diff --git a/.travis.yml b/.travis.yml
index 0cdf80af..22f36925 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -36,7 +36,7 @@ jobs:
       script: octave $OCTFLAGS --eval "results = runTests; assert(all(~[results.Failed]))"
     - stage: "BIDS validator"
       name: "Create and check dataset"
-      script: octave $OCTFLAGS --eval "testmanual_makeRawDataset" && bids-validator `pwd`/../output/rawdata/ --ignoreNiftiHeaders
+      script: cd manualTests && octave $OCTFLAGS --eval "test_makeRawDataset" && bids-validator `pwd`/output/rawdata/ --ignoreNiftiHeaders
     - stage: "Linter"
       name: "miss_hit"
       script: cd .. && mh_style `pwd`
diff --git a/checkCFG.m b/checkCFG.m
index 2dd50246..e7c4d1dd 100644
--- a/checkCFG.m
+++ b/checkCFG.m
@@ -1,110 +1,188 @@
-function [cfg, expParameters] = checkCFG(cfg, expParameters)
+function cfg = checkCFG(cfg)
     % check that we have all the fields that we need in the experiment parameters
+    % reuses a lot of code from the BIDS starter kit
 
     checkCppBidsDependencies();
 
     if nargin < 1 || isempty(cfg)
         cfg = struct();
     end
-    if nargin < 2 || isempty(expParameters)
-        expParameters = struct();
-    end
 
-    %% set the expParameters defaults
+    %% set the cfg defaults
 
     fieldsToSet.verbose = false;
-    fieldsToSet.outputDir = fullfile( ...
+
+    fieldsToSet.fileName.task = '';
+    fieldsToSet.fileName.zeroPadding = 3;
+    fieldsToSet.fileName.dateFormat = 'yyyymmddHHMM';
+
+    fieldsToSet.dir.output = fullfile( ...
         fileparts(mfilename('fullpath')), ...
         '..', ...
         'output');
 
-    fieldsToSet = mriDefaults(fieldsToSet);
+    fieldsToSet.subject.askGrpSess = [true true];
+    fieldsToSet.subject.sessionNb = 1; % in case no session was provided
+    fieldsToSet.subject.subjectGrp = ''; % in case no group was provided
 
-    fieldsToSet.subjectGrp = ''; % in case no group was provided
-    fieldsToSet.sessionNb = 1; % in case no session was provided
-    fieldsToSet.askGrpSess = [true true];
+    fieldsToSet.testingDevice = 'pc';
+
+    fieldsToSet.eyeTracker = struct();
 
-    expParameters = setDefaultFields(expParameters, fieldsToSet);
+    fieldsToSet.eyeTracker.do = false;
+
+    fieldsToSet = mriDefaults(fieldsToSet);
 
     %% BIDS
-    clear fieldsToSet;
-    fieldsToSet.bids = struct();
-    expParameters = setDefaultFields(expParameters, fieldsToSet);
 
-    clear fieldsToSet;
-    fieldsToSet.MRI = struct();
-    fieldsToSet.datasetDescription = struct();
-    expParameters.bids = setDefaultFields(expParameters.bids, fieldsToSet);
+    fieldsToSet = datasetDescriptionDefaults(fieldsToSet);
+    fieldsToSet = mriJsonDefaults(fieldsToSet);
+    fieldsToSet = megJsonDefaults(fieldsToSet);
 
-    clear fieldsToSet;
-    fieldsToSet = datasetDescriptionDefaults();
+    fieldsToSet = transferInfoToBids(fieldsToSet, cfg);
 
-    expParameters.bids.datasetDescription = ...
-        setDefaultFields(expParameters.bids.datasetDescription, fieldsToSet);
+    cfg = setDefaultFields(cfg, fieldsToSet);
 
-    clear fieldsToSet;
-    fieldsToSet = mriJsonDefaults();
-    if isfield(expParameters, 'task')
-        fieldsToSet.TaskName = expParameters.task;
-    end
+end
 
-    expParameters.bids.MRI = ...
-        setDefaultFields(expParameters.bids.MRI, fieldsToSet);
+function fieldsToSet = mriDefaults(fieldsToSet)
 
-    % sort fields alphabetically
-    expParameters = orderfields(expParameters);
+    % for file naming and JSON
+    fieldsToSet.mri.contrastEnhancement = [];
+    fieldsToSet.mri.phaseEncodingDirection = [];
+    fieldsToSet.mri.reconstruction = [];
+    fieldsToSet.mri.echo = [];
+    fieldsToSet.mri.acquisition = [];
+    fieldsToSet.mri.repetitionTime = [];
 
-    %% set the cfg defaults
+    fieldsToSet.mri = orderfields(fieldsToSet.mri);
 
-    clear fieldsToSet;
-    fieldsToSet.verbose = false;
-    fieldsToSet.testingDevice = 'pc';
-    fieldsToSet.eyeTracker = false;
+end
 
-    cfg = setDefaultFields(cfg, fieldsToSet);
+function fieldsToSet = datasetDescriptionDefaults(fieldsToSet)
 
-    % sort fields alphabetically
-    cfg = orderfields(cfg);
+    % REQUIRED name of the dataset
+    fieldsToSet.bids.datasetDescription.Name = '';
 
-end
+    % REQUIRED The version of the BIDS standard that was used
+    fieldsToSet.bids.datasetDescription.BIDSVersion = '';
 
-function fieldsToSet = mriDefaults(fieldsToSet)
+    % RECOMMENDED
+    % what license is this dataset distributed under? The
+    % use of license name abbreviations is suggested for specifying a license.
+    % A list of common licenses with suggested abbreviations can be found in appendix III.
+    fieldsToSet.bids.datasetDescription.License = '';
+
+    % RECOMMENDED List of individuals who contributed to the
+    % creation/curation of the dataset
+    fieldsToSet.bids.datasetDescription.Authors = {''};
+
+    % RECOMMENDED who should be acknowledge in helping to collect the data
+    fieldsToSet.bids.datasetDescription.Acknowledgements = '';
 
-    % for file naming
-    fieldsToSet.MRI.ce = [];
-    fieldsToSet.MRI.dir = []; % phase encoding direction of acquisition for fMRI
-    fieldsToSet.MRI.rec = []; % reconstruction of fMRI images
-    fieldsToSet.MRI.echo = []; % echo fMRI images
-    fieldsToSet.MRI.acq = []; % acquisition of fMRI images
+    % RECOMMENDED Instructions how researchers using this
+    % dataset should acknowledge the original authors. This field can also be used
+    % to define a publication that should be cited in publications that use the
+    % dataset.
+    fieldsToSet.bids.datasetDescription.HowToAcknowledge = '';
+
+    % RECOMMENDED sources of funding (grant numbers)
+    fieldsToSet.bids.datasetDescription.Funding = {''};
+
+    % RECOMMENDED a list of references to
+    % publication that contain information on the dataset, or links.
+    fieldsToSet.bids.datasetDescription.ReferencesAndLinks = {''};
+
+    % RECOMMENDED the Document Object Identifier of the dataset
+    % (not the corresponding paper).
+    fieldsToSet.bids.datasetDescription.DatasetDOI = '';
+
+    % sort fields alphabetically
+    fieldsToSet.bids.datasetDescription = orderfields(fieldsToSet.bids.datasetDescription);
 
 end
 
-function fieldsToSet = datasetDescriptionDefaults()
-    % required
-    fieldsToSet.Name = '';
-    fieldsToSet.BIDSVersion = '';
-    % recommended
-    fieldsToSet.License = '';
-    fieldsToSet.Authors = {''};
-    fieldsToSet.Acknowledgements = '';
-    fieldsToSet.HowToAcknowledge = '';
-    fieldsToSet.Funding = {''};
-    fieldsToSet.ReferencesAndLinks = {''};
-    fieldsToSet.DatasetDOI = '';
+function fieldsToSet = mriJsonDefaults(fieldsToSet)
+    % for json for funcfional MRI data
+
+    % REQUIRED The time in seconds between the beginning of an acquisition of
+    % one volume and the beginning of acquisition of the volume following it
+    % (TR). Please note that this definition includes time between scans
+    % (when no data has been acquired) in case of sparse acquisition schemes.
+    % This value needs to be consistent with the pixdim[4] field
+    % (after accounting for units stored in xyzt_units field) in the NIfTI header
+    fieldsToSet.bids.mri.RepetitionTime = [];
+
+    % REQUIRED for sparse sequences that do not have the DelayTime field set.
+    % This parameter is required for sparse sequences. In addition without this
+    % parameter slice time correction will not be possible.
+    %
+    % In addition without this parameter slice time correction will not be possible.
+    % The time at which each slice was acquired within each volume (frame) of  the acquisition.
+    % The time at which each slice was acquired during the acquisition. Slice
+    % timing is not slice order - it describes the time (sec) of each slice
+    % acquisition in relation to the beginning of volume acquisition. It is
+    % described using a list of times (in JSON format) referring to the acquisition
+    % time for each slice. The list goes through slices along the slice axis in the
+    % slice encoding dimension.
+    fieldsToSet.bids.mri.SliceTiming = [];
+
+    % REQUIRED Name of the task (for resting state use the "rest" prefix). No two tasks
+    % should have the same name. Task label is derived from this field by
+    % removing all non alphanumeric ([a-zA-Z0-9]) characters.
+    fieldsToSet.bids.mri.TaskName = [];
+
+    % RECOMMENDED Text of the instructions given to participants before the scan.
+    % This is especially important in context of resting state fMRI and
+    % distinguishing between eyes open and eyes closed paradigms.
+    fieldsToSet.bids.mri.Instructions = '';
+
+    % RECOMMENDED Longer description of the task.
+    fieldsToSet.bids.mri.TaskDescription = '';
+
+    % fieldsToSet.PhaseEncodingDirection = [];
+    % fieldsToSet.EffectiveEchoSpacing = [];
+    % fieldsToSet.EchoTime = [];
+
+    fieldsToSet.bids.mri = orderfields(fieldsToSet.bids.mri);
+
 end
 
