[ENH] add option to skip slice timing correction

lib/mancoreg/mancoregCallbacks.m

@@ -64,7 +64,7 @@ function mancoregCallbacks(operation)
 
 function moveImage()
 
-  global st mancoregvar;
+  global st mancoregvar
 
   angl_pitch = get(mancoregvar.hpitch, 'Value');
   angl_roll = get(mancoregvar.hroll, 'Value');
@@ -96,7 +96,7 @@ function moveImage()
 
 function toggleOff()
 
-  global st mancoregvar;
+  global st mancoregvar
 
   if get(mancoregvar.htoggle_off, 'value') == 0 % Source is to be displayed
 
@@ -114,7 +114,7 @@ function toggleOff()
 
 function toggleOn()
 
-  global st mancoregvar;
+  global st mancoregvar
 
   if get(mancoregvar.htoggle_on, 'value') == 0 % Source is to be displayed
 
@@ -135,7 +135,7 @@ function toggleOn()
 
 function resetTransformationMatrix()
 
-  global st mancoregvar;
+  global st mancoregvar
 
   set(mancoregvar.hpitch, 'Value', 0);
   set(mancoregvar.hroll, 'Value', 0);
@@ -165,7 +165,7 @@ function resetTransformationMatrix()
 
 function applyTransformationMatrix()
 
-  global st mancoregvar;
+  global st mancoregvar
 
   angl_pitch = get(mancoregvar.hpitch, 'Value');
   angl_roll = get(mancoregvar.hroll, 'Value');
@@ -218,7 +218,7 @@ function applyTransformationMatrix()
 
 function plotMat
 
-  global mancoregvar;
+  global mancoregvar
 
   angl_pitch = get(mancoregvar.hpitch, 'Value');
   angl_roll = get(mancoregvar.hroll, 'Value');

src/batches/setBatchSTC.m

@@ -1,10 +1,10 @@
-function matlabbatch = setBatchSTC(matlabbatch, BIDS, opt, subLabel)
+function matlabbatch = setBatchSTC(varargin)
   %
   % Creates batch for slice timing correction
   %
   % USAGE::
   %
-  %   matlabbatch = setBatchSTC(matlabbatch, BIDS, opt, subID)
+  %   matlabbatch = setBatchSTC(matlabbatch, BIDS, opt, subLabel)
   %
   % :param BIDS: BIDS layout returned by ``getData``.
   % :type BIDS: structure
@@ -30,6 +30,24 @@
   %
   % (C) Copyright 2019 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;
+
+  if opt.stc.skip
+    return
+  end
+
   % get slice order
   sliceOrder = getSliceOrder(opt, 1);
   if isempty(sliceOrder)
@@ -55,10 +73,10 @@
 
   maxSliceTime = max(sliceOrder);
   minSliceTime = min(sliceOrder);
-  if isempty(opt.STC_referenceSlice)
+  if isempty(opt.stc.referenceSlice)
     referenceSlice = (maxSliceTime - minSliceTime) / 2;
   else
-    referenceSlice = opt.STC_referenceSlice;
+    referenceSlice = opt.stc.referenceSlice;
   end
   if TA >= TR || referenceSlice > TA || any(sliceOrder > TA)
 
@@ -80,11 +98,11 @@
     error(errorStruct);
   end
 
-  matlabbatch{end + 1}.spm.temporal.st.nslices = nbSlices;
-  matlabbatch{end}.spm.temporal.st.tr = TR;
-  matlabbatch{end}.spm.temporal.st.ta = TA;
-  matlabbatch{end}.spm.temporal.st.so = sliceOrder * 1000;
-  matlabbatch{end}.spm.temporal.st.refslice = referenceSlice * 1000;
+  temporal.st.nslices = nbSlices;
+  temporal.st.tr = TR;
+  temporal.st.ta = TA;
+  temporal.st.so = sliceOrder * 1000;
+  temporal.st.refslice = referenceSlice * 1000;
 
   [sessions, nbSessions] = getInfo(BIDS, subLabel, opt, 'Sessions');
 
@@ -106,7 +124,7 @@
       file = validationInputFile(subFuncDataDir, fileName);
 
       % add the file to the list
-      matlabbatch{end}.spm.temporal.st.scans{runCounter} = {file};
+      temporal.st.scans{runCounter} = {file};
 
       runCounter = runCounter + 1;
 
