[FIX] Reduce warnings (#1125)

* do not create dir when returning subject level glm dir name

* get all data in circle ci

* change octache templates

* update bids matlab

* reduce warnings in test

* reuce warnings

* fix tests

* reduce number of model to select in bms

* Update demos/MoAE/test_moae.m

* improve warning

* override opt.space with arguments

* toggle

.circleci/config.yml

@@ -61,6 +61,7 @@ jobs:
           datalad get sub-0[1-2]/anat/*MNI*mask.nii.gz \
                 sub-0[1-2]/anat/*MNI*T1w.nii.gz \
                 sub-0[1-2]/func/*MNI*desc-preproc*bold.nii.gz \
+                sub-0[1-2]/func/*MNI*mask.nii.gz \
                 sub-*/func/*tsv	\
                 sub-*/func/*json -J 12
           datalad status

demos/bayes/ds000114_run.m

@@ -27,7 +27,7 @@
 
 models_dir = fullfile(root_dir, 'models');
 
-participant_label = {'[0-9]*'};
+participant_label = {'[0-9]*'}; %#ok<*NASGU>
 if TESTING
   participant_label = {'^0[12]$'};
 end
@@ -56,6 +56,14 @@
 mutliverse.wm_csf = {'none', 'basic', 'full'};
 mutliverse.non_steady_state = [false, true];
 
+if TESTING
+  mutliverse.strategy = {'motion', 'wm_csf', 'scrub', 'non_steady_state'};
+  mutliverse.motion = {'none', 'basic'};
+  mutliverse.scrub = [false, true];
+  mutliverse.wm_csf = {'none'};
+  mutliverse.non_steady_state = false;
+end
+
 create_model_families(models_dir, default_model_file, mutliverse);
 
 %% Statistics
@@ -92,6 +100,12 @@ function create_model_families(models_dir, default_model_file, mutliverse)
   % TODO incorporate into bidspm
 
   % TODO add support for 12 motion regressors
+  strategyToSkip = fieldnames(mutliverse);
+  idxStrategyToSkip = ~ismember(fieldnames(mutliverse), mutliverse.strategy);
+  strategyToSkip = strategyToSkip(idxStrategyToSkip);
+  for i = 1:numel(strategyToSkip)
+    mutliverse.(strategyToSkip{i}) = {''};
+  end
 
   for i = 1:numel(mutliverse.motion)
     for j = 1:numel(mutliverse.scrub)

src/batches/preproc/setBatchSmoothingFunc.m

@@ -1,4 +1,4 @@
-function [matlabbatch, allRT] = setBatchSmoothingFunc(matlabbatch, BIDS, opt, subLabel)
+function [matlabbatch, srcMetadata] = setBatchSmoothingFunc(matlabbatch, BIDS, opt, subLabel)
   %
   % Creates a batch to smooth the bold files of a subject
   %
@@ -42,7 +42,7 @@
   [sessions, nbSessions] = getInfo(BIDS, subLabel, opt, 'Sessions');
 
   allFiles = [];
-  allRT = [];
+  srcMetadata = struct('RepetitionTime', [], 'SliceTimingCorrected', []);
 
   for iSes = 1:nbSessions
 
@@ -66,15 +66,10 @@
       for iFile = 1:size(fileName, 1)
         files{iFile, 1} = validationInputFile(subFuncDataDir(iFile, :), ...
                                               fileName(iFile, :)); %#ok<*AGROW>
-
-        if isfield(metadata{iFile}, 'RepetitionTime')
-          allRT(end + 1) = metadata{iFile}.RepetitionTime;
-        else
-          allRT(end + 1) = nan;
-        end
-
       end
 