-function fieldsToSet = mriJsonDefaults()
-
-    % for json for funcfional data
-    % required
-    fieldsToSet.RepetitionTime = [];
-    fieldsToSet.SliceTiming = [];
-    fieldsToSet.TaskName = [];
-    %     fieldsToSet.PhaseEncodingDirection = [];
-    %     fieldsToSet.EffectiveEchoSpacing = [];
-    %     fieldsToSet.EchoTime = [];
-    % recommended
-    fieldsToSet.Instructions = [];
-    fieldsToSet.TaskDescription = [];
+function fieldsToSet = megJsonDefaults(fieldsToSet)
+    % for json for MEG data
+
+    % REQUIRED Name of the task (for resting state use the "rest" prefix). No two tasks
+    % should have the same name. Task label is derived from this field by
+    % removing all non alphanumeric ([a-zA-Z0-9]) characters.
+    fieldsToSet.bids.meg.TaskName = [];
+
+    % REQUIRED Sampling frequency
+    fieldsToSet.bids.meg.SamplingFrequency = [];
+
+    % REQUIRED Frequency (in Hz) of the power grid at the geographical location of
+    % the MEG instrument (i.e. 50 or 60):
+    fieldsToSet.bids.meg.PowerLineFrequency = [];
+
+    % REQUIRED Position of the dewar during the MEG scan: "upright", "supine" or
+    % "degrees" of angle from vertical: for example on CTF systems,
+    % upright=15°, supine = 90°:
+    fieldsToSet.bids.meg.DewarPosition = [];
+
+    % REQUIRED List of temporal and/or spatial software filters applied, or ideally
+    % key:value pairs of pre-applied software filters and their parameter
+    % values: e.g., {"SSS": {"frame": "head", "badlimit": 7}},
+    % {"SpatialCompensation": {"GradientOrder": Order of the gradient
+    % compensation}}. Write "n/a" if no software filters applied.
+    fieldsToSet.bids.meg.SoftwareFilters = [];
+
+    % REQUIRED Boolean ("true" or "false") value indicating whether anatomical
+    % landmark points (i.e. fiducials) are contained within this recording.
+    fieldsToSet.bids.meg.DigitizedLandmarks = [];
+
+    % REQUIRED Boolean ("true" or "false") value indicating whether head points
+    % outlining the scalp/face surface are contained within this recording
+    fieldsToSet.bids.meg.DigitizedHeadPoints = [];
+
+    fieldsToSet.bids.meg = orderfields(fieldsToSet.bids.meg);
 
 end
diff --git a/checkCppBidsDependencies.m b/checkCppBidsDependencies.m
index 97edb06e..de16d169 100644
--- a/checkCppBidsDependencies.m
+++ b/checkCppBidsDependencies.m
@@ -1,13 +1,13 @@
 function checkCppBidsDependencies
 
     pth = fileparts(mfilename('fullpath'));
-    
-    checkSubmodule(fullfile(pth, 'lib', 'JSONio'))
-    checkSubmodule(fullfile(pth, 'lib', 'bids-matlab'))
-    
+
+    checkSubmodule(fullfile(pth, 'lib', 'JSONio'));
+    checkSubmodule(fullfile(pth, 'lib', 'bids-matlab'));
+
     addpath(fullfile(pth, 'lib', 'utils'));
     addpath(fullfile(pth, 'subfun'));
-    
+
     printCreditsCppBids();
 
 end
diff --git a/convertSourceToRaw.m b/convertSourceToRaw.m
index 10747eef..433d4b5c 100644
--- a/convertSourceToRaw.m
+++ b/convertSourceToRaw.m
@@ -1,11 +1,15 @@
-function convertSourceToRaw(expParameters)
+function convertSourceToRaw(cfg)
 
-    sourceDir = fullfile(expParameters.outputDir, 'source');
-    rawDir = fullfile(expParameters.outputDir, 'rawdata');
+    sourceDir = fullfile(cfg.dir.output, 'source');
+    rawDir = fullfile(cfg.dir.output, 'rawdata');
 
     % add dummy readme and change file
-    copyfile(fullfile('..', 'dummyData', 'README'), sourceDir);
-    copyfile(fullfile('..', 'dummyData', 'CHANGES'), sourceDir);
+    copyfile(fullfile( ...
+        fileparts(mfilename('fullpath')), 'dummyData', 'README'), ...
+        sourceDir);
+    copyfile(fullfile( ...
+        fileparts(mfilename('fullpath')), 'dummyData', 'CHANGES'), ...
+        sourceDir);
 
     copyfile(sourceDir, rawDir);
 
diff --git a/createBoldJson.m b/createBoldJson.m
index fcb14059..b6325fa0 100644
--- a/createBoldJson.m
+++ b/createBoldJson.m
@@ -1,16 +1,16 @@
-function createBoldJson(expParameters)
+function createBoldJson(cfg)
 
     opts.Indent = '    ';
 
-    fileName = strrep(expParameters.fileName.events, '_events', '_bold');
+    fileName = strrep(cfg.fileName.events, '_events', '_bold');
     fileName = strrep(fileName, '.tsv', '.json');
 
     fileName = fullfile( ...
-        expParameters.subjectOutputDir, ...
-        expParameters.modality, ...
+        cfg.dir.outputSubject, ...
+        cfg.fileName.modality, ...
         fileName);
 
-    jsonContent = expParameters.bids.MRI;
+    jsonContent = cfg.bids.mri;
 
     bids.util.jsonencode(fileName, jsonContent, opts);
 
diff --git a/createDataDictionary.m b/createDataDictionary.m
index 828e3918..d9b6d225 100644
--- a/createDataDictionary.m
+++ b/createDataDictionary.m
@@ -1,12 +1,12 @@
-function createDataDictionary(expParameters, logFile)
+function createDataDictionary(cfg, logFile)
 
     opts.Indent = '    ';
 
-    fileName = strrep(expParameters.fileName.events, '.tsv', '.json');
+    fileName = strrep(cfg.fileName.events, '.tsv', '.json');
 
     fileName = fullfile( ...
-        expParameters.subjectOutputDir, ...
-        expParameters.modality, ...
+        cfg.dir.outputSubject, ...
+        cfg.fileName.modality, ...
         fileName);
 
     jsonContent = struct( ...
diff --git a/createDatasetDescription.m b/createDatasetDescription.m
index 4e1cbb8f..0ead3aee 100644
--- a/createDatasetDescription.m
+++ b/createDatasetDescription.m
@@ -1,12 +1,12 @@
-function createDatasetDescription(expParameters)
+function createDatasetDescription(cfg)
 
     opts.Indent = '    ';
 
     fileName = fullfile( ...
-        expParameters.outputDir, 'source', ...
+        cfg.dir.output, 'source', ...
         'dataset_description.json');
 
-    jsonContent = expParameters.bids.datasetDescription;
+    jsonContent = cfg.bids.datasetDescription;
 
     bids.util.jsonencode(fileName, jsonContent, opts);
 
diff --git a/createFilename.m b/createFilename.m
index 40834d4f..08d4391f 100644
--- a/createFilename.m
+++ b/createFilename.m
@@ -1,9 +1,9 @@
-function [cfg, expParameters] = createFilename(cfg, expParameters)
-    % create the BIDS compliant directories and filenames for the behavioral output
+function cfg = createFilename(cfg)
+    % create the BIDS compliant directories and fileNames for the behavioral output
     % for this subject / session / run using the information from cfg and expParameters.
-    % Will also create the right filename for the eyetracking data file.
+    % Will also create the right fileName for the eyetracking data file.
     %
-    % For the moment the date of acquisition is appended to the filename
+    % For the moment the date of acquisition is appended to the fileName
     %
     % can work for behavioral experiment if cfg.device is set to 'PC'
     % can work for fMRI experiment if cfg.device is set to 'scanner'
@@ -12,35 +12,32 @@
     %
     % See test_createFilename in the test folder for more details on how to use it.
 
-    zeroPadding = 3;
-    pattern = ['%0' num2str(zeroPadding) '.0f'];
-    expParameters.pattern = pattern;
+    cfg = checkCFG(cfg);
 
-    dateFormat = 'yyyymmddHHMM';
-    expParameters.date = datestr(now, dateFormat);
+    cfg.fileName.pattern = ['%0' num2str(cfg.fileName.zeroPadding) '.0f'];
+    cfg.fileName.date = datestr(now, cfg.fileName.dateFormat);
 
-    [cfg, expParameters] = checkCFG(cfg, expParameters);
-
-    if ~isfield(expParameters, 'task')
-        error('createFilename: missing a task name. i.e expParameters.task');
+    if ~isfield(cfg, 'task')
+        error('createFilename: missing a task name. i.e cfg.task.name');
     end
 
-    expParameters = getModality(cfg, expParameters);
+    cfg = getModality(cfg);
+
+    cfg = createDirectories(cfg);
 
-    expParameters = createDirectories(cfg, expParameters);
+    cfg = setSuffixes(cfg);
 
-    expParameters = setSuffixes(expParameters);
+    cfg = setFilenames(cfg);
 
-    expParameters = setFilenames(cfg, expParameters);
+    talkToMe(cfg);
 
-    talkToMe(cfg, expParameters);
-    
     cfg = orderfields(cfg);
-    expParameters = orderfields(expParameters);
+    cfg.fileName = orderfields(cfg.fileName);
+    cfg.dir = orderfields(cfg.dir);
 
 end
 
-function expParameters = getModality(cfg, expParameters)
+function cfg = getModality(cfg)
 
     switch lower(cfg.testingDevice)
         case 'pc'
@@ -57,17 +54,17 @@
             modality = 'beh';
     end
 
-    expParameters.modality = modality;
+    cfg.fileName.modality = modality;
 
 end
 
-function [subjectGrp, subjectNb, sessionNb, modality, taskName] = extractInput(expParameters)
+function [subjectGrp, subjectNb, sessionNb, modality, taskName] = extractInput(cfg)
 
