move files to slow

.github/workflows/tests.yml

@@ -121,6 +121,7 @@ jobs:
             run: |
                 cd demos/openneuro/
                 make data_ds000114_mriqc
+                make data_ds000114_fmriprep
 
         -   name: Prepare test data unix
             run: |

.github/workflows/tests_octave.yml

@@ -94,6 +94,12 @@ jobs:
                 unzip download
                 mv moae_fmriprep fmriprep
 
+        -   name: Get data for testing QA
+            run: |
+                cd demos/openneuro/
+                make data_ds000114_mriqc
+                make data_ds000114_fmriprep
+
         -   name: Prepare test data
             run: |
                 cd tests

docs/source/API.rst

@@ -33,7 +33,6 @@ workflows
 .. autofunction:: src.workflows.bidsCheckVoxelSize
 .. autofunction:: src.workflows.bidsCopyInputFolder
 .. autofunction:: src.workflows.bidsInverseNormalize
-.. autofunction:: src.workflows.bidsQAbidspm
 .. autofunction:: src.workflows.bidsRename
 .. autofunction:: src.workflows.bidsReport
 
@@ -42,6 +41,13 @@ roi
 .. autofunction:: src.workflows.roi.bidsCreateROI
 .. autofunction:: src.workflows.roi.bidsRoiBasedGLM
 
+QA
+--
+.. autofunction:: src.workflows.QA.bidsQA
+.. autofunction:: src.workflows.QA.bidsQAbidspm
+.. autofunction:: src.workflows.QA.bidsQAmriqc
+.. autofunction:: src.workflows.QA.bidsQApreproc
+
 lesion
 ------
 .. autofunction:: src.workflows.lesion.bidsLesionAbnormalitiesDetection
@@ -103,7 +109,6 @@ stats
 .. autofunction:: src.batches.stats.setBatchSubjectLevelContrasts
 .. autofunction:: src.batches.stats.setBatchSubjectLevelGLMSpec
 .. autofunction:: src.batches.stats.setBatchSubjectLevelResults
-.. autofunction:: src.batches.stats.setBatchTwoSampleTTest
 
 preproc
 -------
@@ -157,7 +162,6 @@ QA
 .. autofunction:: src.QA.computeFDandRMS
 .. autofunction:: src.QA.computeRobustOutliers
 .. autofunction:: src.QA.createDesignMatrix
-.. autofunction:: src.QA.mriqcQA
 .. autofunction:: src.QA.plotConfounds
 .. autofunction:: src.QA.plotEvents
 .. autofunction:: src.QA.plotRoiTimeCourse
@@ -204,6 +208,9 @@ bidspm
 data
 ----
 
+__pycache__
+-----------
+
 cli
 ===
 .. autofunction:: src.cli.baseInputParser

src/workflows/QA/bidsQA.m

@@ -1,10 +1,25 @@
-function bidsQA(opt, varargin)
+function filename = bidsQA(opt, varargin)
   %
   % Run QA on a BIDS dataset.
   %
+  % Find outliers in MRIQC output
+  % or to view number of outlier timepoints
+  % (for a given metric and threshold) in each functional run
+  %
+  %
+  % USAGE::
+  %
+  %   figurePath = bidsQA(opt, varargin);
+  %
+  % :param opt: Options chosen for the analysis.
+  %             See :func:`checkOptions`.
+  % :type opt:  structure
+  %
 
   % (C) Copyright 2024 Remi Gau
 
+  filename = '';
+
   dsDesc = bids.util.jsondecode(fullfile(opt.dir.input, 'dataset_description.json'));
 
   switch dsDesc.DatasetType
@@ -31,7 +46,7 @@ function bidsQA(opt, varargin)
         bidsQAmriqc(opt, 'bold');
 
       elseif  any(ismember({'fMRIPrep', 'bidspm'}, pipelines))
-        bidsQApreproc(opt, varargin{:});
+        filename = bidsQApreproc(opt, varargin{:});
       end
   end
 end

src/workflows/QA/bidsQAmriqc.m

@@ -1,4 +1,4 @@
-function mriqcQA(opt, suffix)
+function bidsQAmriqc(opt, suffix)
   %
   %  uses the report from MRIQC (bold and T1) identify outliers using
   %  robust statistics (interquartile range).
@@ -8,7 +8,7 @@ function mriqcQA(opt, suffix)
   %
   % USAGE::
   %
-  %   mriqcQA(opt, suffix);
+  %   bidsQAmriqc(opt, suffix);
   %
   % :type opt:  structure
   % :param opt: Options chosen for the analysis.
@@ -18,8 +18,8 @@ function mriqcQA(opt, suffix)
   %
   %   opt.dir.mriqc = '/home/remi/gin/dataset/derivatives/mriqc';
   %
-  %   mriqcQA(opt, 'T1w');
-  %   mriqcQA(opt, 'bold');
+  %   bidsQAmriqc(opt, 'T1w');
+  %   bidsQAmriqc(opt, 'bold');
   %
   % Dependencies (in case you want to use it as standalone):
   %

