[DOC] Add demo for efficiency (#1204)

* start efficiency demo * add efficiency demo * update design * add randomization
cpp-lln-lab · Feb 19, 2024 · 6079826 · 6079826
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diff --git a/demos/efficiency/demo_efficiency.m b/demos/efficiency/demo_efficiency.m
@@ -0,0 +1,106 @@
+% (C) Copyright 2023 bidspm developers
+
+% Example to compute efficiency from
+% https://www.nature.com/articles/s41598-024-52967-8
+%
+% Related to this thread:
+% https://twitter.com/m_wall/status/1757311725777387739
+
+clear;
+clc;
+close all;
+
+addpath(fullfile(pwd, '..', '..'));
+bidspm();
+
+conditions = {'alcohol', 'neutral', 'negative', 'positive'};
+for i = 1:numel(conditions)
+  design_matrix{i} = ['trial_type.' conditions{i}];
+end
+
+%% create stats model JSON
+bm = BidsModel();
+NodeIdx = 1;
+
+% high pass filter
+bm.Nodes{NodeIdx}.Model.Options.HighPassFilterCutoffHz = 1 / 128;
+
+for i = 1:numel(conditions)
+  bm.Nodes{NodeIdx}.Model.X = design_matrix;
+end
+
+% contrast for each condition against baseline
+bm.Nodes{NodeIdx}.DummyContrasts = struct('type', 't', ...
+                                          'Contrasts', {design_matrix});
+
+% contrast of interests
+% alcohol > neural
+% negative > neutral
+% positive > neutral
+conditions_to_check = {'alcohol', 'negative', 'positive'};
+for i = 1:numel(conditions_to_check)
+  contrast = struct('Test', 't', ...
+                    'Name', [conditions_to_check{i} '_gt_neutral'], ...
+                    'Weights', [1, -1], ...
+                    'ConditionList', {{['trial_type.' conditions_to_check{i}], 'trial_type.neutral'}});
+  bm.Nodes{NodeIdx}.Contrasts{i} = contrast;
+end
+
+bm.write('smdl.json');
+
+%% create events TSV file
+IBI = 25;
+ISI = 0;
+stimDuration = 4;
+stimPerBlock = 5;
+nbBlocks = 8;
+
+TR = 1;
+
+randomize = true;
+
+trial_type = {};
+onset = [];
+duration = [];
+
+time = 0;
+
+for iBlock = 1:nbBlocks
+
+  condition_order = 1:4;
+  if randomize
+    condition_order = randperm(4);
+  end
+
+  for i = 1:numel(conditions)
+
+    condition_idx = condition_order(i);
+
+    for iTrial = 1:stimPerBlock
+      trial_type{end + 1} = conditions{condition_idx}; %#ok<*SAGROW>
+      onset(end + 1) = time;
+      duration(end + 1) = stimDuration;
+      time = time + stimDuration + ISI;
+    end
+
+    time = time + IBI;
+
+  end
+end
+
+tsv = struct('trial_type',  {trial_type}, 'onset', onset, 'duration', duration');
+
+bids.util.tsvwrite('events.tsv', tsv);
+
+opt.TR = TR;
+
+opt.model.file = fullfile(pwd, 'smdl.json');
+
+[e, X] = computeDesignEfficiency(fullfile(pwd, 'events.tsv'), opt);
+
+%%
+% saveas(gcf(), 'design_matrix.png');
+% close(gcf());
+%
+% saveas(gcf(), 'events.png');
+% close(gcf());
diff --git a/demos/efficiency/events.tsv b/demos/efficiency/events.tsv
@@ -0,0 +1,161 @@
+trial_type	onset	duration
+neutral	0	4
+neutral	4	4
+neutral	8	4
+neutral	12	4
+neutral	16	4
+positive	45	4
+positive	49	4
+positive	53	4
+positive	57	4
+positive	61	4
+negative	90	4
+negative	94	4
+negative	98	4
+negative	102	4
+negative	106	4
+alcohol	135	4
+alcohol	139	4
+alcohol	143	4
+alcohol	147	4
+alcohol	151	4
+positive	180	4
+positive	184	4
+positive	188	4
+positive	192	4
+positive	196	4
+negative	225	4
+negative	229	4
+negative	233	4
+negative	237	4
+negative	241	4
+neutral	270	4
+neutral	274	4
+neutral	278	4
+neutral	282	4
+neutral	286	4
+alcohol	315	4
+alcohol	319	4
+alcohol	323	4
+alcohol	327	4
+alcohol	331	4
+neutral	360	4
+neutral	364	4
+neutral	368	4
+neutral	372	4
+neutral	376	4
+negative	405	4
+negative	409	4
+negative	413	4
+negative	417	4
+negative	421	4
+positive	450	4
+positive	454	4
+positive	458	4
+positive	462	4
+positive	466	4
+alcohol	495	4
+alcohol	499	4
+alcohol	503	4
+alcohol	507	4
+alcohol	511	4
+negative	540	4
+negative	544	4
+negative	548	4