@@ -116,6 +134,8 @@
 
   end
 
+  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');

src/batches/setBatchSubjectLevelGLMSpec.m

@@ -57,10 +57,10 @@
   % If no reference slice is given for STC, then STC took the mid-volume
   % time point to do the correction.
   % When no STC was done, this is usually a good way to do it too.
-  if isempty(opt.STC_referenceSlice)
+  if isempty(opt.stc.referenceSlice)
     refBin = floor(nbTimeBins / 2);
   else
-    refBin = opt.STC_referenceSlice / opt.metadata.RepetitionTime;
+    refBin = opt.stc.referenceSlice / opt.metadata.RepetitionTime;
   end
   matlabbatch{end}.spm.stats.fmri_spec.timing.fmri_t0 = refBin;
 

src/defaults/checkOptions.m

@@ -50,9 +50,10 @@
   %         will be included in the mask.
   %     - ``opt.funcVoxelDims = []`` - Voxel dimensions to use for resampling of functional data
   %         at normalization.
-  %     - ``opt.STC_referenceSlice = []`` - reference slice for the slice timing correction.
+  %     - ``opt.stc.skip = false`` - boolean flag to skip slice time correction or not.
+  %     - ``opt.stc.referenceSlice = []`` - reference slice for the slice timing correction.
   %         If left emtpy the mid-volume acquisition time point will be selected at run time.
-  %     - ``opt.sliceOrder = []`` - To be used if SPM can't extract slice info. NOT RECOMMENDED,
+  %     - ``opt.stc.sliceOrder = []`` - To be used if SPM can't extract slice info. NOT RECOMMENDED,
   %         if you know the order in which slices were acquired, you should be able to recompute
   %         slice timing and add it to the json files in your BIDS data set.
   %     -  ``opt.glm.roibased.do``
@@ -112,8 +113,9 @@
 
   %% Options for slice time correction
   % all in seconds
-  fieldsToSet.STC_referenceSlice = [];
-  fieldsToSet.sliceOrder = [];
+  fieldsToSet.stc.referenceSlice = [];
+  fieldsToSet.stc.sliceOrder = [];
+  fieldsToSet.stc.skip = false;
 
   %% Options for realign
   fieldsToSet.realign.useUnwarp = true;
@@ -173,13 +175,13 @@ function checkFields(opt)
 
   end
 
-  if ~isempty (opt.STC_referenceSlice) && length(opt.STC_referenceSlice) > 1
+  if ~isempty (opt.stc.referenceSlice) && length(opt.stc.referenceSlice) > 1
 
     errorStruct.identifier = 'checkOptions:refSliceNotScalar';
     errorStruct.message = sprintf( ...
-                                  ['options.STC_referenceSlice should be a scalar.' ...
+                                  ['options.stc.referenceSlice should be a scalar.' ...
                                    '\nCurrent value is: %d'], ...
-                                  opt.STC_referenceSlice);
+                                  opt.stc.referenceSlice);
     error(errorStruct);
 
   end

src/getPrefix.m

@@ -109,9 +109,10 @@
 function prefix = prefixForSTC(prefix, opt)
   % Check the slice timing information is not in the metadata and not added
   % manually in the opt variable.
-  if (isfield(opt.metadata, 'SliceTiming') && ...
-      ~isempty(opt.metadata.SliceTiming)) || ...
-          ~isempty(opt.sliceOrder)
+  if ~opt.stc.skip && ...
+     ((isfield(opt.metadata, 'SliceTiming') && ...
+       ~isempty(opt.metadata.SliceTiming)) || ...
+      ~isempty(opt.stc.sliceOrder))
     prefix = [spm_get_defaults('slicetiming.prefix') prefix];
   end
 end

src/getSliceOrder.m

@@ -41,8 +41,8 @@
     % If slice timing information is not in the metadata, you have the option
     % to add the slice order manually in the "opt" in the "getOptions"
     % function
-    if ~isempty(opt.sliceOrder)
-      sliceOrder = opt.sliceOrder;
+    if ~isempty(opt.stc.sliceOrder)
+      sliceOrder = opt.stc.sliceOrder;
 
       msg{end + 1} = ' SLICE TIMING INFORMATION EXTRACTED FROM OPTIONS.\n\n';
 

tests/test_checkOptions.m

@@ -55,7 +55,7 @@ function test_checkOptionsErrorGroup()
 
 function test_checkOptionsErrorRefSlice()
 
-  opt.STC_referenceSlice = [1:10];
+  opt.stc.referenceSlice = [1:10];
   opt.taskName = 'testTask';
 
   assertExceptionThrown( ...

