feat: bootstrap sample functional connectivity pipe

src/matlab/builders/configurations/BuildFunctionalConnectivityConfiguration.m

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+function [config] = BuildFunctionalConnectivityConfiguration()
+%BUILDFUNCTIONALCONNECTIVITYCONFIGURATION Builds configuration for a pipeline.
+%   Builds a configuration for a pipeline that performs segmentation.
+%
+%   Input:
+%   - ...
+%
+%   Output:
+%   - config: Configuration.
+
+config = struct();
+
+% get data folder relative to this file
+filePath = fileparts(which(mfilename));
+pathToDataFolder = fullfile(filePath, '../../../../../neurochi/data/');
+pathToWorkspace = fullfile(pathToDataFolder, 'w1');
+pathToDataset = fullfile(pathToDataFolder, 'input');
+% for intermediary pipelines, send output to the transfer folder
+pathToOutput = fullfile(pathToDataFolder, 'transfer');
+
+%% pipeline: segmentation
+% common configuration
+config.verbose = true;
+config.clobber = true;
+config.pathToWorkspace = pathToWorkspace;
+config.pathToDataset = pathToDataset;
+config.pathToOutput = pathToOutput;
+% helps debug by not running all subjects
+config.numSubjects = 1;
+config.parallel = false;
+
+% sequence level configurations
+config.sequence.startStep = 1;
+config.sequence.noCleanUp = true;
+
+% step 1: reorient to standard
+config.step1.optional = false;
+config.step1.skip = false;
+config.step1.clobber = config.clobber;
+config.step1.verbose = config.verbose;
+
+
+end
+

src/matlab/builders/pipelines/BuildFunctionalConnectivityPipeline.m

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+function [pipeline] = BuildFunctionalConnectivityPipeline(pathToWorkspace, ...
+                                                          pathToDataset, ...
+                                                          pathToIntermediaryOutputs, ...
+                                                          pathToOutput, ...
+                                                          numSubjects, ...
+                                                          config)
+%BUILDFUNCTIONALCONNECTIVITYPIPELINE Example of a pipeline builder.
+%   This builder creates a pipeline with one sequence per run per subject, based
+%   on the format of a BIDS dataset's participants.tsv file.
+%
+%   Input:
+%   - pathToWorkspace:  Path to the workspace.
+%   - pathToDataset:    Path to input the root of the BIDS dataset.
+%   - pathToOutput:     Path to where we will output the data.
+%
+%   Output:
+%   - pipeline:  Built pipeline.
+
+arguments
+  pathToWorkspace char = '.'
+  pathToDataset char = '.'
+  pathToIntermediaryOutputs char = '.'
+  pathToOutput char = '.'
+  numSubjects int8 {mustBeNonnegative} = 0
+  config = struct()
+end
+
+% names of inputs needed to start the sequence
+inputs = { ...
+  fullfile(pathToIntermediaryOutputs, ...
+           '{subject}/{subject}_T1w_brain_mul.nii.gz'), ...
+  fullfile(pathToIntermediaryOutputs, ...
+           '{subject}/{subject}_T1w_brain_mask_filled.nii.gz'), ...
+  fullfile(pathToDataset, ...
+           '{subject}/func/{subject}_task-convers_{run}_bold.nii.gz'), ...
+};
+numInputs = length(inputs);
+
+% get information about participants
+subjects = readtable(fullfile(pathToDataset, 'participants.tsv'), ...
+                     'Delimiter', ...
+                     '\t', ...
+                     'FileType', ...
+                     'delimitedtext', ...
+                     'PreserveVariableNames', ...
+                     true);
+
+tableHeight = height(subjects);
+if ~numSubjects
+  numSubjects = tableHeight;
+else
+  numSubjects = min(numSubjects, tableHeight);
+end
+
+% there are four runs per subject
+runs = { 'run-01', 'run-02', 'run-03', 'run-04' };
+numRuns = length(runs);
+sequences = cell(1, numSubjects * numRuns);
+
+% create a sequence for each subject
+for i = 1 : numSubjects
+  % get data for one participant
+  subject = subjects(i, :);
+
+  % participant_id is the column name and it's a cell
+  subjectName = subject.participant_id{1};
+
+  % create an input array for each subject
+  subjectInputs = cell(1, numInputs);
+  for j = 1 : numInputs
+    input = inputs{j};
+
+    % replace subject name
+    subjectInputs{j} = strrep(input, '{subject}', subjectName);
+  end
+
+  % now prepare a sequence for each of the subject's runs
+  for k = 1 : numRuns
+    run = runs{k};
+
+    % sequence index
+    sequenceIdx = (i - 1) * numRuns + k;
+
+    % create an input array for each run sequence
+    runInputs = cell(1, numInputs);
+    for l = 1 : numInputs
+      subjectInput = subjectInputs{l};
+
+      % replace subject name
+      runInputs{l} = strrep(subjectInput, '{run}', run);
+    end
+
+    pathToRunWorkspace = fullfile(pathToWorkspace, subjectName, run);
+    pathToRunOutput = fullfile(pathToOutput, subjectName, run);
+
+    % add to sequences at the right index
+    sequences{sequenceIdx} = BuildFunctionalConnectivitySequence(runInputs, ...
+                                                                 subjectName, ...
+                                                                 run, ...
+                                                                 pathToRunWorkspace, ...
+                                                                 pathToRunOutput, ...
+                                                                 config);
+
+  end
+end
+
+% create a pipeline with the sequences
+parallel = config.parallel;
+pipeline = Pipeline(sequences, parallel);
+
+end