-    subjectGrp = expParameters.subjectGrp;
-    subjectNb = expParameters.subjectNb;
-    sessionNb = expParameters.sessionNb;
-    modality = expParameters.modality;
-    taskName = expParameters.task;
+    subjectGrp = cfg.subject.subjectGrp;
+    subjectNb = cfg.subject.subjectNb;
+    sessionNb = cfg.subject.sessionNb;
+    modality = cfg.fileName.modality;
+    taskName = cfg.fileName.task;
 
     if isempty(sessionNb)
         sessionNb = 1;
@@ -75,120 +72,124 @@
 
 end
 
-function expParameters = createDirectories(cfg, expParameters)
+function cfg = createDirectories(cfg)
 
-    [subjectGrp, subjectNb, sessionNb, modality] = extractInput(expParameters);
+    [subjectGrp, subjectNb, sessionNb, modality] = extractInput(cfg);
 
-    pattern = expParameters.pattern;
+    pattern = cfg.fileName.pattern;
 
     % output dir
-    expParameters.subjectOutputDir = fullfile ( ...
-        expParameters.outputDir, ...
+    cfg.dir.outputSubject = fullfile ( ...
+        cfg.dir.output, ...
         'source', ...
         ['sub-' subjectGrp, sprintf(pattern, subjectNb)], ...
         ['ses-', sprintf(pattern, sessionNb)]);
 
-    [~, ~, ~] = mkdir(expParameters.outputDir);
-    [~, ~, ~] = mkdir(expParameters.subjectOutputDir);
-    [~, ~, ~] = mkdir(fullfile(expParameters.subjectOutputDir, modality));
+    [~, ~, ~] = mkdir(cfg.dir.output);
+    [~, ~, ~] = mkdir(cfg.dir.outputSubject);
+    [~, ~, ~] = mkdir(fullfile(cfg.dir.outputSubject, modality));
 
-    if cfg.eyeTracker
-        [~, ~, ~] = mkdir(fullfile(expParameters.subjectOutputDir, 'eyetracker'));
+    if cfg.eyeTracker.do
+        [~, ~, ~] = mkdir(fullfile(cfg.dir.outputSubject, 'eyetracker'));
     end
 
 end
 
-function expParameters = setSuffixes(expParameters)
+function cfg = setSuffixes(cfg)
 
-    expParameters.runSuffix = ['_run-' sprintf(expParameters.pattern, expParameters.runNb)];
+    cfg.fileName.suffix.run = ['_run-' sprintf(cfg.fileName.pattern, cfg.subject.runNb)];
 
     % set values for the suffixes for the different fields in the BIDS name
     fields2Check = { ...
-        'ce', ...
-        'dir', ...  % For BIDS file naming: phase encoding direction of acquisition for fMRI
-        'rec', ...  % For BIDS file naming: reconstruction of fMRI images
-        'echo', ... % For BIDS file naming: echo fMRI images
-        'acq'       % For BIDS file naming: acquisition of fMRI images
+        'contrastEnhancement', ...
+        'phaseEncodingDirection', ...
+        'reconstruction', ...
+        'echo', ...
+        'acquisition'
         };
 
     for iField = 1:numel(fields2Check)
-        if isempty (expParameters.MRI.(fields2Check{iField})) %#ok<*GFLD>
-            expParameters.MRI.([fields2Check{iField} 'Suffix']) = ''; %#ok<*SFLD>
+        if isempty (cfg.mri.(fields2Check{iField})) %#ok<*GFLD>
+            cfg.fileName.suffix.mri.(fields2Check{iField}) = ''; %#ok<*SFLD>
         else
-            expParameters.MRI.([fields2Check{iField} 'Suffix']) = ...
-                ['_' fields2Check{iField} '-' getfield(expParameters.MRI, fields2Check{iField})];
+            cfg.fileName.suffix.mri.(fields2Check{iField}) = ...
+                ['_' fields2Check{iField} '-' getfield(cfg.mri, fields2Check{iField})];
         end
     end
 
+    cfg.fileName.suffix = orderfields(cfg.fileName.suffix);
+
 end
 
-function expParameters = setFilenames(cfg, expParameters)
+function cfg = setFilenames(cfg)
 
-    [subjectGrp, subjectNb, sessionNb, modality, taskName] = extractInput(expParameters);
+    [subjectGrp, subjectNb, sessionNb, modality, taskName] = extractInput(cfg);
 
-    runSuffix = expParameters.runSuffix;
-    pattern = expParameters.pattern;
-    acqSuffix = expParameters.MRI.acqSuffix ;
-    ceSuffix = expParameters.MRI.ceSuffix ;
-    dirSuffix = expParameters.MRI.dirSuffix ;
-    recSuffix = expParameters.MRI.recSuffix ;
-    echoSuffix = expParameters.MRI.echoSuffix;
+    pattern = cfg.fileName.pattern;
 
-    expParameters.datasetDescription.filename = fullfile ( ...
-        expParameters.outputDir, ...
+    runSuffix = cfg.fileName.suffix.run;
+    acqSuffix = cfg.fileName.suffix.mri.acquisition ;
+    ceSuffix = cfg.fileName.suffix.mri.contrastEnhancement ;
+    dirSuffix = cfg.fileName.suffix.mri.phaseEncodingDirection ;
+    recSuffix = cfg.fileName.suffix.mri.reconstruction ;
+    echoSuffix = cfg.fileName.suffix.mri.echo;
+
+    thisDate = cfg.fileName.date;
+
+    cfg.fileName.datasetDescription = fullfile ( ...
+        cfg.dir.output, ...
         'dataset_description.json');
 
-    % create base filename
+    % create base fileName
     fileNameBase = ...
         ['sub-', subjectGrp, sprintf(pattern, subjectNb), ...
         '_ses-', sprintf(pattern, sessionNb), ...
         '_task-', taskName];
-    expParameters.fileName.base = fileNameBase;
+    cfg.fileName.base = fileNameBase;
 
     switch modality
 
         case 'func'
 
-            expParameters.fileName.events = ...
+            cfg.fileName.events = ...
                 [fileNameBase, ...
                 acqSuffix, ceSuffix, ...
                 dirSuffix, recSuffix, ...
                 runSuffix, echoSuffix, ...
-                '_events_date-' expParameters.date '.tsv'];
+                '_events_date-' thisDate '.tsv'];
 
         otherwise
 
-            expParameters.fileName.events = ...
-                [fileNameBase, runSuffix, '_events_date-' expParameters.date '.tsv'];
+            cfg.fileName.events = ...
+                [fileNameBase, runSuffix, '_events_date-' thisDate '.tsv'];
 
     end
 
-    expParameters.fileName.stim = strrep(expParameters.fileName.events, 'events', 'stim');
+    cfg.fileName.stim = strrep(cfg.fileName.events, 'events', 'stim');
 
-    if cfg.eyeTracker
-        expParameters.fileName.eyetracker = ...
+    if cfg.eyeTracker.do
+        cfg.fileName.eyetracker = ...
             [fileNameBase, acqSuffix, ...
-            runSuffix, '_eyetrack_date-' expParameters.date '.edf'];
-
+            runSuffix, '_eyetrack_date-' thisDate '.edf'];
     end
 
 end
 
-function talkToMe(cfg, expParameters)
+function talkToMe(cfg)
 
     fprintf(1, '\nData will be saved in this directory:\n\t%s\n', ...
-        fullfile(expParameters.subjectOutputDir, expParameters.modality));
+        fullfile(cfg.dir.outputSubject, cfg.fileName.modality));
 
     fprintf(1, '\nData will be saved in this file:\n\t%s\n', ...
-        expParameters.fileName.events);
+        cfg.fileName.events);
 
-    if cfg.eyeTracker
+    if cfg.eyeTracker.do
 
         fprintf(1, '\nEyetracking data will be saved in this directory:\n\t%s\n', ...
-            fullfile(expParameters.subjectOutputDir, 'eyetracker'));
+            fullfile(cfg.dir.outputSubject, 'eyetracker'));
 
         fprintf(1, '\nEyetracking data will be saved in this file:\n\t%s\n', ...
-            expParameters.fileName.eyetracker);
+            cfg.fileName.eyetracker);
 
     end
 
diff --git a/printCreditsCppBids.m b/printCreditsCppBids.m
index 678130c8..bfb3f252 100644
--- a/printCreditsCppBids.m
+++ b/printCreditsCppBids.m
@@ -1,16 +1,18 @@
 function printCreditsCppBids()
-    
+
     version = '0.0.1';
-    
+
     contributors = { ...
         'Rémi Gau', ...
         'Marco Barilari', ...
         'Ceren Battal'};
-    
+
     % DOI_URL = 'https://doi.org/10.5281/zenodo.3554331.';
-    
+
     repoURL = 'https://github.com/cpp-lln-lab/CPP_BIDS';
-    
+
+    fprintf('\n\n');
+
     disp('___________________________________________________');
     disp('___________________________________________________');
     disp('                                                   ');
@@ -19,25 +21,24 @@ function printCreditsCppBids()
     disp('       | (__|  _/  _/ | _ \| || |) \__ \');
     disp('        \___|_| |_|   |___/___|___/|___/');
     disp('                                                   ');
-    
-    
+
     splash = 'Thank you for using the CPP BIDS - version %s. ';
     fprintf(splash, version);
     fprintf('\n\n');
-    
+
     fprintf('Current list of contributors includes:\n');
     for iCont = 1:numel(contributors)
         fprintf(' %s\n', contributors{iCont});
     end
     fprintf('\b\n\n');
-    
+
     % fprintf('Please cite using the following DOI: \n %s\n\n', DOI_URL)
-    
+
     fprintf('For bug report, suggestions or contributions see: \n %s\n\n', repoURL);
-    
+
     disp('___________________________________________________');
     disp('___________________________________________________');
-    
+
     fprintf('\n\n');
-    
+
 end
diff --git a/saveEventsFile.m b/saveEventsFile.m
index 9945bdf6..76891037 100644
--- a/saveEventsFile.m
+++ b/saveEventsFile.m
@@ -1,4 +1,4 @@
-function [logFile] = saveEventsFile(action, expParameters, logFile)
+function [logFile] = saveEventsFile(action, cfg, logFile)
     % Function to save output files for events that will be BIDS compliant.
     %
     % INPUTS
@@ -47,7 +47,7 @@
     end
 
     if nargin < 2
-        expParameters = struct();
+        cfg = struct();
     end
 
     if nargin < 3 || isempty(logFile)
@@ -62,50 +62,22 @@
 
         case 'open'
 
