protocol creator

scripts-01-protocolcreator/Main_Behav_D12.m

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+clear, clc;
+
+outputFolder = fullfile('..','data','prt');
+
+%% PRT Parameters
+PRTParameters = struct();
+
+PRTParameters.FileVersion = 2;
+PRTParameters.Resolution = 'Volumes';
+PRTParameters.ExperimentName = 'VisualPerception_CrossInhibition';
+PRTParameters.BackgroundColor = [0 0 0];
+PRTParameters.TextColor = [255 255 255];
+PRTParameters.TimeCourseColor = [1 1 1];
+PRTParameters.TimeCourseThick = 3;
+PRTParameters.ReferenceFuncColor = [0 0 80];
+PRTParameters.ReferenceFuncThick = 2;
+
+%% PRT Conditions
+condNames = {'Static','Coherent','Incoherent','NonAdapt','Ambiguous_aCoh','Ambiguous_aInCoh','Ambiguous_aNA','MAE'};
+
+blockDuration = [ 6 12 12 12 6 6 6 3 ]; %in volumes (think TR = 1000ms)
+
+blockColor = [170 170 170 ; 150 210 240 ; 150 170 200 ; 150 130 160 ; ...
+                            200 170 100 ; 200 170 120 ; 200 170 140 ; ...
+                            120 120 120];
+
+PRTParameters.nCond = length(condNames);
+
+PRTConditions = struct();
+
+for c = 1:PRTParameters.nCond
+
+    PRTConditions.(condNames{c}).Color = blockColor(c,:);
+    PRTConditions.(condNames{c}).BlockDuration = blockDuration(c);
+    PRTConditions.(condNames{c}).Intervals = [];
+    PRTConditions.(condNames{c}).NumBlocks = 0;
+
+end
+
+%% Run Behav D12 R1
+%SEQ = [ 1 2 5 6 1 3 5 6 1 4 5 6 1 2 5 6 1 3 5 6 1 4 5 6 1 2 5 6 1 3 5 6 1 4 5 6 1 2 5 6 1 3 5 6 1 4 5 6];
+SEQ = [ 1 2 5 8 1 3 6 8 1 4 7 8 1 2 5 8 1 3 6 8 1 4 7 8 1 2 5 8 1 3 6 8 1 4 7 8 1 2 5 8 1 3 6 8 1 4 7 8 ];
+
+[ PRTConditions_R1 ] = buildIntervals( SEQ , PRTConditions );
+
+generatePRT( PRTParameters , PRTConditions_R1 , 'RunBehav_D12_R1' , outputFolder );
+
+%% Run Behav D12 R2
+%SEQ = [ 1 2 5 6 1 4 5 6 1 3 5 6 1 2 5 6 1 4 5 6 1 3 5 6 1 2 5 6 1 4 5 6 1 3 5 6 1 2 5 6 1 4 5 6 1 3 5 6 ];
+SEQ = [ 1 2 5 8 1 4 7 8 1 3 6 8 1 2 5 8 1 4 7 8 1 3 6 8 1 2 5 8 1 4 7 8 1 3 6 8 1 2 5 8 1 4 7 8 1 3 6 8 ];
+
+[ PRTConditions_R2 ] = buildIntervals( SEQ , PRTConditions );
+
+generatePRT( PRTParameters , PRTConditions_R2 , 'RunBehav_D12_R2' , outputFolder );
+
+%% Run Behav D12 R3
+%SEQ = [ 1 3 5 6 1 4 5 6 1 2 5 6 1 3 5 6 1 4 5 6 1 2 5 6 1 3 5 6 1 4 5 6 1 2 5 6 1 3 5 6 1 4 5 6 1 2 5 6 ];
+SEQ = [ 1 3 6 8 1 4 7 8 1 2 5 8 1 3 6 8 1 4 7 8 1 2 5 8 1 3 6 8 1 4 7 8 1 2 5 8 1 3 6 8 1 4 7 8 1 2 5 8 ];
+
+[ PRTConditions_R3 ] = buildIntervals( SEQ , PRTConditions );
+
+generatePRT( PRTParameters , PRTConditions_R3 , 'RunBehav_D12_R3' , outputFolder );

