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feat: split register parcellation into two pipelines
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79
src/matlab/builders/configurations/BuildRegisterToStandardConfiguration.m
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| function [config] = BuildRegisterToStandardConfiguration() | ||
| %BUILDREGISTERTOSTANDARDCONFIGURATION Builds configuration for pipeline. | ||
| % Builds a configuration for a pipeline that registers volumes to a standard. | ||
| % | ||
| % Input: | ||
| % - ... | ||
| % | ||
| % Output: | ||
| % - config: Configuration. | ||
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| config = struct(); | ||
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| % get data folder relative to this file | ||
| filePath = fileparts(which(mfilename)); | ||
| pathToDataFolder = fullfile(filePath, '../../../../../neurochi/data/'); | ||
| pathToWorkspace = fullfile(pathToDataFolder, 'w1'); | ||
| pathToDataset = fullfile(pathToDataFolder, 'input'); | ||
| pathToParcellations = fullfile(pathToDataFolder, 'parcs'); | ||
| % for intermediary pipelines, send output to the transfer folder | ||
| pathToOutput = fullfile(pathToDataFolder, 'transfer'); | ||
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| %% pipeline: register to standard | ||
| % common configuration | ||
| config.verbose = true; | ||
| config.clobber = true; | ||
| config.pathToWorkspace = pathToWorkspace; | ||
| config.pathToDataset = pathToDataset; | ||
| config.pathToParcellations = pathToParcellations; | ||
| config.pathToOutput = pathToOutput; | ||
| % helps debug by not running all subjects | ||
| config.numSubjects = 1; | ||
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| % step 1 | ||
| config.step1.dof = 6; | ||
| config.step1.interp = 'spline'; | ||
| config.step1.optional = false; | ||
| config.step1.clobber = config.clobber; | ||
| config.step1.verbose = config.verbose; | ||
| % step 2: flirt | ||
| config.step2.dof = 6; | ||
| config.step2.applyxfm = true; | ||
| config.step2.nosearch = true; | ||
| config.step2.interp = 'spline'; | ||
| config.step2.optional = false; | ||
| config.step2.clobber = config.clobber; | ||
| config.step2.verbose = config.verbose; | ||
| % step 3 | ||
| config.step3.optional = false; | ||
| config.step3.clobber = config.clobber; | ||
| config.step3.verbose = config.verbose; | ||
| % step 4 | ||
| config.step4.dof = 12; | ||
| config.step4.interp = 'spline'; | ||
| config.step4.optional = false; | ||
| config.step4.clobber = config.clobber; | ||
| config.step4.verbose = config.verbose; | ||
| % step 5 | ||
| config.step5.dof = 12; | ||
| config.step5.applyxfm = true; | ||
| config.step5.nosearch = true; | ||
| config.step5.interp = 'spline'; | ||
| config.step5.optional = false; | ||
| config.step5.clobber = config.clobber; | ||
| config.step5.verbose = config.verbose; | ||
| % step 6 | ||
| config.step6.optional = false; | ||
| config.step6.clobber = config.clobber; | ||
| config.step6.verbose = config.verbose; | ||
| % step 7 | ||
| config.step7.optional = false; | ||
| config.step7.clobber = config.clobber; | ||
| config.step7.verbose = config.verbose; | ||
| % step 8 | ||
| config.step8.optional = false; | ||
| config.step8.clobber = config.clobber; | ||
| config.step8.verbose = config.verbose; | ||
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| end |
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62
src/matlab/builders/configurations/BuildTransformParcellationConfiguration.m
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| Original file line number | Diff line number | Diff line change |
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| function [config] = BuildTransformParcellationConfiguration() | ||
| %BUILDTRANSFORMPARCELLATIONCONFIGURATION Builds configuration for pipeline. | ||
| % Builds a configuration for a pipeline that transforms a parcellation. | ||
| % | ||
| % Input: | ||
| % - ... | ||
| % | ||
| % Output: | ||
| % - config: Configuration. | ||
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| config = struct(); | ||
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| % get data folder relative to this file | ||
| filePath = fileparts(which(mfilename)); | ||
| pathToDataFolder = fullfile(filePath, '../../../../../neurochi/data/'); | ||
| pathToWorkspace = fullfile(pathToDataFolder, 'w1'); | ||
| pathToDataset = fullfile(pathToDataFolder, 'input'); | ||
| pathToParcellations = fullfile(pathToDataFolder, 'parcs'); | ||
| % for intermediary pipelines, send output to the transfer folder | ||
| pathToOutput = fullfile(pathToDataFolder, 'transfer'); | ||
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| %% pipeline: transform parcellation | ||
| % common configuration | ||
| config.verbose = true; | ||
| config.clobber = true; | ||
| config.pathToWorkspace = pathToWorkspace; | ||
| config.pathToDataset = pathToDataset; | ||
| config.pathToParcellations = pathToParcellations; | ||
| config.pathToOutput = pathToOutput; | ||
| % helps debug by not running all subjects | ||
| config.numSubjects = 1; | ||
