[FIX] inconsistent slice timing throw errors and not warnings (#982)

* inconsistent slice timing throw errors and not warnings

* update doc

* fix tests

* update doc

Author: Remi-Gau

src/batches/stats/setBatchSubjectLevelGLMSpec.m

@@ -241,7 +241,7 @@
     try
       hdr = spm_vol(fullpathBoldFilename);
     catch
-      warning('Could not open %s.\nThis expected during testing.', fullpathBoldFilename);
+      warning('Could not open %s.\nExpected during testing.', fullpathBoldFilename);
       % TODO a value should be passed by user for this
       % hard coded value for test
       hdr = ones(200, 1);

src/bids/getAndCheckSliceOrder.m

@@ -1,8 +1,8 @@
 function sliceOrder = getAndCheckSliceOrder(BIDS, opt, filter)
   %
   % Get the slice order information from the BIDS metadata.
-  % If inconsistent slice timing is found across files it returns empty and
-  % throws a warning.
+  % If inconsistent slice timing is found across files
+  % it throws an error.
   %
   % USAGE::
   %
@@ -20,10 +20,10 @@
   %   - :sliceOrder: a vector of the time when each slice was acquired in
   %                  in a volume or indicating the order of acquisition of the slices.
   %
-  % ``getAndCheckSliceOrder`` will try to read the ``opt`` structure for any relevant information
-  % about slice timing.
-  % If this is empty, it queries the BIDS dataset to ee if there is any
-  % consistent slice timing information for a given ``filter``
+  % ``getAndCheckSliceOrder`` will try to read the ``opt`` structure
+  % for any relevant information about slice timing.
+  % If this is empty, it queries the BIDS dataset to see if there is any
+  % consistent slice timing information for a given ``filter``.
   %
   % See also: bidsSTC, setBatchSTC
   %
@@ -57,10 +57,11 @@
 
     sliceOrder = [];
 
-    msg = sprintf('inconsistent slice timing found for filter:\n%s.\n\n', ...
+    msg = sprintf(['Inconsistent slice timing found for filter:\n%s.\n\n', ...
+                   'Number of slice per volume seems different across bold files.'], ...
                   bids.internal.create_unordered_list(filter));
-    id = 'inconsistentSliceTiming';
-    logger('WARNING', msg, 'id', id, 'filename', mfilename(), 'options', opt);
+    id = 'inconsistentSliceTimingLength';
+    logger('ERROR', msg, 'id', id, 'filename', mfilename(), 'options', opt);
 
     return
 
@@ -76,9 +77,9 @@
 
       sliceOrder = [];
 
-      wng = sprintf('inconsistent slice timing found for filter:\n%s.\n\n', ...
+      msg = sprintf('Inconsistent slice timing found for filter:\n%s.\n\n', ...
                     bids.internal.create_unordered_list(filter));
-      id = 'inconsistentSliceTiming';
+      id = 'inconsistentSliceTimingValues';
       logger('WARNING', msg, 'id', id, 'filename', mfilename(), 'options', opt);
 
       return

src/messages/bidspmHelp.m

@@ -75,7 +75,7 @@ function bidspmHelp()
   %                           Se to ``true`` to overwrites previous versions.
   % :type  boilerplate_only:  logical
   %
-  % :param verbosity:         can be ``0``, ``1`` or ``2``. Defaults to ``2``
+  % :param verbosity:         can be any value between ``0`` and ``3``. Defaults to ``2``
   % :type  verbosity:         positive integer
   %
   % :param space:             Defaults to ``{'individual', 'IXI549Space'}``

tests/tests_batches/stats/test_setBatchSubjectLevelGLMSpec.m

@@ -170,7 +170,7 @@ function test_setBatchSubjectLevelGLMSpec_inconsistent_metadata()
   %% WHEN
   matlabbatch = {};
   assertExceptionThrown(@()setBatchSubjectLevelGLMSpec(matlabbatch, BIDS, opt, subLabel), ...
-                        'getAndCheckRepetitionTime:differentRepetitionTime');
+                        'getAndCheckSliceOrder:inconsistentSliceTimingLength');
 
 end
 

tests/tests_bids/unit_tests/test_getAndCheckSliceOrder.m

@@ -38,9 +38,8 @@ function test_getAndCheckSliceOrder_inconsistent_slice_timing()
 
   [BIDS, opt, filter] = setUp({'vismotion', 'vislocalizer'});
 
-  sliceOrder = getAndCheckSliceOrder(BIDS, opt, filter);
-
-  assert(isempty(sliceOrder));
+  assertExceptionThrown(@()getAndCheckSliceOrder(BIDS, opt, filter), ...
+                        'getAndCheckSliceOrder:inconsistentSliceTimingLength');
 
 end