scripts-01-protocolcreator/Main_Behav_D6.m

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+clear, clc;
+
+outputFolder = fullfile('..','data','prt');
+
+%% PRT Parameters
+PRTParameters = struct();
+
+PRTParameters.FileVersion = 2;
+PRTParameters.Resolution = 'Volumes';
+PRTParameters.ExperimentName = 'VisualPerception_CrossInhibition';
+PRTParameters.BackgroundColor = [0 0 0];
+PRTParameters.TextColor = [255 255 255];
+PRTParameters.TimeCourseColor = [1 1 1];
+PRTParameters.TimeCourseThick = 3;
+PRTParameters.ReferenceFuncColor = [0 0 80];
+PRTParameters.ReferenceFuncThick = 2;
+
+%% PRT Conditions
+condNames = {'Static','Coherent','Incoherent','NonAdapt','Ambiguous_aCoh','Ambiguous_aInCoh','Ambiguous_aNA','MAE'};
+
+blockDuration = [ 6 6 6 6 6 6 6 3 ]; %in volumes (think TR = 1000ms)
+
+blockColor = [170 170 170 ; 150 210 240 ; 150 170 200 ; 150 130 160 ; ...
+                            200 170 100 ; 200 170 120 ; 200 170 140 ; ...
+                            120 120 120];
+
+PRTParameters.nCond = length(condNames);
+
+PRTConditions = struct();
+
+for c = 1:PRTParameters.nCond
+
+    PRTConditions.(condNames{c}).Color = blockColor(c,:);
+    PRTConditions.(condNames{c}).BlockDuration = blockDuration(c);
+    PRTConditions.(condNames{c}).Intervals = [];
+    PRTConditions.(condNames{c}).NumBlocks = 0;
+
+end
+
+%% Run Behav D6 R1
+%SEQ = [ 1 2 5 6 1 3 5 6 1 4 5 6 1 2 5 6 1 3 5 6 1 4 5 6 1 2 5 6 1 3 5 6 1 4 5 6 1 2 5 6 1 3 5 6 1 4 5 6];
+SEQ = [ 1 2 5 8 1 3 6 8 1 4 7 8 1 2 5 8 1 3 6 8 1 4 7 8 1 2 5 8 1 3 6 8 1 4 7 8 1 2 5 8 1 3 6 8 1 4 7 8];
+
+[ PRTConditions_R1 ] = buildIntervals( SEQ , PRTConditions );
+
+generatePRT( PRTParameters , PRTConditions_R1 , 'RunBehav_D6_R1' , outputFolder );
+
+%% Run Behav D6 R2
+%SEQ = [ 1 2 5 6 1 4 5 6 1 3 5 6 1 2 5 6 1 4 5 6 1 3 5 6 1 2 5 6 1 4 5 6 1 3 5 6 1 2 5 6 1 4 5 6 1 3 5 6 ];
+SEQ = [ 1 2 5 8 1 4 7 8 1 3 6 8 1 2 5 8 1 4 7 8 1 3 6 8 1 2 5 8 1 4 7 8 1 3 6 8 1 2 5 8 1 4 7 8 1 3 6 8 ];
+
+[ PRTConditions_R2 ] = buildIntervals( SEQ , PRTConditions );
+
+generatePRT( PRTParameters , PRTConditions_R2 , 'RunBehav_D6_R2' , outputFolder );
+
+%% Run Behav D6 R3
+%SEQ = [ 1 3 5 6 1 4 5 6 1 2 5 6 1 3 5 6 1 4 5 6 1 2 5 6 1 3 5 6 1 4 5 6 1 2 5 6 1 3 5 6 1 4 5 6 1 2 5 6 ];
+SEQ = [ 1 3 6 8 1 4 7 8 1 2 5 8 1 3 6 8 1 4 7 8 1 2 5 8 1 3 6 8 1 4 7 8 1 2 5 8 1 3 6 8 1 4 7 8 1 2 5 8 ];
+
+[ PRTConditions_R3 ] = buildIntervals( SEQ , PRTConditions );
+
+generatePRT( PRTParameters , PRTConditions_R3 , 'RunBehav_D6_R3' , outputFolder );