-            logFile.filename = expParameters.fileName.events;
+            logFile.filename = cfg.fileName.events;
 
-            logFile = initializeFile(expParameters, logFile);
+            logFile = initializeFile(cfg, logFile);
 
         case 'open_stim'
 
-            logFile.filename = expParameters.fileName.stim;
+            logFile.filename = cfg.fileName.stim;
 
-            logFile = initializeFile(expParameters, logFile);
+            logFile = initializeFile(cfg, logFile);
 
         case 'save'
 
             checklLogFile('checkID', logFile);
             checklLogFile('type&size', logFile);
 
-            % appends to the logfile all the data stored in the structure
-            % first with the standard BIDS data and then any extra things
-            for iEvent = 1:size(logFile, 1)
-
-                logFile = checklLogFile('fields', logFile, iEvent);
-
-                onset = logFile(iEvent).onset;
-                duration = logFile(iEvent).duration;
-                trial_type = logFile(iEvent).trial_type;
-
-                if isnan(onset) || ischar(onset) || any(isempty({onset trial_type})) || ...
-                        strcmp(trial_type, 'n/a')
-
-                    warning('\nSkipping saving this event.\n onset: %f \n trial_type: %s\n', ...
-                        onset, ...
-                        trial_type);
-
-                else
-
-                    printData(logFile(1).fileID, onset);
-                    printData(logFile(1).fileID, duration);
-                    printData(logFile(1).fileID, trial_type);
-
-                    printExtraColumns(logFile, iEvent);
-
-                    fprintf(logFile(1).fileID, '\n');
-
-                end
-            end
+            logFile = saveToLogFile(logFile);
 
         case 'close'
 
@@ -116,8 +88,8 @@
 
             fprintf(1, '\nData were saved in this file:\n\n%s\n\n', ...
                 fullfile( ...
-                expParameters.subjectOutputDir, ...
-                expParameters.modality, ...
+                cfg.dir.outputSubject, ...
+                cfg.fileName.modality, ...
                 logFile.filename));
 
         otherwise
@@ -153,14 +125,10 @@
 
         case 'fields'
 
-            if ~isfield(logFile, 'onset') || isempty(logFile(iEvent).onset)
-                logFile(iEvent).onset = nan;
-            end
-            if ~isfield(logFile, 'trial_type') || isempty(logFile(iEvent).trial_type)
-                logFile(iEvent).trial_type = nan;
-            end
-            if ~isfield(logFile, 'duration') || isempty(logFile(iEvent).duration)
-                logFile(iEvent).duration = nan;
+            for iFields = {'onset', 'trial_type', 'duration'}
+                if ~isfield(logFile, iFields) || isempty(logFile(iEvent).(iFields{1}))
+                    logFile(iEvent).(iFields{1}) = nan;
+                end
             end
 
             logFile = checkExtracolumns(logFile, iEvent);
@@ -169,18 +137,18 @@
 
 end
 
-function logFile = initializeFile(expParameters, logFile)
+function logFile = initializeFile(cfg, logFile)
 
     logFile = initializeExtraColumns(logFile);
 
-    createDataDictionary(expParameters, logFile);
+    createDataDictionary(cfg, logFile);
 
     % Initialize txt logfiles and empty fields for the standard BIDS
     %  event file
     logFile.fileID = fopen( ...
         fullfile( ...
-        expParameters.subjectOutputDir, ...
-        expParameters.modality, ...
+        cfg.dir.outputSubject, ...
+        cfg.fileName.modality, ...
         logFile.filename), ...
         'w');
 
@@ -232,7 +200,9 @@ function printHeaderExtraColumns(logFile)
             data = logFile(iEvent).(namesExtraColumns{iExtraColumn});
         end
 
-        data = checkInput(data, nbCol);
+        data = checkInput(data);
+
+        data = nanPadding(data, nbCol);
 
         logFile(iEvent).(namesExtraColumns{iExtraColumn}) = data;
 
@@ -248,15 +218,11 @@ function printHeaderExtraColumns(logFile)
 
 end
 
-function data = checkInput(data, expectedLength)
+function data = checkInput(data)
     % check the data to write
     % default will be 'n/a' for chars and NaN for numeric data
     % for numeric data that don't have the expected length, it will be padded with NaNs
 
-    if nargin < 2
-        expectedLength = [];
-    end
-
     if islogical(data) && data
         data = 'true';
     elseif islogical(data) && ~data
@@ -271,12 +237,54 @@ function printHeaderExtraColumns(logFile)
         data = nan;
     end
 
+end
+
+function data = nanPadding(data, expectedLength)
+
+    if nargin < 2
+        expectedLength = [];
+    end
+
     if ~isempty(expectedLength) && isnumeric(data) && max(size(data)) < expectedLength
         padding = expectedLength - max(size(data));
         data(end + 1:end + padding) = nan(1, padding);
     elseif ~isempty(expectedLength) && isnumeric(data) && max(size(data)) > expectedLength
-        data = data(1:expectedLength);
         warning('A field for this event is longer than expected. Truncating the extra values.');
+        data = data(1:expectedLength);
+    end
+
+end
+
+function logFile = saveToLogFile(logFile)
+
+    % appends to the logfile all the data stored in the structure
+    % first with the standard BIDS data and then any extra things
+    for iEvent = 1:size(logFile, 1)
+
+        logFile = checklLogFile('fields', logFile, iEvent);
+
+        onset = logFile(iEvent).onset;
+        duration = logFile(iEvent).duration;
+        trial_type = logFile(iEvent).trial_type;
+
+        if isnan(onset) || ischar(onset) || any(isempty({onset trial_type})) || ...
+                strcmp(trial_type, 'n/a')
+
+            warning('\nSkipping saving this event.\n onset: %f \n trial_type: %s\n', ...
+                onset, ...
+                trial_type);
+
+        else
+
+            printData(logFile(1).fileID, onset);
+            printData(logFile(1).fileID, duration);
+            printData(logFile(1).fileID, trial_type);
+
+            printExtraColumns(logFile, iEvent);
+
+            fprintf(logFile(1).fileID, '\n');
+
+        end
     end
 
 end
diff --git a/subfun/createTaskName.m b/subfun/createTaskName.m
new file mode 100644
index 00000000..6b3fd62b
--- /dev/null
+++ b/subfun/createTaskName.m
@@ -0,0 +1,17 @@
+function [taskName, taskNameValid] = createTaskName(taskName)
+    % [taskName, taskNameValid] = createTaskName(taskName)
+    %
+    % Name of the task (for resting state use the "rest" prefix). No two tasks
+    % should have the same name. Task label is derived from this field by
+    % removing all non alphanumeric ([a-zA-Z0-9]) characters.
+
+    % camel case: upper case for first letter for all words but the first one
+    spaceIdx = regexp(taskName, '[a-zA-Z0-9]*', 'start');
+    taskName(spaceIdx(2:end)) = upper(taskName(spaceIdx(2:end)));
+
+    % remove invalid characters
+    [unvalidCharacters] = regexp(taskName, '[^a-zA-Z0-9]');
+    taskNameValid = taskName;
+    taskNameValid(unvalidCharacters) = [];
+
+end
diff --git a/subfun/setDefaultFields.m b/subfun/setDefaultFields.m
index 75669017..e54f805f 100644
--- a/subfun/setDefaultFields.m
+++ b/subfun/setDefaultFields.m
@@ -1,5 +1,10 @@
 function structure = setDefaultFields(structure, fieldsToSet)
-    % loop through the defaults fiels to set and update if they don't exist
+    % structure = setDefaultFields(structure, fieldsToSet)
+    %
+    % recursively loop through the fields of a structure and sets a value if they don't exist
+    %
+
+    fieldsToSet = orderfields(fieldsToSet);
 
     names = fieldnames(fieldsToSet);
 
@@ -7,13 +12,23 @@
 
         thisField = fieldsToSet.(names{i});
 
-        structure = setFieldToIfNotPresent( ...
-            structure, ...
-            names{i}, ...
-            thisField);
+        if isfield(structure, names{i}) && isstruct(structure.(names{i}))
+
+            structure.(names{i}) = ...
+                setDefaultFields(structure.(names{i}), fieldsToSet.(names{i}));
+
+        else
+
+            structure = setFieldToIfNotPresent( ...
+                structure, ...
+                names{i}, ...
+                thisField);
+        end
 
     end
 
+    structure = orderfields(structure);
+
 end
 
 function structure = setFieldToIfNotPresent(structure, fieldName, value)
diff --git a/subfun/transferInfoToBids.m b/subfun/transferInfoToBids.m
new file mode 100644
index 00000000..7f239cf7
--- /dev/null
+++ b/subfun/transferInfoToBids.m
@@ -0,0 +1,16 @@
+function fieldsToSet = transferInfoToBids(fieldsToSet, cfg)
+    % transfer any info that might have been provided by the user to the
+    % relevant field for its reuse for BIDS filenames or JSON later
+
+    if isfield(cfg, 'task') && isfield(cfg.task, 'name')
+        [taskName, taskNameValid] = createTaskName(cfg.task.name);
+        fieldsToSet.fileName.task = taskNameValid;
+        fieldsToSet.bids.meg.TaskName = taskName;
+        fieldsToSet.bids.mri.TaskName = taskName;
+    end
+
+    if isfield(cfg, 'mri') && isfield(cfg.mri, 'repetitionTime')
+        fieldsToSet.bids.mri.RepetitionTime = cfg.mri.repetitionTime;
+    end
+
+end
diff --git a/tests/manualTests/miss_hit.cfg b/tests/manualTests/miss_hit.cfg
new file mode 100644
index 00000000..074b1ea7
--- /dev/null
+++ b/tests/manualTests/miss_hit.cfg
@@ -0,0 +1,3 @@
+line_length: 100
+regex_function_name: "(test_[a-z]+)(([A-Z]){1}[A-Za-z]+)*"
+suppress_rule: "copyright_notice"
\ No newline at end of file
diff --git a/tests/testmanual_makeRawDataset.m b/tests/manualTests/test_makeRawDataset.m
similarity index 61%
rename from tests/testmanual_makeRawDataset.m
rename to tests/manualTests/test_makeRawDataset.m
index ce176a41..e3ca4b3d 100644
--- a/tests/testmanual_makeRawDataset.m
+++ b/tests/manualTests/test_makeRawDataset.m
@@ -4,7 +4,7 @@ function test_makeRawDataset()
 
     clear;
 