+      srcMetadata = collectSrcMetadata(srcMetadata, metadata);
+
       % add the files to list
       allFilesTemp = cellstr(char(files));
       allFiles = [allFiles; allFilesTemp];
@@ -91,3 +86,21 @@
                                    num2str(opt.fwhm.func)]);
 
 end
+
+function srcMetadata = collectSrcMetadata(srcMetadata, metadata)
+  for iFile = 1:numel(metadata)
+
+    if isfield(metadata{iFile}, 'RepetitionTime')
+      srcMetadata.RepetitionTime(end + 1) = metadata{iFile}.RepetitionTime;
+    else
+      srcMetadata.RepetitionTime(end + 1) = nan;
+    end
+
+    if isfield(metadata{iFile}, 'SliceTimingCorrected')
+      srcMetadata.SliceTimingCorrected(end + 1) = metadata{iFile}.SliceTimingCorrected;
+    else
+      srcMetadata.SliceTimingCorrected(end + 1) = false;
+    end
+
+  end
+end

src/bids/getAnatFilename.m

@@ -72,9 +72,14 @@
   end
 
   if numel(anat) > nbImgToReturn
-    tmp = bids.internal.format_path(anat(1:nbImgToReturn));
-    msg = sprintf('More than %i anat file. Found: %i.\n\nTaking the first %i:%s\n', ...
+
+    tmp = anat(1:nbImgToReturn);
+    tmp = strrep(tmp, [BIDS.pth filesep], '');
+    tmp = bids.internal.format_path(tmp);
+    msg = sprintf(['More than %i anat file in:\n%s.', ...
+                   '\n\nFound: %i.\nTaking the first %i:%s'], ...
                   nbImgToReturn, ...
+                  bids.internal.format_path(BIDS.pth), ...
                   numel(anat), ...
                   nbImgToReturn, ...
                   bids.internal.create_unordered_list(tmp));

src/bids/getAndCheckSliceOrder.m

@@ -32,6 +32,22 @@
 
   % TODO support for DelayTime and AcquisitionDuration
 
+  warning('OFF', 'query:unknowMetadata');
+
+  filter.target = 'SliceTimingCorrected';
+  sliceTimingCorrected = bids.query(BIDS, 'metadata', filter);
+  stCorrected = areAllSliceTimeCorrected(sliceTimingCorrected);
+
+  % for GLM if data is not slice time corrected
+  % we will rely on the number of slices
+  % to figure out the temporal resolution
+  % to do convolution at.
+  if strcmp(opt.pipeline.type, 'stats') && ~stCorrected
+    sliceOrder = [];
+    warning('ON', 'query:unknowMetadata');
+    return
+  end
+
   filter.target = 'SliceTiming';
   sliceTiming = bids.query(BIDS, 'metadata', filter);
 
@@ -48,23 +64,20 @@
     id = 'noSliceTimingFound';
     logger('WARNING', msg, 'id', id, 'filename', mfilename(), 'options', opt);
 
+    warning('ON', 'query:unknowMetadata');
     return
 
   end
 
   sliceTimingLengths = cellfun('length', sliceTiming);
   if length(unique(sliceTimingLengths)) > 1
-
-    sliceOrder = [];
+    warning('ON', 'query:unknowMetadata');
 
     msg = sprintf(['Inconsistent slice timing found for filter:\n%s.\n\n', ...
                    'Number of slice per volume seems different across bold files.'], ...
                   bids.internal.create_unordered_list(filter));
     id = 'inconsistentSliceTimingLength';
     logger('ERROR', msg, 'id', id, 'filename', mfilename(), 'options', opt);
-
-    return
-
   end
 
   % all slice timing should be the same,
@@ -82,6 +95,7 @@
       id = 'inconsistentSliceTimingValues';
       logger('WARNING', msg, 'id', id, 'filename', mfilename(), 'options', opt);
 
+      warning('ON', 'query:unknowMetadata');
       return
     end
 
@@ -90,4 +104,21 @@
   msg = ' SLICE TIMING INFORMATION EXTRACTED FROM METADATA.';
   logger('INFO', msg, 'options', opt, 'filename', mfilename());
 