scripts-01-protocolcreator/Main_MRI_D12.m

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+clear, clc;
+
+outputFolder = fullfile('..','data','prt');
+
+%% PRT Parameters
+PRTParameters = struct();
+
+PRTParameters.FileVersion = 2;
+PRTParameters.Resolution = 'Volumes';
+PRTParameters.ExperimentName = 'VisualPerception_CrossInhibition';
+PRTParameters.BackgroundColor = [0 0 0];
+PRTParameters.TextColor = [255 255 255];
+PRTParameters.TimeCourseColor = [1 1 1];
+PRTParameters.TimeCourseThick = 3;
+PRTParameters.ReferenceFuncColor = [0 0 80];
+PRTParameters.ReferenceFuncThick = 2;
+
+%% PRT Conditions
+condNames = {'Static','Coherent','Incoherent','NonAdapt',...
+    'Coh_aCoh','Coh_aInCoh','Coh_aNA',...
+    'InCoh_aCoh','InCoh_aInCoh','InCoh_aNA',...
+    'MAE','Report','Discard'};
+
+blockDuration = [ 6 12 12 12 6 6 6 6 6 6 3 3 4 ]; %in volumes (think TR = 1000ms)
+
+blockColor = [170 170 170 ; 0 115 190 ; 216 83 25 ; 236 177 32 ; ...
+                            110 115 190 ; 150 83 25 ; 190 177 32 ; ...
+                            150 115 190 ; 100 83 25 ; 120 177 32 ; ...
+                            120 160 120; 120 220 120; 50 50 50];
+
+PRTParameters.nCond = length(condNames);
+
+PRTConditions = struct();
+
+for c = 1:PRTParameters.nCond
+
+    PRTConditions.(condNames{c}).Color = blockColor(c,:);
+    PRTConditions.(condNames{c}).BlockDuration = blockDuration(c);
+    PRTConditions.(condNames{c}).Intervals = [];
+    PRTConditions.(condNames{c}).NumBlocks = 0;
+
+end
+
+%% Trials
+trials = [ 1 2 5 11 12 ;
+           1 2 8 11 12 ;
+           1 3 6 11 12 ;
+           1 3 9 11 12 ;
+           1 4 7 11 12 ;
+           1 4 10 11 12 ];
+
+%% Run MRI D12 R1
+SEQ = [13 reshape(trials([1 3 2 6 5 4 1 3 2 6 5 4],:)',1,60) 1 13];
+
+[ PRTConditions_R1 ] = buildIntervals( SEQ , PRTConditions );
+
+generatePRT( PRTParameters , PRTConditions_R1 , 'RunMRI_D12_R1' , outputFolder );
+
+%% Run MRI D12 R2
+SEQ = [13 reshape(trials([1 3 5 2 4 6 1 3 5 2 4 6],:)',1,60) 1 13];
+
+[ PRTConditions_R2 ] = buildIntervals( SEQ , PRTConditions );
+
+generatePRT( PRTParameters , PRTConditions_R2 , 'RunMRI_D12_R2' , outputFolder );
+
+%% Run MRI D12 R3
+SEQ = [13 reshape(trials([5 3 1 6 4 2 5 3 1 6 4 2],:)',1,60) 1 13];
+
+[ PRTConditions_R3 ] = buildIntervals( SEQ , PRTConditions );
+
+generatePRT( PRTParameters , PRTConditions_R3 , 'RunMRI_D12_R3' , outputFolder );
+
+%% Run MRI D12 R4
+SEQ = [13 reshape(trials([4 5 6 2 3 1 4 5 6 2 3 1],:)',1,60) 1 13];
+
+[ PRTConditions_R4 ] = buildIntervals( SEQ , PRTConditions );
+
+generatePRT( PRTParameters , PRTConditions_R4 , 'RunMRI_D12_R4' , outputFolder );
+
+%% Run MRI D12 R5
+SEQ = [13 reshape(trials([1 6 2 5 3 4 1 6 2 5 3 4],:)',1,60) 1 13];
+
+[ PRTConditions_R5 ] = buildIntervals( SEQ , PRTConditions );
+
+generatePRT( PRTParameters , PRTConditions_R5 , 'RunMRI_D12_R5' , outputFolder );
+
+%% Run MRI D12 R6
+SEQ = [13 reshape(trials([6 1 5 2 4 3 6 1 5 2 4 3],:)',1,60) 1 13];
+
+[ PRTConditions_R6 ] = buildIntervals( SEQ , PRTConditions );
+
+generatePRT( PRTParameters , PRTConditions_R6 , 'RunMRI_D12_R6' , outputFolder );

scripts-01-protocolcreator/README.md

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+# scripts-01-protocolcreator
+Scripts for generating the protocol files for the Inhibition experiment. These files are in BrainVoyager format (.prt).
+
+## Files:
+- `Main_Behav_D6.m`: generate the protocol files for the behavioral runs with adaptation duration of 6 seconds.
+- `Main_Behav_D12.m`: generate the protocol files for the behavioral runs with adaptation duration of 12 seconds.
+- `Main_MRI_D12.m`: generate the protocol files for the MRI runs with adaptation duration of 12 seconds.