-    outputDir = fullfile(fileparts(mfilename('fullpath')), '..', 'output');
+    outputDir = fullfile(fileparts(mfilename('fullpath')), 'output');
 
     if isdir(outputDir)
         rmdir(outputDir, 's');
@@ -14,16 +14,16 @@ function test_makeRawDataset()
 
     %%% set up
 
-    expParameters.subjectNb = 1;
-    expParameters.runNb = 1;
-    expParameters.task = 'testtask';
-    expParameters.outputDir = outputDir;
+    cfg.subject.subjectNb = 1;
+    cfg.subject.runNb = 1;
+    cfg.task.name = 'testtask';
+    cfg.dir.output = outputDir;
 
-    expParameters.bids.datasetDescription.Name = 'dummy';
-    expParameters.bids.datasetDescription.BIDSVersion = '1.0.0';
-    expParameters.bids.datasetDescription.Authors = {'Jane Doe', 'John Doe'};
+    cfg.bids.datasetDescription.Name = 'dummy';
+    cfg.bids.datasetDescription.BIDSVersion = '1.0.0';
+    cfg.bids.datasetDescription.Authors = {'Jane Doe', 'John Doe'};
 
-    expParameters.bids.MRI.RepetitionTime = 1.56;
+    cfg.bids.mri.RepetitionTime = 1.56;
 
     cfg.testingDevice = 'mri';
 
@@ -33,13 +33,13 @@ function test_makeRawDataset()
 
     %%% do stuff
 
-    [cfg, expParameters] = createFilename(cfg, expParameters); %#ok<*ASGLU>
+    cfg = createFilename(cfg);
 
     % create the events file and header
-    logFile = saveEventsFile('open', expParameters, logFile);
+    logFile = saveEventsFile('open', cfg, logFile);
 
-    createBoldJson(expParameters);
-    createDatasetDescription(expParameters);
+    createBoldJson(cfg);
+    createDatasetDescription(cfg);
 
     % ROW 2: normal events : all info is there
     logFile(1, 1).onset = 2;
@@ -68,19 +68,19 @@ function test_makeRawDataset()
     logFile(end, 1).duration = 3;
     logFile(end, 1).LHL24 = rand(1, 2);
 
-    saveEventsFile('save', expParameters, logFile);
+    saveEventsFile('save', cfg, logFile);
 
     % close the file
-    saveEventsFile('close', expParameters, logFile);
+    saveEventsFile('close', cfg, logFile);
 
     % add dummy functional data
-    funcDir = fullfile(expParameters.outputDir, 'source', 'sub-001', 'ses-001', 'func');
+    funcDir = fullfile(cfg.dir.output, 'source', 'sub-001', 'ses-001', 'func');
     boldFilename = 'sub-001_ses-001_task-testtask_run-001_bold.nii.gz';
     copyfile( ...
-        fullfile('..', 'dummyData', 'dummyData.nii.gz'), ...
+        fullfile('..', '..', 'dummyData', 'dummyData.nii.gz'), ...
         fullfile(funcDir, boldFilename));
 
     %%
 
-    convertSourceToRaw(expParameters);
+    convertSourceToRaw(cfg);
 end
diff --git a/tests/manualTests/test_userInput.m b/tests/manualTests/test_userInput.m
new file mode 100644
index 00000000..ce3edab0
--- /dev/null
+++ b/tests/manualTests/test_userInput.m
@@ -0,0 +1,41 @@
+clear;
+clc;
+
+%%
+fprintf('Debug\n');
+cfg.debug = true;
+
+cfg = userInputs(cfg);
+disp(cfg.subject);
+
+%%
+fprintf('No Group\n');
+cfg.debug = false;
+cfg.subject.askGrpSess = 0;
+
+cfg = userInputs(cfg);
+disp(cfg.subject);
+
+%%
+fprintf('No Group or session\n');
+cfg.debug = false;
+cfg.subject.askGrpSess = [0 0];
+
+cfg = userInputs(cfg);
+disp(cfg.subject);
+
+%%
+fprintf('No session\n');
+cfg.debug = false;
+cfg.subject.askGrpSess = [1 0];
+
+cfg = userInputs(cfg);
+disp(cfg.subject);
+
+%%
+fprintf('Default\n');
+cfg.debug = false;
+cfg.subject.askGrpSess = [];
+
+cfg = userInputs(cfg);
+disp(cfg.subject);
diff --git a/tests/test_checkCFG.m b/tests/test_checkCFG.m
index 2db865f2..8c2155ed 100644
--- a/tests/test_checkCFG.m
+++ b/tests/test_checkCFG.m
@@ -1,12 +1,13 @@
 function test_checkCFG()
 
-    expParameters.outputDir = fullfile(fileparts(mfilename('fullpath')), '..', 'output');
-    [cfg, expParameters] = checkCFG([], expParameters);
+    cfg.dir.output = fullfile(fileparts(mfilename('fullpath')), '..', 'output');
+    cfg = checkCFG(cfg);
 
     expectedStructure = returnExpectedStructure();
-    expectedStructure.outputDir = expParameters.outputDir;
+    expectedStructure.dir.output = cfg.dir.output;
+    expectedStructure.testingDevice = 'pc';
 
-    assert(isequal(expectedStructure, expParameters));
+    testSubFields(expectedStructure, cfg);
 
     %%
     fprintf('\n--------------------------------------------------------------------');
@@ -15,34 +16,44 @@ function test_checkCFG()
 
     outputDir = fullfile(fileparts(mfilename('fullpath')), '..', 'output');
 
-    expParameters.subjectNb = 1;
-    expParameters.runNb = 1;
-    expParameters.task = 'testtask';
-    expParameters.outputDir = outputDir;
+    cfg.subject.subjectNb = 1;
+    cfg.subject.runNb = 1;
 
-    expParameters.bids.datasetDescription.Name = 'dummy';
-    expParameters.bids.datasetDescription.BIDSVersion = '1.0.0';
-    expParameters.bids.datasetDescription.Authors = {'Jane Doe', 'John Doe'};
+    cfg.task.name = 'test task';
 
-    expParameters.bids.MRI.RepetitionTime = 1.56;
+    cfg.dir.output = outputDir;
+
+    cfg.bids.datasetDescription.Name = 'dummy';
+    cfg.bids.datasetDescription.BIDSVersion = '1.0.0';
+    cfg.bids.datasetDescription.Authors = {'Jane Doe', 'John Doe'};
+
+    cfg.mri.repetitionTime = 1.56;
 
     cfg.testingDevice = 'mri';
 
-    [~, expParameters] = checkCFG(cfg, expParameters);
+    cfg = checkCFG(cfg);
 
     %%% test
 
     % test data
     expectedStructure = returnExpectedStructure();
-    expectedStructure.subjectNb = 1;
-    expectedStructure.runNb = 1;
+    expectedStructure.subject.subjectNb = 1;
+    expectedStructure.subject.runNb = 1;
+
+    expectedStructure.dir.output = outputDir;
+
+    expectedStructure.task.name = 'test task';
+
+    expectedStructure.testingDevice = 'mri';
+
+    expectedStructure.mri.repetitionTime = 1.56;
 
-    expectedStructure.outputDir = outputDir;
+    expectedStructure.fileName.task = 'testTask';
 
-    expectedStructure.task = 'testtask';
+    expectedStructure.bids.mri.RepetitionTime = 1.56;
+    expectedStructure.bids.mri.TaskName = 'test Task';
 
-    expectedStructure.bids.MRI.RepetitionTime = 1.56;
-    expectedStructure.bids.MRI.TaskName = 'testtask';
+    expectedStructure.bids.meg.TaskName = 'test Task';
 
     expectedStructure.bids.datasetDescription.Name = 'dummy';
     expectedStructure.bids.datasetDescription.BIDSVersion =  '1.0.0';
@@ -50,7 +61,7 @@ function test_checkCFG()
 
     expectedStructure = orderfields(expectedStructure);
 
-    assert(isequal(expectedStructure, expParameters));
+    testSubFields(expectedStructure, cfg);
 
     fprintf('\n');
 
@@ -58,26 +69,38 @@ function test_checkCFG()
 
 function expectedStructure = returnExpectedStructure()
 
