Merge pull request #57 from CerenB/master

cfg conversion

Author: Remi-Gau

.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`

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

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

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);
 

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);
 

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( ...

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);