[DOC] update templates

src/batches/preproc/setBatchSTC.m

@@ -30,6 +30,10 @@
   %
   % (C) Copyright 2019 CPP_SPM developers
 
+  % TODO with multitask support it is even more needed to check
+  % that all files have the same slice timing and that might not be the case
+  % reflected in opt.metadata
+
   p = inputParser;
 
   addRequired(p, 'matlabbatch', @iscell);
@@ -60,12 +64,10 @@
   printBatchName('slice timing correction', opt);
 
   % get metadata for STC
-  % Note that slice ordering is assumed to be from foot to head. If it is not, enter
-  % instead: TR - INTRASCAN_TIME - SLICE_TIMING_VECTOR
 
-  % SPM accepts slice time acquisition as inputs for slice order (simplifies
-  % things when dealing with multiecho data)
-  nbSlices = length(sliceOrder); % unique is necessary in case of multi echo
+  % SPM accepts slice time acquisition as inputs for slice order
+  % (simplifies things when dealing with multiecho data)
+  nbSlices = length(sliceOrder);
   TR = opt.metadata.RepetitionTime;
   TA = TR - (TR / nbSlices);
   % round acquisition time to the upper millisecond
@@ -125,7 +127,6 @@
                                                    BIDS, ...
                                                    subLabel, sessions{iSes}, runs{iRun}, opt);
 
-      % % TODO remove this validation
       file = validationInputFile(subFuncDataDir, fileName);
 
       % add the file to the list
@@ -141,8 +142,4 @@
 
   matlabbatch{end + 1}.spm.temporal = temporal;
 
-  % The following lines are commented out because those parameters
-  % can be set in the spm_my_defaults.m
-  % matlabbatch{1}.spm.temporal.st.prefix = spm_get_defaults('slicetiming.prefix');
-
 end

src/workflows/preproc/bidsSTC.m

@@ -23,7 +23,7 @@ function bidsSTC(opt)
   % If no slice timing information is available from the file metadata or from
   % the ``opt`` strcuture this step will be skipped.
   %
-  % See also: getSliceOrder()
+  % See also: setBatchSTC, getSliceOrder
   %
   % See the documentation for more information about slice timing correction.
   %

templates/batch.m

@@ -0,0 +1,70 @@
+function matlabbatch = batch(varargin)
+  %
+  % Short batch description
+  %
+  % USAGE::
+  %
+  %   matlabbatch = setBatchTemplate(matlabbatch, BIDS, opt, subLabel)
+  %
+  % :param matlabbatch: matlabbatch to append to.
+  % :type matlabbatch: cell
+  % :param BIDS: BIDS layout returned by ``getData`` or ``bids.layout`.
+  % :type BIDS: structure
+  % :param opt: structure or json filename containing the options. See
+  %             ``checkOptions()`` and ``loadAndCheckOptions()``.
+  % :type opt: structure
+  % :param subLabel: subject label
+  % :type subLabel: string
+  %
+  %
+  % :returns: - :matlabbatch: (cell) The matlabbatch ready to run the spm job
+  %
+  %
+  % Example::
+  %
+  %
+  % (C) Copyright 2021 CPP_SPM developers
+
+  p = inputParser;
+
+  addRequired(p, 'matlabbatch', @iscell);
+  addRequired(p, 'BIDS', @isstruct);
+  addRequired(p, 'opt', @isstruct);
+  addRequired(p, 'subLabel', @ischar);
+
+  parse(p, varargin{:});
+
+  matlabbatch = p.Results.matlabbatch;
+  BIDS = p.Results.BIDS;
+  opt = p.Results.opt;
+  subLabel = p.Results.subLabel;
+
+  printBatchName('name for this batch');
+
+  for iTask = 1:numel(opt.taskName)
+
+    opt.query.task = opt.taskName{iTask};
+
+    [sessions, nbSessions] = getInfo(BIDS, subLabel, opt, 'Sessions');
+
+    for iSes = 1:nbSessions
+
+      % get all runs for that subject across all sessions
+      [runs, nbRuns] = getInfo(BIDS, subLabel, opt, 'Runs', sessions{iSes});
+
+      for iRun = 1:nbRuns
+
+        something = foo();
+
+      end
+
+      runCounter = runCounter + 1;
+    end
+
+  end
+
+  matlabbatch{end + 1}.spm.something = something;
+  matlabbatch{end}.spm.else = faa;
+  matlabbatch{end}.spm.other = fii;
+
+end

templates/getOption.m

@@ -0,0 +1,44 @@
+function opt = getOption()
+  %
+  % returns a structure that contains the options chosen for preprocessing
+  %
+  %
+  % (C) Copyright 2021 CPP_SPM developers
+
+  if nargin < 1
+    opt = [];
+  end
+
+  % task to analyze
+  opt.taskName = 'balloonanalogrisktask';
+
+  % The directory where the data are located
+  opt.dir.raw = FIXME;
+  opt.dir.derivatives = FIXME;
+
+  % Options for slice time correction
+  % If left unspecified the slice timing will be done using the mid-volume acquisition
+  % time point as reference.
+  % opt.STC_referenceSlice = [];
+
+  % when opt.ignoreFieldmaps is set to false, the
+  % preprocessing pipeline will look for the voxel displacement maps (created by
+  % the corresponding workflow) and will use them for realign and unwarp
+  % opt.ignoreFieldmaps = false;
+
+  % session number and type of the anatomical reference
+  % opt.anatReference.type = 'T1w';
+  % opt.anatReference.session = 1;
+
+  % any voxel with p(grayMatter) +  p(whiteMatter) + p(CSF) > threshold
+  % will be included in the skull stripping mask
+  % opt.skullstrip.threshold = 0.75;
+
+  % space where we conduct the analysis
+  % opt.space = 'MNI';
+
+  % Options for normalize
+  % Voxel dimensions for resampling at normalization of functional data or leave empty [ ].
+  % opt.funcVoxelDims = [];
+
+end

templates/newFunction.m

@@ -0,0 +1,43 @@
+function vargarout = newFunction(varargin)
+  %
+  % Short description of what the function does goes here.
+  %
+  % USAGE::
+  %
+  %   [foo, faa, fi] = newFunction(foo, faa, fii, 'boo')
+  %
+  % :param foo: obligatory argument. Lorem ipsum dolor sit amet,
+  % :type foo: cell
+  % :param faa: optional argument. Lorem ipsum dolor sit amet,
+  % :type faa: structure
+  % :param fii: parameter. default: ``boo``
+  % :type fii: string
+  %
+  % :returns: - :foo: (type) (dimension)
+  %           - :faa: (type) (dimension)
+  %           - :fii: (type) (dimension)
+  %
+  % Example::
+  %
+  % (C) Copyright 2021 CPP_SPM developers
+
+  % The code goes below
+
+  p = inputParser;
+
+  default_faa = [];
+  default_fii = 'boo';
+
+  addRequired(p, 'foo', @iscell);
+  addOptional(p, 'faa', default_faa, @isstruct);
+  addParameter(p, 'fii', default_fii, @ischar);
+
+  parse(p, varargin{:});
+
+  foo = p.Results.foo;
+  faa = p.Results.faa;
+  fii = p.Results.fii;
+
+  vargarout = {foo, faa, fii};
+
+end