-    expectedStructure.subjectGrp = '';
-    expectedStructure.sessionNb = 1;
+    expectedStructure.subject.subjectGrp = '';
+    expectedStructure.subject.sessionNb = 1;
+    expectedStructure.subject.askGrpSess = [true true];
 
     expectedStructure.verbose = 0;
-    expectedStructure.askGrpSess = [true true];
-
-    expectedStructure.MRI.ce = [];
-    expectedStructure.MRI.dir = [];
-    expectedStructure.MRI.rec = [];
-    expectedStructure.MRI.echo = [];
-    expectedStructure.MRI.acq = [];
-
-    expectedStructure.bids.MRI.RepetitionTime = [];
-    expectedStructure.bids.MRI.SliceTiming = '';
-    expectedStructure.bids.MRI.TaskName = '';
-    %     expectedStructure.bids.MRI.PhaseEncodingDirection = '';
-    %     expectedStructure.bids.MRI.EffectiveEchoSpacing = '';
-    %     expectedStructure.bids.MRI.EchoTime = '';
-    expectedStructure.bids.MRI.Instructions = '';
-    expectedStructure.bids.MRI.TaskDescription = '';
+
+    expectedStructure.fileName.task = '';
+    expectedStructure.fileName.zeroPadding = 3;
+    expectedStructure.fileName.dateFormat = 'yyyymmddHHMM';
+
+    expectedStructure.eyeTracker.do = false;
+
+    expectedStructure.mri.contrastEnhancement = [];
+    expectedStructure.mri.phaseEncodingDirection = [];
+    expectedStructure.mri.reconstruction = [];
+    expectedStructure.mri.echo = [];
+    expectedStructure.mri.acquisition = [];
+    expectedStructure.mri.repetitionTime = [];
+
+    expectedStructure.bids.mri.RepetitionTime = [];
+    expectedStructure.bids.mri.SliceTiming = '';
+    expectedStructure.bids.mri.TaskName = '';
+    expectedStructure.bids.mri.Instructions = '';
+    expectedStructure.bids.mri.TaskDescription = '';
+
+    expectedStructure.bids.meg.TaskName = '';
+    expectedStructure.bids.meg.SamplingFrequency = [];
+    expectedStructure.bids.meg.PowerLineFrequency = [];
+    expectedStructure.bids.meg.DewarPosition = [];
+    expectedStructure.bids.meg.SoftwareFilters = [];
+    expectedStructure.bids.meg.DigitizedLandmarks = [];
+    expectedStructure.bids.meg.DigitizedHeadPoints = [];
 
     expectedStructure.bids.datasetDescription.Name = '';
     expectedStructure.bids.datasetDescription.BIDSVersion =  '';
@@ -90,4 +113,35 @@ function test_checkCFG()
     expectedStructure.bids.datasetDescription.DatasetDOI = '';
 
     expectedStructure = orderfields(expectedStructure);
+
+end
+
+function testSubFields(expectedStructure, cfg)
+    % check that that the structures match
+    % if it fails it check from which subfield the error comes from
+
+    try
+
+        assert(isequal(expectedStructure, cfg));
+
+    catch ME
+
+        if isstruct(expectedStructure)
+
+            names = fieldnames(expectedStructure);
+
+            for i = 1:numel(names)
+
+                disp(names{i});
+                testSubFields(expectedStructure.(names{i}), cfg.(names{i}));
+
+            end
+
+        end
+
+        expectedStructure;
+        cfg;
+
+        rethrow(ME);
+    end
 end
diff --git a/tests/test_createBoldJson.m b/tests/test_createBoldJson.m
index b5bd9130..72348bfa 100644
--- a/tests/test_createBoldJson.m
+++ b/tests/test_createBoldJson.m
@@ -4,26 +4,26 @@ function test_createBoldJson()
 
     %%% set up part
 
-    expParameters.subjectNb = 1;
-    expParameters.runNb = 1;
-    expParameters.task = 'testtask';
-    expParameters.outputDir = outputDir;
+    cfg.subject.subjectNb = 1;
+    cfg.subject.runNb = 1;
+    cfg.task.name = 'testtask';
+    cfg.dir.output = outputDir;
 
-    cfg = struct();
+    % cfg = struct();
     cfg.testingDevice = 'mri';
 
-    [cfg, expParameters] = createFilename(cfg, expParameters);  %#ok<*ASGLU>
+    cfg = createFilename(cfg);
 
-    logFile = saveEventsFile('init', expParameters); %#ok<*NASGU>
+    logFile = saveEventsFile('init', cfg); %#ok<*NASGU>
 
-    createBoldJson(expParameters);
+    createBoldJson(cfg);
 
     %%% test part
 
     % test data
     funcDir = fullfile(outputDir, 'source', 'sub-001', 'ses-001', 'func');
     eventFilename = ['sub-001_ses-001_task-testtask_run-001_bold_date-' ...
-        expParameters.date '.json'];
+        cfg.fileName.date '.json'];
 
     % check that the file has the right path and name
     assert(exist(fullfile(funcDir, eventFilename), 'file') == 2);
diff --git a/tests/test_createDataDictionary.m b/tests/test_createDataDictionary.m
index d5875706..c9bf1a81 100644
--- a/tests/test_createDataDictionary.m
+++ b/tests/test_createDataDictionary.m
@@ -6,28 +6,27 @@ function test_createDataDictionary()
 
     %%% set up part
 
-    expParameters.subjectNb = 1;
-    expParameters.runNb = 1;
-    expParameters.task = 'testtask';
-    expParameters.outputDir = outputDir;
+    cfg.subject.subjectNb = 1;
+    cfg.subject.runNb = 1;
+    cfg.task.name = 'testtask';
+    cfg.dir.output = outputDir;
 
-    cfg = struct();
     cfg.testingDevice = 'mri';
 
-    [cfg, expParameters] = createFilename(cfg, expParameters); %#ok<ASGLU>
+    cfg = createFilename(cfg);
 
     logFile.extraColumns.Speed.length = 1;
     logFile.extraColumns.LHL24.length = 3;
-    logFile = saveEventsFile('init', expParameters, logFile);
+    logFile = saveEventsFile('init', cfg, logFile);
 
-    createDataDictionary(expParameters, logFile);
+    createDataDictionary(cfg, logFile);
 
     %%% test part
 
     % test data
     funcDir = fullfile(outputDir, 'source', 'sub-001', 'ses-001', 'func');
     jsonFilename = ['sub-001_ses-001_task-testtask_run-001_events_date-' ...
-        expParameters.date '.json'];
+        cfg.fileName.date '.json'];
 
     % check that the file has the right path and name
     assert(exist(fullfile(funcDir, jsonFilename), 'file') == 2);
diff --git a/tests/test_createDatasetDescription.m b/tests/test_createDatasetDescription.m
index 07ee42f5..629fe432 100644
--- a/tests/test_createDatasetDescription.m
+++ b/tests/test_createDatasetDescription.m
@@ -4,18 +4,16 @@ function test_createDatasetDescription()
 
     %%% set up part
 
-    expParameters.outputDir = outputDir;
+    cfg.dir.output = outputDir;
 
-    expParameters.bids.datasetDescription.json.Name = 'dummy_dataset';
-    expParameters.bids.datasetDescription.json.BIDSVersion = '1.0.0';
-    expParameters.bids.datasetDescription.json.License = 'none';
-    expParameters.bids.datasetDescription.json.Authors = {'Jane Doe'};
+    cfg.bids.datasetDescription.json.Name = 'dummy_dataset';
+    cfg.bids.datasetDescription.json.BIDSVersion = '1.0.0';
+    cfg.bids.datasetDescription.json.License = 'none';
+    cfg.bids.datasetDescription.json.Authors = {'Jane Doe'};
 
-    cfg = struct();
+    cfg = checkCFG(cfg);
 
-    [cfg, expParameters] = checkCFG(cfg, expParameters); %#ok<*ASGLU>
-
-    createDatasetDescription(expParameters);
+    createDatasetDescription(cfg);
 
     %%% test part
 
diff --git a/tests/test_createFilename.m b/tests/test_createFilename.m
index 171ed583..ebce891f 100644
--- a/tests/test_createFilename.m
+++ b/tests/test_createFilename.m
@@ -7,25 +7,23 @@ function test_createFilename()
 
     %%% set up part
 
-    expParameters.subjectNb = 1;
-    expParameters.runNb = 1;
-    expParameters.task = 'testtask';
-    expParameters.outputDir = outputDir;
-
-    cfg = struct();
+    cfg.subject.subjectNb = 1;
+    cfg.subject.runNb = 1;
+    cfg.task.name = 'test task';
+    cfg.dir.output = outputDir;
 
     %%% run part
-    [cfg, expParameters] = createFilename(cfg, expParameters);
+    cfg = createFilename(cfg);
 
     %%% test part
 
     % test data
     behDir = fullfile(outputDir, 'source', 'sub-001', 'ses-001', 'beh');
     eyetrackerDir = fullfile(outputDir, 'source', 'sub-001', 'ses-001', 'eyetracker');
-    eventFilename = ['sub-001_ses-001_task-testtask_run-001_events_date-'...
-        expParameters.date '.tsv'];
-    stimFilename =  ['sub-001_ses-001_task-testtask_run-001_stim_date-'...
-        expParameters.date '.tsv'];
+    eventFilename = ['sub-001_ses-001_task-testTask_run-001_events_date-'...
+        cfg.fileName.date '.tsv'];
+    stimFilename =  ['sub-001_ses-001_task-testTask_run-001_stim_date-'...
+        cfg.fileName.date '.tsv'];
 
     % make sure the beh dir is created
     assert(exist(behDir, 'dir') == 7);
@@ -34,10 +32,10 @@ function test_createFilename()
     assert(exist(eyetrackerDir, 'dir') == 0);
 
     % make sure the events filename is created
-    assert(strcmp(expParameters.fileName.events, eventFilename));
+    assert(strcmp(cfg.fileName.events, eventFilename));
 
     % make sure the stim filename is created
-    assert(strcmp(expParameters.fileName.stim, stimFilename));
+    assert(strcmp(cfg.fileName.stim, stimFilename));
 
     %% fMRI and eye tracker
     fprintf('\n--------------------------------------------------------------------');
@@ -48,28 +46,28 @@ function test_createFilename()
 