tests/test_setBatchSTC.m

@@ -8,6 +8,22 @@
   initTestSuite;
 end
 
+function test_setBatchSTCSkip()
+
+  subLabel = '02';
+
+  opt = setOptions('vislocalizer', subLabel);
+
+  [BIDS, opt] = getData(opt);
+
+  opt.stc.skip = true;
+
+  matlabbatch = {};
+  matlabbatch = setBatchSTC(matlabbatch, BIDS, opt, subLabel);
+  assertEqual(matlabbatch, {});
+
+end
+
 function test_setBatchSTCEmpty()
 
   subLabel = '02';
@@ -16,11 +32,11 @@ function test_setBatchSTCEmpty()
 
   [BIDS, opt] = getData(opt);
 
-  matlabbatch = [];
+  matlabbatch = {};
   matlabbatch = setBatchSTC(matlabbatch, BIDS, opt, subLabel);
 
   % no slice timing info for this run so nothing should be returned.
-  assertEqual(matlabbatch, []);
+  assertEqual(matlabbatch, {});
 
 end
 
@@ -31,19 +47,19 @@ function test_setBatchSTCForce()
   opt = setOptions('vislocalizer', subLabel);
 
   % we give it some slice timing value to force slice timing to happen
-  opt.sliceOrder = linspace(0, 1.6, 10);
-  opt.sliceOrder(end - 1:end) = [];
-  opt.STC_referenceSlice = 1.6 / 2;
+  opt.stc.sliceOrder = linspace(0, 1.6, 10);
+  opt.stc.sliceOrder(end - 1:end) = [];
+  opt.stc.referenceSlice = 1.6 / 2;
 
   opt = checkOptions(opt);
 
   [BIDS, opt] = getData(opt);
 
-  matlabbatch = [];
+  matlabbatch = {};
   matlabbatch = setBatchSTC(matlabbatch, BIDS, opt, subLabel);
 
   TR = 1.55;
-  expectedBatch = returnExpectedBatch(opt.sliceOrder, opt.STC_referenceSlice, TR);
+  expectedBatch = returnExpectedBatch(opt.stc.sliceOrder, opt.stc.referenceSlice, TR);
 
   runCounter = 1;
   for iSes = 1:2
@@ -69,17 +85,17 @@ function test_setBatchSTCBasic()
 
   [BIDS, opt] = getData(opt);
 
-  matlabbatch = [];
+  matlabbatch = {};
   matlabbatch = setBatchSTC(matlabbatch, BIDS, opt, subLabel);
 
   TR = 1.5;
   sliceOrder = repmat([ ...
                        0.5475, 0, 0.3825, 0.055, 0.4375, 0.11, 0.4925, 0.22, 0.6025, ...
                        0.275, 0.6575, ...
                        0.3275, 0.71, 0.165], 1, 3)';
-  STC_referenceSlice = 0.355;
+  referenceSlice = 0.355;
 
-  expectedBatch = returnExpectedBatch(sliceOrder, STC_referenceSlice, TR);
+  expectedBatch = returnExpectedBatch(sliceOrder, referenceSlice, TR);
 
   runCounter = 1;
   for iSes = 1:2
@@ -106,14 +122,13 @@ function test_setBatchSTCErrorInvalidInputTime()
 
   opt = setOptions('vislocalizer', subLabel);
 
-  opt.sliceOrder = linspace(0, 1.6, 10);
-  opt.sliceOrder(end) = [];
-  opt.STC_referenceSlice = 2; % impossible reference value
+  opt.stc.sliceOrder = linspace(0, 1.6, 10);
+  opt.stc.sliceOrder(end) = [];
+  opt.stc.referenceSlice = 2; % impossible reference value
 
   [BIDS, opt] = getData(opt);
 
-  matlabbatch = [];
-
+  matlabbatch = {};
   assertExceptionThrown( ...
                         @()setBatchSTC(matlabbatch, BIDS, opt, subLabel), ...
                         'setBatchSTC:invalidInputTime');
@@ -126,10 +141,12 @@ function test_setBatchSTCErrorInvalidInputTime()
   TA = TR - (TR / nbSlices);
   TA = ceil(TA * 1000) / 1000;
 
-  expectedBatch{1}.spm.temporal.st.nslices = nbSlices;
-  expectedBatch{1}.spm.temporal.st.tr = TR;
-  expectedBatch{1}.spm.temporal.st.ta = TA;
-  expectedBatch{1}.spm.temporal.st.so = sliceOrder * 1000;
-  expectedBatch{1}.spm.temporal.st.refslice = referenceSlice * 1000;
+  temporal.st.nslices = nbSlices;
+  temporal.st.tr = TR;
+  temporal.st.ta = TA;
+  temporal.st.so = sliceOrder * 1000;
+  temporal.st.refslice = referenceSlice * 1000;
+
+  expectedBatch{1}.spm.temporal = temporal;
 
 end