src/workflows/QA/bidsQApreproc.m

@@ -1,11 +1,25 @@
-function bidsQApreproc(opt, varargin)
+function filename = bidsQApreproc(opt, varargin)
   %
   % Use confounds preprocessed datasets to estimate
   % the number of timepoints with values superior to threshold.
   %
+  % Plots the proportion of timepoints per run
+  % (to identify runs with that goes above a limit).
+  %
+  % USAGE::
+  %
+  %   figurePath = bidsQApreproc(opt, 'metric', metric, 'threshold', threshold);
+  %
+  % :param opt: Options chosen for the analysis.
+  %             See :func:`checkOptions`.
+  % :type opt:  structure
+  %
+  % :param metric: default = 'framewise_displacement'
+  % :type  metric: char
+  %
+  % :param threshold: default = 0.2
+  % :param threshold: numeric
   %
-  % plots the proportion of timepoints per run
-  % (to identify runs with that goes above a limit)
 
   % (C) Copyright 2024 bidspm developers
 
@@ -81,6 +95,9 @@ function bidsQApreproc(opt, varargin)
 
   plotFigure(df, metric, threshold);
 
+  output_path = fullfile(opt.dir.output, 'reports');
+  filename = printFigure(output_path, metric);
+
 end
 
 function plotFigure(df, metric, threshold)
@@ -128,3 +145,16 @@ function plotFigure(df, metric, threshold)
       'fontsize', 8, 'tickdir', 'out');
 
 end
+
+function filename = printFigure(outputPath, metric)
+  bids.util.mkdir(outputPath);
+
+  filename = regexprep(['outliers_', metric, '.png'], ' - ', '_');
+  filename = regexprep(filename, ' ', '-');
+  filename = regexprep(filename, '[\(\)]', '');
+  filename = fullfile(outputPath, filename);
+
+  print(filename, '-dpng');
+  fprintf('Figure saved:\n\t%s\n', filename);
+
+end

tests/tests_slow/tests_workflows/QA/test_bidsQA.m

@@ -0,0 +1,100 @@
+function test_suite = test_bidsQA %#ok<*STOUT>
+
+  % (C) Copyright 2024 bidspm developers
+
+  try % assignment of 'localfunctions' is necessary in Matlab >= 2016
+    test_functions = localfunctions(); %#ok<*NASGU>
+  catch % no problem; early Matlab versions can use initTestSuite fine
+  end
+  initTestSuite;
+end
+
+function test_bidsQA_raw()
+
+  %   markTestAs('slow');
+  %
+  %     opt = setOptions('vislocalizer');
+  %
+  %      expectedOutput = fullfile(opt.dir.output, ...
+  %         'reports', ...
+  %         'bidspm-raw_split_by-task.png');
+  %
+  %     if exist(expectedOutput, 'file')
+  %         delete(expectedOutput)
+  %     end
+  %
+  %     bidsQA(opt)
+  %
+  %     assertEqual(exist(expectedOutput, 'file'), 2)
+
+end
+
+function test_bidsQA_mriqc()
+
+  %   markTestAs('slow');
+  %
+  % if ispc()
+  % moxunit_throw_test_skipped_exception('requires datalad setup');
+  % end
+  %
+  %   ds000114mriqc = spm_file(fullfile(getTestDir(), ...
+  %                                     '..', 'demos', 'openneuro', ...
+  %                                     'inputs', 'ds000114-mriqc'), 'cpath');
+  %
+  %   opt.dir.input = ds000114mriqc;
+  %
+  %   bidsQA(opt);
+
+end
+
+function test_bidsQA_bidspm()
+
+  markTestAs('slow');
+
+  if ispc()
+    moxunit_throw_test_skipped_exception('requires datalad setup');
+  end
+
+  opt = setOptions('vislocalizer');
+
+  opt.dir.input = opt.dir.preproc;
+
+  opt.dir.output = '';
+  opt.dir.derivatives = tempName();
+
+  opt = checkOptions(opt);
+
+  threshold = 0.0001;
+  metric = 'rot_x';
+
+  filename = bidsQA(opt, 'metric', metric, 'threshold', threshold);
+
+  assertEqual(exist(filename, 'file'), 2);
+
+end
+
+function test_bidsQA_fmriprep()
+
+  markTestAs('slow');
+
+  ds000114fmriprep = spm_file(fullfile(getTestDir(), ...
+                                       '..', 'demos', 'openneuro', ...
+                                       'inputs', 'ds000114-fmriprep'), 'cpath');
+
+  opt.dir.input = ds000114fmriprep;
+  opt.dir.preproc = ds000114fmriprep;
+  opt.dir.derivatives = tempName();
+  opt.pipeline.type = 'preproc';
+  opt.verbosity = 0;
+
+  opt.taskName = {'overtverbgeneration', 'linebisection'};
+
+  opt = checkOptions(opt);
+
+  opt.subjects = {'01', '02', '03', '10'};
+
+  filename = bidsQA(opt);
+
+  assertEqual(exist(filename, 'file'), 2);
+
+end