     %%% set up part
 
-    expParameters.subjectGrp = 'ctrl';
-    expParameters.subjectNb = 2;
-    expParameters.sessionNb = 2;
-    expParameters.runNb = 2;
-    expParameters.task = 'testtask';
-    expParameters.outputDir = outputDir;
+    cfg.subject.subjectGrp = 'ctrl';
+    cfg.subject.subjectNb = 2;
+    cfg.subject.sessionNb = 2;
+    cfg.subject.runNb = 2;
+    cfg.task.name = 'test task';
+    cfg.dir.output = outputDir;
 
-    cfg.eyeTracker = true;
+    cfg.eyeTracker.do = true;
     cfg.testingDevice = 'mri';
 
-    [cfg, expParameters] = createFilename(cfg, expParameters);
+    cfg = createFilename(cfg);
 
     %%% test part
 
     % test data
     funcDir = fullfile(outputDir, 'source', 'sub-ctrl002', 'ses-002', 'func');
     eyetrackerDir = fullfile(outputDir, 'source', 'sub-ctrl002', 'ses-002', 'eyetracker');
-    baseFilename = 'sub-ctrl002_ses-002_task-testtask';
-    eventFilename = ['sub-ctrl002_ses-002_task-testtask_run-002_events_date-' ...
-        expParameters.date '.tsv'];
-    eyetrackerFilename =  ['sub-ctrl002_ses-002_task-testtask_run-002_eyetrack_date-' ...
-        expParameters.date '.edf'];
+    baseFilename = 'sub-ctrl002_ses-002_task-testTask';
+    eventFilename = ['sub-ctrl002_ses-002_task-testTask_run-002_events_date-' ...
+        cfg.fileName.date '.tsv'];
+    eyetrackerFilename =  ['sub-ctrl002_ses-002_task-testTask_run-002_eyetrack_date-' ...
+        cfg.fileName.date '.edf'];
 
     % make sure the func dir is created
     assert(exist(funcDir, 'dir') == 7);
@@ -78,9 +76,9 @@ function test_createFilename()
     assert(exist(eyetrackerDir, 'dir') == 7);
 
     % make sure the right filenames are created
-    assert(strcmp(expParameters.fileName.base, baseFilename));
-    assert(strcmp(expParameters.fileName.events, eventFilename));
-    assert(strcmp(expParameters.fileName.eyetracker, eyetrackerFilename));
+    assert(strcmp(cfg.fileName.base, baseFilename));
+    assert(strcmp(cfg.fileName.events, eventFilename));
+    assert(strcmp(cfg.fileName.eyetracker, eyetrackerFilename));
 
     %% EEG
     fprintf('\n--------------------------------------------------------------------');
@@ -91,16 +89,16 @@ function test_createFilename()
 
     %%% set up part
 
-    expParameters.subjectGrp = 'blind';
-    expParameters.subjectNb = 3;
-    expParameters.sessionNb = 1;
-    expParameters.runNb = 1;
-    expParameters.task = 'testtask';
-    expParameters.outputDir = outputDir;
+    cfg.subject.subjectGrp = 'blind';
+    cfg.subject.subjectNb = 3;
+    cfg.subject.sessionNb = 1;
+    cfg.subject.runNb = 1;
+    cfg.task.name = 'test task';
+    cfg.dir.output = outputDir;
 
     cfg.testingDevice = 'eeg';
 
-    [cfg, expParameters] = createFilename(cfg, expParameters); %#ok<ASGLU>
+    cfg = createFilename(cfg);
 
     %%% test part
 
diff --git a/tests/test_createTaskName.m b/tests/test_createTaskName.m
new file mode 100644
index 00000000..6f30fe35
--- /dev/null
+++ b/tests/test_createTaskName.m
@@ -0,0 +1,25 @@
+function test_createTaskName()
+    %
+
+    taskName = '&|@#-_(§!{})[]ù%£+/=:;.?,\<> visual task';
+
+    [taskName, taskNameValid] = createTaskName(taskName);
+
+    [unvalidCharacters] = regexp(taskNameValid, '[^a-zA-Z0-9]');
+
+    assert(isempty(unvalidCharacters));
+
+    taskName = ' 09 visual task';
+
+    [taskName, taskNameValid] = createTaskName(taskName);
+
+    [unvalidCharacters] = regexp(taskNameValid, '[^a-zA-Z0-9]');
+
+    assert(isempty(unvalidCharacters));
+
+    taskName = 'foo bar';
+    [taskName, taskNameValid] = createTaskName(taskName);
+    assert(isequal(taskName, 'foo Bar'));
+    assert(isequal(taskNameValid, 'fooBar'));
+
+end
diff --git a/tests/test_saveEventsFileInit.m b/tests/test_saveEventsFileInit.m
index 765f96f3..ca0ecf02 100644
--- a/tests/test_saveEventsFileInit.m
+++ b/tests/test_saveEventsFileInit.m
@@ -21,11 +21,11 @@ function test_saveEventsFileInit()
     clear;
 
     %%% set up
-    [cfg, expParameters] = checkCFG(); %#ok<ASGLU>
+    cfg = checkCFG();
     logFile.extraColumns = {'Speed'};
 
     %%% do stuff
-    [logFile] = saveEventsFile('init', expParameters, logFile);
+    [logFile] = saveEventsFile('init', cfg, logFile);
 
     %%% test section
     expectedStrcut(1).extraColumns.Speed.length = 1;
@@ -42,12 +42,12 @@ function test_saveEventsFileInit()
     clear;
 
     %%% set up
-    [cfg, expParameters] = checkCFG(); %#ok<ASGLU>
+    cfg = checkCFG();
     logFile.extraColumns.Speed.length = 1;
     logFile.extraColumns.LHL24.length = 3;
 
     %%% do stuff
-    [logFile] = saveEventsFile('init', expParameters, logFile);
+    [logFile] = saveEventsFile('init', cfg, logFile);
 
     %%% test section
     expectedStrcut(1).extraColumns.Speed.length = 1;
diff --git a/tests/test_saveEventsFileOpen.m b/tests/test_saveEventsFileOpen.m
index 21d52954..032f5f47 100644
--- a/tests/test_saveEventsFileOpen.m
+++ b/tests/test_saveEventsFileOpen.m
@@ -7,37 +7,36 @@ function test_saveEventsFileOpen()
 
     %%% set up
 
-    expParameters.subjectNb = 1;
-    expParameters.runNb = 1;
-    expParameters.task = 'testtask';
-    expParameters.outputDir = outputDir;
+    cfg.subject.subjectNb = 1;
+    cfg.subject.runNb = 1;
+    cfg.task.name = 'testtask';
+    cfg.dir.output = outputDir;
 
     cfg.testingDevice = 'mri';
 
     %%% do stuff
 
-    [cfg, expParameters] = createFilename(cfg, expParameters);
+    cfg = createFilename(cfg);
 
     % create the events file and header
-    logFile = saveEventsFile('open', expParameters);
+    logFile = saveEventsFile('open', cfg);
 
     % close the file
-    saveEventsFile('close', expParameters, logFile);
+    saveEventsFile('close', cfg, logFile);
 
     %%% test section
 
     % test data
     funcDir = fullfile(outputDir, 'source', 'sub-001', 'ses-001', 'func');
     eventFilename = ['sub-001_ses-001_task-testtask_run-001_events_date-' ...
-        expParameters.date '.tsv'];
-
-    % open the file
-    FID = fopen(fullfile(funcDir, eventFilename), 'r');
-    C = textscan(FID, repmat('%s', 1, 3), 'Delimiter', '\t', 'EndOfLine', '\n');
+        cfg.fileName.date '.tsv'];
 
     % check that the file has the right path and name
     assert(exist(fullfile(funcDir, eventFilename), 'file') == 2);
 
+    FID = fopen(fullfile(funcDir, eventFilename), 'r');
+    C = textscan(FID, repmat('%s', 1, 3), 'Delimiter', '\t', 'EndOfLine', '\n');
+
     % check the extra columns of the header
     assert(isequal(C{1}{1}, 'onset'));
     assert(isequal(C{2}{1}, 'duration'));
@@ -52,10 +51,10 @@ function test_saveEventsFileOpen()
 
     %%% set up
 
-    expParameters.subjectNb = 1;
-    expParameters.runNb = 1;
-    expParameters.task = 'testtask';
-    expParameters.outputDir = outputDir;
+    cfg.subject.subjectNb = 1;
+    cfg.subject.runNb = 1;
+    cfg.task.name = 'testtask';
+    cfg.dir.output = outputDir;
 
     cfg.testingDevice = 'mri';
 
@@ -64,23 +63,22 @@ function test_saveEventsFileOpen()
 
     %%% do stuff
 
-    [cfg, expParameters] = createFilename(cfg, expParameters); %#ok<ASGLU>
+    cfg = createFilename(cfg);
 
     % create the events file and header
-    logFile = saveEventsFile('open', expParameters, logFile);
+    logFile = saveEventsFile('open', cfg, logFile);
 
     % close the file
-    saveEventsFile('close', expParameters, logFile);
+    saveEventsFile('close', cfg, logFile);
 
     %%% test section
 
     % open the file
+    funcDir = fullfile(cfg.dir.outputSubject, cfg.fileName.modality);
+    eventFilename = cfg.fileName.events;
+
     nbExtraCol = 2;
-    FID = fopen(fullfile( ...
-        expParameters.subjectOutputDir, ...
-        expParameters.modality, ...
-        expParameters.fileName.events), ...
-        'r');
+    FID = fopen(fullfile(funcDir, eventFilename), 'r');
     C = textscan(FID, repmat('%s', 1, nbExtraCol + 3), 'Delimiter', '\t', 'EndOfLine', '\n');
 
     % check the extra columns of the header
diff --git a/tests/test_saveEventsFileOpenMultiColumn.m b/tests/test_saveEventsFileOpenMultiColumn.m
index d1415fbf..69b0dc5b 100644
--- a/tests/test_saveEventsFileOpenMultiColumn.m
+++ b/tests/test_saveEventsFileOpenMultiColumn.m
@@ -7,14 +7,14 @@ function test_saveEventsFileOpenMultiColumn()
 