+negative	552	4
+negative	556	4
+positive	585	4
+positive	589	4
+positive	593	4
+positive	597	4
+positive	601	4
+neutral	630	4
+neutral	634	4
+neutral	638	4
+neutral	642	4
+neutral	646	4
+alcohol	675	4
+alcohol	679	4
+alcohol	683	4
+alcohol	687	4
+alcohol	691	4
+negative	720	4
+negative	724	4
+negative	728	4
+negative	732	4
+negative	736	4
+positive	765	4
+positive	769	4
+positive	773	4
+positive	777	4
+positive	781	4
+neutral	810	4
+neutral	814	4
+neutral	818	4
+neutral	822	4
+neutral	826	4
+alcohol	855	4
+alcohol	859	4
+alcohol	863	4
+alcohol	867	4
+alcohol	871	4
+positive	900	4
+positive	904	4
+positive	908	4
+positive	912	4
+positive	916	4
+alcohol	945	4
+alcohol	949	4
+alcohol	953	4
+alcohol	957	4
+alcohol	961	4
+neutral	990	4
+neutral	994	4
+neutral	998	4
+neutral	1002	4
+neutral	1006	4
+negative	1035	4
+negative	1039	4
+negative	1043	4
+negative	1047	4
+negative	1051	4
+alcohol	1080	4
+alcohol	1084	4
+alcohol	1088	4
+alcohol	1092	4
+alcohol	1096	4
+negative	1125	4
+negative	1129	4
+negative	1133	4
+negative	1137	4
+negative	1141	4
+neutral	1170	4
+neutral	1174	4
+neutral	1178	4
+neutral	1182	4
+neutral	1186	4
+positive	1215	4
+positive	1219	4
+positive	1223	4
+positive	1227	4
+positive	1231	4
+negative	1260	4
+negative	1264	4
+negative	1268	4
+negative	1272	4
+negative	1276	4
+neutral	1305	4
+neutral	1309	4
+neutral	1313	4
+neutral	1317	4
+neutral	1321	4
+alcohol	1350	4
+alcohol	1354	4
+alcohol	1358	4
+alcohol	1362	4
+alcohol	1366	4
+positive	1395	4
+positive	1399	4
+positive	1403	4
+positive	1407	4
+positive	1411	4
diff --git a/demos/efficiency/smdl.json b/demos/efficiency/smdl.json
@@ -0,0 +1,105 @@
+{
+  "Name": "empty_model",
+  "BIDSModelVersion": "1.0.0",
+  "Description": "This is an empty BIDS stats model.",
+  "Input": {
+    "task": [
+      ""
+    ]
+  },
+  "Nodes": [
+    {
+      "Level": "Run",
+      "Name": "run",
+      "GroupBy": [
+        ""
+      ],
+      "Transformations": {
+        "Transformer": "",
+        "Instructions": [
+          {
+            "Name": "",
+            "Inputs": [
+              ""
+            ]
+          }
+        ]
+      },
+      "Model": {
+        "X": [
+          "trial_type.alcohol",
+          "trial_type.neutral",
+          "trial_type.negative",
+          "trial_type.positive"
+        ],
+        "Type": "glm",
+        "HRF": {
+          "Variables": [
+            ""
+          ],
+          "Model": "DoubleGamma"
+        },
+        "Options": {
+          "HighPassFilterCutoffHz": 0.0078125,
+          "Mask": {
+            "desc": [
+              "brain"
+            ],
+            "suffix": [
+              "mask"
+            ]
+          }
+        },
+        "Software": []
+      },
+      "Contrasts": [
+        {
+          "Test": "t",
+          "Name": "alcohol_gt_neutral",
+          "Weights": [
+            1,
+            -1
+          ],
+          "ConditionList": [
+            "trial_type.alcohol",
+            "trial_type.neutral"
+          ]
+        },
+        {
+          "Test": "t",
+          "Name": "negative_gt_neutral",
+          "Weights": [
+            1,
+            -1
+          ],
+          "ConditionList": [
+            "trial_type.negative",
+            "trial_type.neutral"
+          ]
+        },
+        {
+          "Test": "t",
+          "Name": "positive_gt_neutral",
+          "Weights": [
+            1,
+            -1
+          ],
+          "ConditionList": [
+            "trial_type.positive",
+            "trial_type.neutral"
+          ]
+        }
+      ],
+      "DummyContrasts": {
+        "type": "t",
+        "Contrasts": [
+          "trial_type.alcohol",
+          "trial_type.neutral",
+          "trial_type.negative",
+          "trial_type.positive"
+        ]
+      }
+    }
+  ],
+  "Edges": []
+}