Further cosmetic changes

CheckTargets.m

@@ -1,22 +1,25 @@
 function CheckTargets(MRS_struct)
 
 filepath = fullfile(fileparts(which(mfilename('fullpath'))), 'GannetPreInitialise.m');
-msg      = 'Incorrect targets entered in GannetPreInitialise.m. Check spelling, allowable options and order of targets.';
+msg      = 'Incorrect targets entered in GannetPreInitialise.m. Check spelling, allowable options, and order of targets.';
 msg      = hyperlink(['matlab: opentoline(''' filepath ''', 4, 0)'], 'Incorrect targets entered in GannetPreInitialise.m', msg);
 
 switch num2str(length(MRS_struct.p.target))
     case '1'
         if any(strcmp(MRS_struct.p.target, {'GABA', 'Glx', 'GABAGlx', 'GSH', 'Lac', 'EtOH'}))
             if MRS_struct.p.phantom && strcmp(MRS_struct.p.target, 'GABAGlx')
+                fprintf('\n');
                 error(msg);
             end
             if MRS_struct.p.HERMES
                 msg = 'MRS_struct.p.HERMES is set to 1 in GannetPreInitialise.m. Add a second target metabolite or set flag to 0.';
                 msg = hyperlink(['matlab: opentoline(''' filepath ''', 4, 0)'], 'Add a second target metabolite', msg);
                 msg = hyperlink(['matlab: opentoline(''' filepath ''', 33, 0)'], 'set flag to 0', msg);
+                fprintf('\n');
                 error(msg);
             end
         else
+            fprintf('\n');
             error(msg);
         end
     case '2'
@@ -25,24 +28,29 @@ function CheckTargets(MRS_struct)
                 all(strcmp(MRS_struct.p.target, {'Glx', 'GSH'})) ...
                 all(strcmp(MRS_struct.p.target, {'Lac', 'GSH'}))])
             if MRS_struct.p.phantom && any(strcmp(MRS_struct.p.target, 'GABAGlx'))
+                fprintf('\n');
                 error(msg);
             end
             if ~MRS_struct.p.HERMES
                 msg = 'Two target metabolites detected. MRS_struct.p.HERMES must be set to 1 in GannetPreInitialise.m.';
                 msg = hyperlink(['matlab: opentoline(''' filepath ''', 33, 0)'], 'MRS_struct.p.HERMES must be set to 1', msg);
+                fprintf('\n');
                 error(msg);
             end
         else
+            fprintf('\n');
             error(msg);
         end
     case '3'
         if all(strcmp(MRS_struct.p.target, {'EtOH', 'GABA', 'GSH'}))
             if ~MRS_struct.p.HERMES
                 msg = 'Three target metabolites detected. MRS_struct.p.HERMES must be set to 1 in GannetPreInitialise.m.';
                 msg = hyperlink(['matlab: opentoline(''' filepath ''', 33, 0)'], 'MRS_struct.p.HERMES must be set to 1', msg);
+                fprintf('\n');
                 error(msg);
             end
         else
+            fprintf('\n');
             error(msg);
         end
 end

CoRegStandAlone/CoReg.m

@@ -17,17 +17,20 @@
 spm_version = fileparts(which('spm'));
 if isempty(spm_version)
     msg = 'SPM not found! Please install SPM12 and make sure it is in your search path.';
-    msg = hyperlink('https://www.fil.ion.ucl.ac.uk/spm/software/spm12', 'SPM12', msg);
+    msg = hyperlink('https://www.fil.ion.ucl.ac.uk/spm/software/spm12/', 'SPM12', msg);
+    fprintf('\n');
     error(msg);
 elseif strcmpi(spm_version(end-3:end),'spm8')
     msg = ['SPM8 detected. Gannet no longer supports SPM8. ' ...
            'Please install SPM12 and make sure it is in your search path.'];
-    msg = hyperlink('https://www.fil.ion.ucl.ac.uk/spm/software/spm12', 'SPM12', msg);
+    msg = hyperlink('https://www.fil.ion.ucl.ac.uk/spm/software/spm12/', 'SPM12', msg);
+    fprintf('\n');
     error(msg);
 end
 
 if MRS_struct.ii ~= length(struc)
-    error('The number of NIfTI files does not match the number of MRS files processed by CoRegStandAlone.');
+    fprintf('\n');
+    error('The number of structural image files does not match the number of MRS files.');
 end
 
 numscans = numel(MRS_struct.metabfile);

CoRegStandAlone/CoRegStandAlone.m

@@ -44,7 +44,8 @@
 %                   already exists in the output directory
 
 if nargin == 0
-    error('MATLAB:minrhs','Not enough input arguments.');
+    fprintf('\n');
+    error('MATLAB:minrhs', 'Not enough input arguments.');
 end
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