scripts-01-protocolcreator/buildIntervals.m

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+function [ PRTConditions ] = buildIntervals( Sequence , PRTConditions )
+
+condNames = fieldnames(PRTConditions);
+currentTime = 0;
+
+for t = 1:length(Sequence)
+
+    PRTConditions.(condNames{Sequence(t)}).Intervals = ...
+        [PRTConditions.(condNames{Sequence(t)}).Intervals ; ...
+        currentTime+1 currentTime+PRTConditions.(condNames{Sequence(t)}).BlockDuration];
+
+    PRTConditions.(condNames{Sequence(t)}).NumBlocks = PRTConditions.(condNames{Sequence(t)}).NumBlocks + 1;
+
+    currentTime = currentTime+PRTConditions.(condNames{Sequence(t)}).BlockDuration;
+
+end
+
+end

scripts-01-protocolcreator/generatePRT.m

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+function [  ] = generatePRT( PRTParameters , PRTConditions , runName , outputFolder )
+
+%outputFolder = fullfile(pwd,'PRTs_AF');
+
+if ~exist(outputFolder,'dir')
+    mkdir(outputFolder);
+end
+
+outputFileName = [ runName '.prt'];
+
+% --- Create new file using parameters
+
+prtFile = fopen( fullfile(outputFolder,outputFileName) , 'wt' );
+
+% delimiter tab
+del = char(9);
+
+% --- FILE HEADER
+fprintf(prtFile, '\n');
+fprintf(prtFile, 'FileVersion:%s%s%i \n\n', del, del, PRTParameters.FileVersion);
+fprintf(prtFile, 'ResolutionOfTime:%s%s \n\n', del, PRTParameters.Resolution);
+fprintf(prtFile, 'Experiment:%s%s%s%s \n\n', del, del, del, PRTParameters.ExperimentName);
+fprintf(prtFile, 'BackgroundColor:%s%s \n', del, num2str(PRTParameters.BackgroundColor));
+fprintf(prtFile, 'TextColor:%s%s%s%s \n\n', del, del, del, num2str(PRTParameters.TextColor));
+fprintf(prtFile, 'TimeCourseColor:%s%s \n', del, num2str(PRTParameters.TimeCourseColor));
+fprintf(prtFile, 'TimeCourseThick:%s%i \n', del, PRTParameters.TimeCourseThick);
+fprintf(prtFile, 'ReferenceFuncColor:%s%s \n', del, num2str(PRTParameters.ReferenceFuncColor));
+fprintf(prtFile, 'ReferenceFuncThick:%s%i \n\n', del, PRTParameters.ReferenceFuncThick);
+fprintf(prtFile, 'NrOfConditions:%s%s%i \n \n', del, del, PRTParameters.nCond);
+
+% -- Conditions
+condNames = fieldnames(PRTConditions);
+
+for c = 1:PRTParameters.nCond
+
+    % Write the name of the condition
+    fprintf(prtFile, '%s \n', condNames{c});
+
+    % Write the number of blocks
+    fprintf(prtFile, '%i \n', PRTConditions.(condNames{c}).NumBlocks);
+
+    for i = 1:size(PRTConditions.(condNames{c}).Intervals,1)
+
+        % Write to file
+        fprintf(prtFile, '%i%s%i \n', PRTConditions.(condNames{c}).Intervals(i,1), del, PRTConditions.(condNames{c}).Intervals(i,2));
+
+    end
+
+    % Write condition color
+    fprintf(prtFile, 'Color:%s%i %i %i \n', del, PRTConditions.(condNames{c}).Color);
+
+    fprintf(prtFile, '\n');
+
+end
+
+fclose(prtFile);
+
+fprintf('[generatePRT] %s file exported.\n',outputFileName);
+
+end