src/matlab/builders/sequences/BuildFunctionalConnectivitySequence.m

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+function [sequence] = BuildFunctionalConnectivitySequence(inputs, ...
+                                                          subjectName, ...
+                                                          run, ...
+                                                          pathToWorkspace, ...
+                                                          pathToOutput, ...
+                                                          config)
+%BUILDFUNCTIONALCONNECTIVITYSEQUENCE Example of a sequence builder.
+%   This builder creates the typical sequence to generate functional
+%   connectomes.
+%
+%   Input:
+%   - inputs:           Inputs that will be copied into the workspace.
+%   - pathToWorkspace:  Path to the sequence's workspace.
+%   - pathToOutput:     Path to where we will output the data.
+%
+%   Output:
+%   - sequence:  Built sequence.
+
+%% step 1
+% reorient to standard
+step1Params = struct();
+step1Config = config.step1;
+step1Params.inputVolume = sprintf('%s_task-convers_%s_bold.nii.gz', ...
+                                  subjectName, ...
+                                  run);
+step1Params.outputVolume = sprintf('%s_task-convers_%s_bold_std.nii.gz', ...
+                                   subjectName, ...
+                                   run);
+deps1 = { step1Params.inputVolume };
+outputs1 = { step1Params.outputVolume };
+step1 = Step(@ReorientToStandard, ...
+             step1Params, ...
+             deps1, ...
+             step1Config, ...
+             outputs1);
+
+
+
+%% prepare the sequence
+% set up steps in order
+steps = { step1 };
+
+% these files will be copied from the workspace to the output path
+outputs = { step1Params.outputVolume };
+
+sequence = Sequence(steps, ...
+                    inputs, ...
+                    outputs, ...
+                    pathToWorkspace, ...
+                    pathToOutput, ...
+                    config.sequence);
+
+end
+

src/matlab/scripts/functionalConnectivityScript.m

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+% ensure variables are cleared
+clearvars;
+
+% ensure src/matlab and subfolders are in the path
+filePath = fileparts(which(mfilename));
+addpath(genpath(fullfile(filePath, '../../matlab')));
+
+% build configuration
+config = BuildFunctionalConnectivityConfiguration();
+
+pipeline = BuildFunctionalConnectivityPipeline(config.pathToWorkspace, ...
+                                               config.pathToDataset, ...
+                                               config.pathToOutput, ...
+                                               config.pathToOutput, ...
+                                               config.numSubjects, ...
+                                               config);
+
+pipelineExecution = pipeline.run();
+