diff --git a/job/OspreyJob.m b/job/OspreyJob.m
index f94ec9ae..ddb53829 100755
--- a/job/OspreyJob.m
+++ b/job/OspreyJob.m
@@ -256,21 +256,46 @@
     % and save them as separate cells to be saved into the MRSCont
     % container.
     if isfield(jobStruct, 'files')
-        files = jobStruct.files';
+        if ~iscell(jobStruct.files{1}) || size(jobStruct.files,1) == 1
+            files = jobStruct.files';
+        end
+        if iscell(files{1})
+            files = cellfun(@transpose,files,'UniformOutput',false);
+        end
     else
         error('Invalid job file! A job file needs to contain at least metabolite data in the field ''files''.');
     end
     if isfield(jobStruct, 'files_mm')  %re_mm Adding functionality for MM
-        files_mm = jobStruct.files_mm';   %re_mm
+        if ~iscell(jobStruct.files_mm{1}) || size(jobStruct.files_mm,1) == 1
+            files_mm = jobStruct.files_mm';   %re_mm
+        end
+        if iscell(files_mm{1})
+            files_mm = cellfun(@transpose,files_mm,'UniformOutput',false);
+        end
     end %re_mm
     if isfield(jobStruct, 'files_mm_ref')
-        files_mm_ref = jobStruct.files_mm_ref';
+        if ~iscell(jobStruct.files_mm_ref{1}) || size(jobStruct.files_mm_ref,1) == 1
+            files_mm_ref = jobStruct.files_mm_ref';
+        end
+        if iscell(files_mm_ref{1})
+            files_mm_ref = cellfun(@transpose,files_mm_ref,'UniformOutput',false);
+        end
     end
     if isfield(jobStruct, 'files_ref')
-        files_ref = jobStruct.files_ref';
+        if ~iscell(jobStruct.files_ref{1}) || size(jobStruct.files_ref,1) == 1
+            files_ref = jobStruct.files_ref';
+        end
+        if iscell(files_ref{1})
+            files_ref = cellfun(@transpose,files_ref,'UniformOutput',false);
+        end
     end
     if isfield(jobStruct, 'files_w')
-        files_w = jobStruct.files_w';
+        if ~iscell(jobStruct.files_w{1}) || size(jobStruct.files_w,1) == 1
+            files_w = jobStruct.files_w';
+        end
+        if iscell(files_w{1})
+            files_w = cellfun(@transpose,files_w,'UniformOutput',false);
+        end
     end
     if isfield(jobStruct, 'files_nii')
         files_nii = jobStruct.files_nii';
diff --git a/load/osp_LoadSDAT.m b/load/osp_LoadSDAT.m
index 53b409d9..1eceb214 100644
--- a/load/osp_LoadSDAT.m
+++ b/load/osp_LoadSDAT.m
@@ -33,21 +33,21 @@
             MRSCont.files_mm{kk} = MRSCont.files_mm{1}; % re_mm allowable to specify one MM file for the whole batch
         end %re_mm 
     end   %re_mm 
-    if ((length(MRSCont.files_mm) ~= MRSCont.nDatasets(1)) )   %re_mm 
+    if ((size(MRSCont.files_mm,2) ~= MRSCont.nDatasets(1)) )   %re_mm 
         msg = 'Number of specified MM files does not match number of specified metabolite files.'; %re_mm 
         fprintf(msg);
         error(msg);
     end   %re_mm 
 end   %re_mm 
 if MRSCont.flags.hasRef
-    if length(MRSCont.files_ref) ~= MRSCont.nDatasets(1)
+    if size(MRSCont.files_ref,2) ~= MRSCont.nDatasets(1)
         msg = 'Number of specified reference files does not match number of specified metabolite files.'; %re_mm 
         fprintf(msg);
         error(msg);
     end
 end
 if MRSCont.flags.hasWater
-    if length(MRSCont.files_w) ~= MRSCont.nDatasets(1)
+    if size(MRSCont.files_w,2) ~= MRSCont.nDatasets(1)
         msg = 'Number of specified water files does not match number of specified metabolite files.'; %re_mm 
         fprintf(msg);
         error(msg);