain atlas.

⑤ loads group 1 from XLS.

⑥ loads group 2 from XLS.

⑦ loads group 3 from XLS. This is added.

⑧ performs the graph analysis for group 1. The default value of 'DENSITIES' is set to [10 20 30 40 50].

⑨ performs the graph analysis for group 2 with the same analysis template as with group 1.

⑩ performs the graph analysis for group 3 with the same analysis template as with group 1. This is added.

⑩ compares graph measures between groups 1 group 2. The default value of the number of permutations is 'P' set to 1000.

⑫ compares graph measures between groups 1 and 3. This is added.

⑬ compares graph measures between groups 2 and 3. This is added.