| % select the parcellation to transform | ||
| % (must be present in `pathToParcellations`) | ||
| config.parcellation = 'mask_ventricles_MNIch2.nii.gz'; | ||
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| % step 1 | ||
| config.step1.numDilations = 0; | ||
| config.step1.clobber = config.clobber; | ||
| config.step1.verbose = config.verbose; | ||
| % step 2 | ||
| config.step2.interp = 'nn'; | ||
| config.step2.clobber = config.clobber; | ||
| config.step2.verbose = config.verbose; | ||
| % step 3 | ||
| config.step3.interp = 'nearestneighbour'; | ||
| config.step3.applyxfm = true; | ||
| config.step3.nosearch = true; | ||
| config.step3.optional = true; | ||
| config.step3.clobber = config.clobber; | ||
| config.step3.verbose = config.verbose; | ||
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| % step 4 | ||
| config.step4.interp = 'nearestneighbour'; | ||
| config.step4.applyxfm = true; | ||
| config.step4.nosearch = true; | ||
| config.step4.optional = true; | ||
| config.step4.clobber = config.clobber; | ||
| config.step4.verbose = config.verbose; | ||
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| end | ||
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95 changes: 95 additions & 0 deletions
95
src/matlab/builders/pipelines/BuildTransformParcellationPipeline.m
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| Original file line number | Diff line number | Diff line change |
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| function [pipeline] = BuildTransformParcellationPipeline(parcellation, ... | ||
| pathToWorkspace, ... | ||
| pathToDataset, ... | ||
| pathToParcellations, ... | ||
| pathToIntermediaryOutputs, ... | ||
| pathToOutput, ... | ||
| numSubjects, ... | ||
| config) | ||
| %BUILDSAMPLEPIPELINE Example of a pipeline builder. | ||
| % This builder creates a pipeline with one sequence 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. | ||
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| arguments | ||
| parcellation char | ||
| pathToWorkspace char = '.' | ||
| pathToDataset char = '.' | ||
| pathToParcellations char = '.' | ||
| pathToIntermediaryOutputs char = '.' | ||
| pathToOutput char = '.' | ||
| numSubjects int8 {mustBeNonnegative} = 0 | ||
| config = {} | ||
| end | ||
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| % names of inputs needed to start the sequence | ||
| inputs = { ... | ||
| fullfile(pathToDataset, '%s/anat/%s_T1w.nii.gz'), ... | ||
| fullfile(pathToIntermediaryOutputs, '%s/%s_T1w_brain_mul.nii.gz'), ... | ||
| fullfile(pathToIntermediaryOutputs, '%s/%s_MNI2T1w_dof6.mat'), ... | ||
| fullfile(pathToIntermediaryOutputs, '%s/%s_MNI2T1w_dof12.mat'), ... | ||
| fullfile(pathToIntermediaryOutputs, '%s/%s_MNI2T1w_warp.nii.gz'), ... | ||
| fullfile(pathToIntermediaryOutputs, '%s/%s_T1w_brain_dof6.nii.gz'), ... | ||
| fullfile(pathToIntermediaryOutputs, '%s/%s_T1w_brain_dof12.nii.gz'), ... | ||
| fullfile(pathToParcellations, parcellation) }; | ||
| numInputs = length(inputs); | ||
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| % get information about participants | ||
| subjects = readtable(fullfile(pathToDataset, 'participants.tsv'), ... | ||
| 'Delimiter', ... | ||
| '\t', ... | ||
| 'FileType', ... | ||
| 'delimitedtext', ... | ||
| 'PreserveVariableNames', ... | ||
| true); | ||
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| tableHeight = height(subjects); | ||
| if ~numSubjects | ||
| numSubjects = tableHeight; | ||
| else | ||
| numSubjects = min(numSubjects, tableHeight); | ||
| end | ||
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| sequences = cell(1, numSubjects); | ||
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| % create a sequence for each subject | ||
| for i = 1 : numSubjects | ||
| % get data for one participant | ||
| subject = subjects(i, :); | ||
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| % participant_id is the column name and it's a cell | ||
| subjectName = subject.participant_id{1}; | ||
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| % create an input array for each sequence | ||
| subjectInputs = cell(1, numInputs); | ||
| for j = 1 : numInputs | ||
| input = inputs{j}; | ||
| % get number of times subject name is needed | ||
| subjectNameOccurences = count(input, '%s'); | ||
| [subjectNameArray{1:subjectNameOccurences}] = deal(subjectName); | ||
| subjectInputs{j} = sprintf(input, subjectNameArray{:}); | ||
| end | ||
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| pathToSubjectWorkspace = fullfile(pathToWorkspace, subjectName); | ||
| pathToSubjectOutput = fullfile(pathToOutput, subjectName); | ||
| sequences{i} = BuildTransformParcellationSequence(subjectInputs, ... | ||
| parcellation, ... | ||
| subjectName, ... | ||
| pathToSubjectWorkspace, ... | ||
| pathToSubjectOutput, ... | ||
| config); | ||
| end | ||
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| % create a pipeline with the sequences | ||
| parallel = false; | ||
| pipeline = Pipeline(sequences, parallel); | ||
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| end | ||
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