     %%% set up
 
-    expParameters.subjectNb = 1;
-    expParameters.runNb = 1;
-    expParameters.task = 'testtask';
-    expParameters.outputDir = outputDir;
+    cfg.subject.subjectNb = 1;
+    cfg.subject.runNb = 1;
+    cfg.task.name = 'testtask';
+    cfg.dir.output = outputDir;
 
     cfg.testingDevice = 'mri';
 
-    [cfg, expParameters] = createFilename(cfg, expParameters); %#ok<ASGLU>
+    cfg = createFilename(cfg);
 
     % define the extra columns: here we specify how many columns we want for
     % each variable
@@ -25,23 +25,23 @@ function test_saveEventsFileOpenMultiColumn()
     %%% do stuff
 
     % create the events file and header
-    logFile = saveEventsFile('open', expParameters, logFile);
+    logFile = saveEventsFile('open', cfg, logFile);
 
     % close the file
-    saveEventsFile('close', expParameters, logFile);
+    saveEventsFile('close', cfg, logFile);
 
     %%% test section
 
     % check the extra columns of the header and some of the content
+    funcDir = fullfile(cfg.dir.outputSubject, cfg.fileName.modality);
+    eventFilename = cfg.fileName.events;
+
     nbExtraCol = ...
         logFile(1).extraColumns.Speed.length + ...
         logFile(1).extraColumns.LHL24.length + ...
         logFile(1).extraColumns.is_Fixation.length;
-    FID = fopen(fullfile( ...
-        expParameters.subjectOutputDir, ...
-        expParameters.modality, ...
-        expParameters.fileName.events), ...
-        'r');
+
+    FID = fopen(fullfile(funcDir, eventFilename), 'r');
     C = textscan(FID, repmat('%s', 1, nbExtraCol + 3), 'Delimiter', '\t', 'EndOfLine', '\n');
 
     % check the extra columns of the header
diff --git a/tests/test_saveEventsFileSave.m b/tests/test_saveEventsFileSave.m
index ad3bfe84..9cc610c5 100644
--- a/tests/test_saveEventsFileSave.m
+++ b/tests/test_saveEventsFileSave.m
@@ -7,21 +7,21 @@ function test_saveEventsFileSave()
 
     %%% set up
 
-    expParameters.subjectNb = 1;
-    expParameters.runNb = 1;
-    expParameters.task = 'testtask';
-    expParameters.outputDir = outputDir;
+    cfg.subject.subjectNb = 1;
+    cfg.subject.runNb = 1;
+    cfg.task.name = 'testtask';
+    cfg.dir.output = outputDir;
 
     cfg.testingDevice = 'mri';
 
-    [cfg, expParameters] = createFilename(cfg, expParameters); %#ok<ASGLU>
+    cfg = createFilename(cfg);
 
     logFile.extraColumns.Speed.length = 1;
     logFile.extraColumns.LHL24.length = 12;
     logFile.extraColumns.is_Fixation.length = 1;
 
     % create the events file and header
-    logFile = saveEventsFile('open', expParameters, logFile);
+    logFile = saveEventsFile('open', cfg, logFile);
 
     %%% do stuff
 
@@ -33,7 +33,7 @@ function test_saveEventsFileSave()
     logFile(end, 1).is_Fixation = true;
     logFile(end, 1).LHL24 = 1:12;
 
-    logFile = saveEventsFile('save', expParameters, logFile);
+    logFile = saveEventsFile('save', cfg, logFile);
 
     % ROW 3: missing info (speed, LHL24)
     logFile(1, 1).onset = 3;
@@ -68,10 +68,10 @@ function test_saveEventsFileSave()
     %     logFile(end, 1).duration = 3;
     %     logFile(end, 1).LHL24 = rand(1, 15);
 
-    saveEventsFile('save', expParameters, logFile);
+    saveEventsFile('save', cfg, logFile);
 
     % close the file
-    saveEventsFile('close', expParameters, logFile);
+    saveEventsFile('close', cfg, logFile);
 
     %%% test section
 
@@ -80,11 +80,10 @@ function test_saveEventsFileSave()
         logFile(1).extraColumns.Speed.length + ...
         logFile(1).extraColumns.LHL24.length + ...
         logFile(1).extraColumns.is_Fixation.length;
-    FID = fopen(fullfile( ...
-        expParameters.subjectOutputDir, ...
-        expParameters.modality, ...
-        expParameters.fileName.events), ...
-        'r');
+
+    funcDir = fullfile(cfg.dir.outputSubject, cfg.fileName.modality);
+    eventFilename = cfg.fileName.events;
+    FID = fopen(fullfile(funcDir, eventFilename), 'r');
     C = textscan(FID, repmat('%s', 1, nbExtraCol + 3), 'Delimiter', '\t', 'EndOfLine', '\n');
 
     % event 1/ ROW 2: check that values are entered correctly
diff --git a/tests/test_setDefaultFields.m b/tests/test_setDefaultFields.m
new file mode 100644
index 00000000..b0aea0fc
--- /dev/null
+++ b/tests/test_setDefaultFields.m
@@ -0,0 +1,29 @@
+function test_setDefaultFields()
+
+    structure = struct();
+
+    fieldsToSet.field = 1;
+
+    structure = setDefaultFields(structure, fieldsToSet);
+
+    expectedStructure.field = 1;
+
+    assert(isequal(expectedStructure, structure));
+
+    fprintf('\n--------------------------------------------------------------------');
+
+    clear;
+
+    structure.field.subfield_1 = 3;
+
+    fieldsToSet.field.subfield_1 = 1;
+    fieldsToSet.field.subfield_2 = 1;
+
+    structure = setDefaultFields(structure, fieldsToSet);
+
+    expectedStructure.field.subfield_1 = 3;
+    expectedStructure.field.subfield_2 = 1;
+
+    assert(isequal(expectedStructure, structure));
+
+end
diff --git a/tests/test_transferInfoToBids.m b/tests/test_transferInfoToBids.m
new file mode 100644
index 00000000..5af1816f
--- /dev/null
+++ b/tests/test_transferInfoToBids.m
@@ -0,0 +1,35 @@
+function test_transferInfoToBids()
+
+    %%
+    cfg = struct();
+    fieldsToSet = struct();
+    cfg = transferInfoToBids(fieldsToSet, cfg);
+
+    expectedStruct = struct();
+
+    assert(isequal(expectedStruct, fieldsToSet));
+
+    %%
+    cfg.task.name = 'foo bar';
+
+    fieldsToSet = transferInfoToBids(fieldsToSet, cfg);
+
+    expectedStruct.fileName.task = 'fooBar';
+    expectedStruct.bids.meg.TaskName = 'foo Bar';
+    expectedStruct.bids.mri.TaskName = 'foo Bar';
+
+    assert(isequal(expectedStruct, fieldsToSet));
+
+    %%
+    clear cfg fieldsToSet expectedStruct;
+
+    cfg.mri.repetitionTime = 1.56;
+
+    fieldsToSet = struct();
+    fieldsToSet = transferInfoToBids(fieldsToSet, cfg);
+
+    expectedStruct.bids.mri.RepetitionTime = 1.56;
+
+    assert(isequal(expectedStruct, fieldsToSet));
+
+end
diff --git a/tests/userInput_test.m b/tests/userInput_test.m
deleted file mode 100644
index eae757a7..00000000
--- a/tests/userInput_test.m
+++ /dev/null
@@ -1,34 +0,0 @@
-%%
-cfg = struct('debug', true);
-expParameters = struct();
-
-[expParameters] = userInputs(cfg, expParameters);
-disp(expParameters);
-
-%%
-cfg = struct('debug', false);
-expParameters = struct('askGrpSess', 0);
-
-[expParameters] = userInputs(cfg, expParameters);
-disp(expParameters);
-
-%%
-cfg = struct('debug', false);
-expParameters = struct('askGrpSess', [0 0]);
-
-[expParameters] = userInputs(cfg, expParameters);
-disp(expParameters);
-
-%%
-cfg = struct('debug', false);
-expParameters = struct('askGrpSess', [0 1]);
-
-[expParameters] = userInputs(cfg, expParameters);
-disp(expParameters);
-
-%%
-cfg = struct('debug', false);
-expParameters = struct('askGrpSess', []);
-
-[expParameters] = userInputs(cfg, expParameters);
-disp(expParameters);
diff --git a/userInputs.m b/userInputs.m
index a6433949..8b153471 100644
--- a/userInputs.m
+++ b/userInputs.m
@@ -1,4 +1,4 @@
-function [expParameters] = userInputs(cfg, expParameters)
+function cfg = userInputs(cfg)
     % Get subject, run and session number and make sure they are
     % positive integer values
     %
@@ -8,16 +8,20 @@
     %    group
     %    - the second value set to false will skip asking for the session
 
-    if nargin < 1 || isempty(cfg.debug)
-        cfg.debug = false;
+    if nargin < 1
+        cfg = [];
     end
-    if nargin < 2
-        expParameters = [];
+    if isempty(cfg.debug)
+        cfg.debug = false;
     end
 
     askGrpSess = [true true];
-    if isfield(expParameters, 'askGrpSess') && ~isempty(expParameters.askGrpSess)
-        askGrpSess = expParameters.askGrpSess;
+    if isfield(cfg, 'subject') && ...
+            isfield(cfg.subject, 'askGrpSess') && ...
+            ~isempty(cfg.subject.askGrpSess)
+
+        askGrpSess = cfg.subject.askGrpSess;
+
     end
     if numel(askGrpSess) < 2
         askGrpSess(2) = 1;
@@ -59,10 +63,10 @@
 
     end
 
-    expParameters.subjectGrp = subjectGrp;
-    expParameters.subjectNb = subjectNb;
-    expParameters.sessionNb = sessionNb;
-    expParameters.runNb = runNb;
+    cfg.subject.subjectGrp = subjectGrp;
+    cfg.subject.subjectNb = subjectNb;
+    cfg.subject.sessionNb = sessionNb;
+    cfg.subject.runNb = runNb;
 
 end