+  warning('ON', 'query:unknowMetadata');
+
+end
+
+function stCorrected = areAllSliceTimeCorrected(values)
+  if isempty(values) || ...
+          (~iscell(values) && ~values)
+    stCorrected = false;
+    return
+  end
+  if iscell(values) && any(cellfun('isempty', values))
+    stCorrected = false;
+    return
+  end
+
+  stCorrected = all(values{1});
+
 end

src/bids_model/getInclusiveMask.m

@@ -40,12 +40,14 @@
           file = file{1};
 
         elseif numel(file) > 1
-          file = bids.internal.format_path(file);
-          msg = sprintf(['More than 1 mask image found for %s.\n\n' ...
-                         'Taking the first one:\n\t%s\n\nfrom:%s\n\n'], ...
+          tmp = strrep(file, [BIDS.pth, filesep], '');
+          tmp = bids.internal.format_path(tmp);
+          msg = sprintf(['More than 1 mask image found in:\n %s\nfor filter: %s.\n\n' ...
+                         'Taking the first one:\n\t%s\n\nfrom:%s'], ...
+                        BIDS.pth, ...
                         bids.internal.create_unordered_list(mask), ...
-                        file{1}, ...
-                        bids.internal.create_unordered_list(file));
+                        tmp{1}, ...
+                        bids.internal.create_unordered_list(tmp));
           id = 'tooManyMasks';
           logger('WARNING', msg, 'id', id, 'options', opt, 'filename', mfilename());
           file = file{1};

src/cli/getOptionsFromCliArgument.m

@@ -204,14 +204,15 @@
   if ~isfield(args.Results, 'space')
     return
   end
-  if ~isempty(args.Results.space)
-    if isfield(opt, 'space') && ~all(ismember(args.Results.space, opt.space))
+
+  if isfield(opt, 'space') && ~all(ismember(args.Results.space, opt.space))
+    if ~isempty(args.Results.space)
       overrideMsg('space', convertToString(args.Results.space), ...
                   'space', convertToString(opt.space), ...
                   opt);
     end
-    opt.space = args.Results.space;
   end
+  opt.space = args.Results.space;
 end
 
 function output = convertToString(input)

src/reports/boilerplate_preprocess.mustache

@@ -7,8 +7,8 @@ The (f)MRI data were pre-processed with {{>computing_environment}}.
 {{! TODO mention which task were processed}}
 
 The preprocessing of the functional images was performed in the following order:
-{{#dummy_scans}}- removing of dummy scans
-{{/dummy_scans}}
+{{#dummyScans}}- removing of dummy scans
+{{/dummyScans}}
 {{#stc}}- slice timing correction
 {{/stc}}
 - realignment{{#unwarp}} and unwarping{{/unwarp}}

src/reports/partials/remove_dummies.mustache

@@ -1,2 +1,2 @@
-{{#dummy_scans}}{{nb}} dummy scans were removed to allow for signal stabilization.
-{{/dummy_scans}}
+{{#dummyScans}}{{nb}} dummy scans were removed to allow for signal stabilization.
+{{/dummyScans}}

src/stats/subject_level/createAndReturnCounfoundMatFile.m

@@ -59,6 +59,9 @@
   opt.query.task = opt.taskName;
 
   ffxDir = getFFXdir(bf.entities.sub, opt);
+  if exist(ffxDir, 'dir') == 0
+    spm_mkdir(ffxDir);
+  end
   counfoundFile = fullfile(ffxDir, bf.filename);
 
   if isempty(names) || isempty(R)

src/stats/subject_level/getFFXdir.m

@@ -1,6 +1,6 @@
 function ffxDir = getFFXdir(subLabel, opt)
   %
-  % Sets the name the FFX directory and creates it if it does not exist
+  % Sets the name the FFX directory
   %
   % USAGE::
   %
@@ -39,8 +39,6 @@
     ffxDir = [ffxDir '_roi'];
   end
 
-  spm_mkdir(ffxDir);
-
 end
 
 function string = deregexify(string)

src/workflows/preproc/bidsSmoothing.m

@@ -1,4 +1,4 @@
-function bidsSmoothing(opt)
+function srcMetadata = bidsSmoothing(opt)
   %
   % This performs smoothing to the functional data using a full width
   % half maximum smoothing kernel of size "opt.fwhm.func".
@@ -33,7 +33,7 @@ function bidsSmoothing(opt)
     opt.taskName = bids.query(BIDS, 'tasks');
   end
 
