Add 3 setbatches for lesion detection

src/batches/setBatchLesionAbnormalitiesDetection.m

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+%-----------------------------------------------------------------------
+% Job saved on 08-Mar-2021 12:47:16 by cfg_util (rev $Rev: 7345 $)
+% spm SPM - SPM12 (7771)
+% cfg_basicio BasicIO - Unknown
+%-----------------------------------------------------------------------
+matlabbatch{1}.spm.tools.ali.outliers_detection.step3tissue.step3patients = '<UNDEFINED>';
+matlabbatch{1}.spm.tools.ali.outliers_detection.step3tissue.step3controls = '<UNDEFINED>';
+matlabbatch{1}.spm.tools.ali.outliers_detection.step3tissue.step3Alpha = 0.5;
+matlabbatch{1}.spm.tools.ali.outliers_detection.step3tissue.step3Lambda = -4;
+spmDir = spm('dir');
+lesionMask = fullfile(spmDir, 'toolbox', 'ALI', 'Mask_image', 'mask_controls_vox2mm.nii');
+matlabbatch{1}.spm.tools.ali.outliers_detection.step3mask_thr = 0;
+matlabbatch{1}.spm.tools.ali.outliers_detection.step3binary_thr = 0.3;
+matlabbatch{1}.spm.tools.ali.outliers_detection.step3binary_size = 0.8;

src/batches/setBatchLesionOverlapMap.m

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+%-----------------------------------------------------------------------
+% Job saved on 08-Mar-2021 12:48:14 by cfg_util (rev $Rev: 7345 $)
+% spm SPM - SPM12 (7771)
+% cfg_basicio BasicIO - Unknown
+%-----------------------------------------------------------------------
+matlabbatch{1}.spm.tools.ali.lesion_overlap.lom = '<UNDEFINED>';

src/batches/setBatchLesionSegmentation.m

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+% (C) Copyright 2021 CPP BIDS SPM-pipeline developers
+
+function matlabbatch = setBatchLesionSegmentation(matlabbatch, BIDS, opt, subID)
+  %
+  % Creates a batch to segment the anatomical image for lesion detection
+  %
+  % USAGE::
+  %
+  %   matlabbatch = setBatchSegmentationDetectLesion(matlabbatch, BIDS, opt, subID)
+  %
+  % :param matlabbatch: list of SPM batches
+  % :type matlabbatch: structure
+  %
+  % :returns: - :matlabbatch: (structure)
+
+  printBatchName('Lesion segmentation');
+
+% find anatomical file
+[anatImage, anatDataDir] = getAnatFilename(BIDS, subID, opt);
+matlabbatch{1}.spm.tools.ali.unified_segmentation.step1data = [anatImage, anatDataDir];
+
+% define SPM folder 
+spmDir = spm('dir');
+
+% specify Prior EXTRA class (lesion prior map)
+lesionPriorMap = fullfile(spmDir, 'toolbox', 'ALI', 'Priors_extraClass', 'wc4prior0.nii');
+
+unified_segmentation.step1prior = {lesionPriorMap};
+unified_segmentation.step1niti = 2;                       % number of iterations
+unified_segmentation.step1thr_prob = 0.333333333333333;   % threshold probability
+unified_segmentation.step1thr_size = 0.8;                 % threshold size (in cm3) 
+unified_segmentation.step1coregister = 1;                  % coregister in MNI space (yes: 1)
+unified_segmentation.step1mask = {''};                     % specify cost function mask CFM (optional)
+unified_segmentation.step1vox = 2;                         % Voxel sizes (in mm)
+unified_segmentation.step1fwhm = [8 8 8];                  % Smooth: FWHM
+
+matlabbatch{end+1}.spm.tools.ali.unified_segmentation = unified_segmentation;
+
+end

src/workflows/bidsLesionSegmentation.m

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+% (C) Copyright 2021 CPP BIDS SPM-pipeline developers
+
+function bidsLesionSegmentation(opt)
+  %
+  % Performs segmentation to detect lesions of anatomical image.
+  %
+  % USAGE::
+  %
+  %  bidsLesionSegmentation(opt)
+  %
+  % :param opt: structure or json filename containing the options. See
+  %             ``checkOptions()`` and ``loadAndCheckOptions()``.
+  % :type opt: structure
+  %
+  % Segmentation will be performed using the information provided in the BIDS data set.
+  %
+
+
+  if nargin < 1
+    opt = [];
+  end
+
+  [BIDS, opt] = setUpWorkflow(opt, 'lesion segmentation');
+
+  parfor iSub = 1:numel(opt.subjects)
+
+    subLabel = opt.subjects{iSub};
+
+    printProcessingSubject(iSub, subLabel);
+
+    matlabbatch = [];
+    matlabbatch = setBatchSTC(matlabbatch, BIDS, opt, subLabel);
+
+    saveAndRunWorkflow(matlabbatch, 'LesionSegmentation', opt, subLabel);
+
+  end
+
+end  
+