-  allRT = {};
+  srcMetadata = struct('RepetitionTime', [], 'SliceTimingCorrected', []);
   unRenamedFiles = {};
 
   for iSub = 1:numel(opt.subjects)
@@ -49,10 +49,10 @@ function bidsSmoothing(opt)
       switch modality
         case 'func'
           matlabbatch = {};
-          [matlabbatch, allRT{iSub}] = setBatchSmoothingFunc(matlabbatch, ...
-                                                             BIDS, ...
-                                                             opt, ...
-                                                             subLabel);
+          [matlabbatch, srcMetadata(iSub)] = setBatchSmoothingFunc(matlabbatch, ...
+                                                                   BIDS, ...
+                                                                   opt, ...
+                                                                   subLabel);
           [~, unRenamedFiles{iSub}] = saveAndRunWorkflow(matlabbatch, ...
                                                          ['smoothing_FWHM-', ...
                                                           num2str(opt.fwhm.func)], ...
@@ -81,25 +81,41 @@ function bidsSmoothing(opt)
   opt.query.space = opt.space;
   createdFiles = bidsRename(opt);
 
+  transferMetadata(opt, createdFiles, unRenamedFiles, srcMetadata);
+
+end
+
+function transferMetadata(opt, createdFiles, unRenamedFiles, srcMetadata)
   % add Repetition Time to smoothed files metadata
+
+  metadataToTransfer = fieldnames(srcMetadata);
+
   for iSub = 1:numel(opt.subjects)
+
     subLabel = opt.subjects{iSub};
+
     for iFile = 1:numel(createdFiles)
+
       bf = bids.File(createdFiles{iFile});
       if ~strcmp(bf.suffix, 'bold') || ~strcmp(bf.entities.sub, subLabel)
         continue
       end
+
       jsonFile = spm_file(createdFiles{iFile}, 'ext', '.json');
       if exist(jsonFile, 'file')
+
         metadata = bids.util.jsondecode(jsonFile);
         idx = ~cellfun('isempty', ...
                        strfind(unRenamedFiles{iSub}{1}.files, ...
                                metadata.SpmFilename));
-        rt = allRT{iSub}(idx);
-        metadata.RepetitionTime = rt;
+
+        for i = 1:numel(metadataToTransfer)
+          metadata.(metadataToTransfer{i}) = srcMetadata(iSub).(metadataToTransfer{i})(idx);
+        end
+
         bids.util.jsonencode(jsonFile, metadata);
       end
+
     end
   end
-
 end

tests/data/derivatives/bidspm-preproc/task-vislocalizer_bold.json

@@ -9,5 +9,6 @@
   "SliceThickness": 3,
   "FlipAngle": 54,
   "NumberOfVolumesDiscardedByUser": 4,
-  "TaskName": "vislocalizer"
+  "TaskName": "vislocalizer",
+  "SliceTimingCorrected": false
 }

tests/data/derivatives/bidspm-preproc/task-vismotion_bold.json

@@ -2,6 +2,16 @@
   "ImageType": "ORIGINAL\\PRIMARY\\M\\ND\\MOSAIC",
   "Modality": "MR",
   "TotalReadoutTime": 1.0035123,
+  "SliceTimingCorrected": true,
+  "RepetitionTime": 1.5,
+  "PhaseEncodingDirection": "j-",
+  "EffectiveEchoSpacing": 0.00024499812,
+  "EchoTime": 0.03,
+  "SliceThickness": 3,
+  "FlipAngle": 54,
+  "NumberOfVolumesDiscardedByUser": 8,
+  "TaskName": "vismotion",
+  "PixelBandwidth": 15.873,
   "SliceTiming": [
     0.5475,
     0,
@@ -45,14 +55,5 @@
     0.3275,
     0.71,
     0.165
-  ],
-  "RepetitionTime": 1.5,
-  "PhaseEncodingDirection": "j-",
-  "EffectiveEchoSpacing": 0.00024499812,
-  "EchoTime": 0.03,
-  "SliceThickness": 3,
-  "FlipAngle": 54,
-  "NumberOfVolumesDiscardedByUser": 8,
-  "TaskName": "vismotion",
-  "PixelBandwidth": 15.873
+  ]
 }