CoRegStandAlone/Seg.m

@@ -26,12 +26,14 @@
 spm_version = fileparts(which('spm'));
 if isempty(spm_version)
     msg = 'SPM not found! Please install SPM12 and make sure it is in your search path.';
-    msg = hyperlink('https://www.fil.ion.ucl.ac.uk/spm/software/spm12', 'SPM12', msg);
+    msg = hyperlink('https://www.fil.ion.ucl.ac.uk/spm/software/spm12/', 'SPM12', msg);
+    fprintf('\n');
     error(msg);
 elseif strcmpi(spm_version(end-3:end),'spm8')
     msg = ['SPM8 detected. Gannet no longer supports SPM8. ' ...
            'Please install SPM12 and make sure it is in your search path.'];
-    msg = hyperlink('https://www.fil.ion.ucl.ac.uk/spm/software/spm12', 'SPM12', msg);
+    msg = hyperlink('https://www.fil.ion.ucl.ac.uk/spm/software/spm12/', 'SPM12', msg);
+    fprintf('\n');
     error(msg);
 end
 

DiscernDataType.m

@@ -22,7 +22,7 @@
     case '.sdat'
         MRS_struct.p.vendor = 'Philips';
     otherwise
-        error('Unrecognized file type! Extension should be .7, .dat, .data, .dcm, .gz, .ima, .nii, .raw, .rda, or, .sdat.');
+        error('Unrecognized file type! Extension must be .7, .dat, .data, .dcm, .gz, .ima, .nii, .raw, .rda, or, .sdat.');
 end
 
 end

GERead.m

@@ -325,7 +325,7 @@
     MRS_struct.p.nrows_water(ii) = refframes;
 
     if totalframes ~= (dataframes + refframes + 1) * nechoes % RTN 2017
-        error('# of totalframes not same as (dataframes + refframes + 1) * nechoes');
+        error('Number of totalframes does not equal (dataframes + refframes + 1) * nechoes');
     end
 
     ShapeData = reshape(raw_data, [2 MRS_struct.p.npoints(ii) totalframes nreceivers]);

GannetCoRegister.m

@@ -3,23 +3,26 @@
 % Coregistration of MRS voxel volumes to imaging datasets, based on headers.
 
 if nargin < 2
-    error('MATLAB:minrhs','Not enough input arguments.');
+    fprintf('\n');
+    error('MATLAB:minrhs', 'Not enough input arguments.');
 end
 
-MRS_struct.version.coreg = '230313';
+MRS_struct.version.coreg = '230314';
 
 warning('off'); % temporarily suppress warning messages
 
 % First check if SPM12 is installed and on the search path
 spm_version = fileparts(which('spm'));
 if isempty(spm_version)
     msg = 'SPM not found! Please install SPM12 and make sure it is in your search path.';
-    msg = hyperlink('https://www.fil.ion.ucl.ac.uk/spm/software/spm12', 'SPM12', msg);
+    msg = hyperlink('https://www.fil.ion.ucl.ac.uk/spm/software/spm12/', 'SPM12', msg);
+    fprintf('\n');
     error(msg);
 elseif strcmpi(spm_version(end-3:end), 'spm8')
     msg = ['SPM8 detected. Gannet no longer supports SPM8. ' ...
            'Please install SPM12 and make sure it is in your search path.'];
-    msg = hyperlink('https://www.fil.ion.ucl.ac.uk/spm/software/spm12', 'SPM12', msg);
+    msg = hyperlink('https://www.fil.ion.ucl.ac.uk/spm/software/spm12/', 'SPM12', msg);
+    fprintf('\n');
     error(msg);
 end
 
@@ -32,6 +35,7 @@
 struc = GetFullPath(struc);
 
 if MRS_struct.p.numScans ~= length(struc)
+    fprintf('\n');
     error('The number of structural image files does not match the number of MRS files processed by GannetLoad.');
 end
 

GannetFit.m

@@ -3,10 +3,11 @@
 % Signal fitting in the frequency domain using nonlinear least-squares optimization
 
 if nargin == 0
-    error('MATLAB:minrhs','Not enough input arguments.');
+    fprintf('\n');
+    error('MATLAB:minrhs', 'Not enough input arguments.');
 end
 
-MRS_struct.version.fit = '230313';
+MRS_struct.version.fit = '230314';
 
 if MRS_struct.p.PRIAM
     vox = MRS_struct.p.vox;
@@ -551,7 +552,7 @@
 
                     otherwise
 
-                        error('Fitting %s not recognised',target{jj});
+                        error('Metabolite ''%s'' not recognized.', target{jj});
 
                 end
 

GannetFitPhantom.m

@@ -3,10 +3,11 @@
 % Updates by MM 2018-2020
 
 if nargin == 0
-    error('MATLAB:minrhs','Not enough input arguments.');
+    fprintf('\n');
+    error('MATLAB:minrhs', 'Not enough input arguments.');
 end
 
-MRS_struct.version.fit_phantom = '230125';
+MRS_struct.version.fit_phantom = '230314';
 
 if MRS_struct.p.PRIAM
     vox = MRS_struct.p.vox;
@@ -281,7 +282,7 @@
 
                 otherwise
 
-                    error('Fitting %s not recognised',target{jj});
+                    error('Metabolite ''%s'' not recognized.', target{jj});
 
             end
 

GannetLoad.m

@@ -14,11 +14,12 @@
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 if nargin == 0
-    error('MATLAB:minrhs','Not enough input arguments.');
+    fprintf('\n');
+    error('MATLAB:minrhs', 'Not enough input arguments.');
 end
 
 MRS_struct.version.Gannet = '3.3.1';
-MRS_struct.version.load   = '230313';
+MRS_struct.version.load   = '230314';
 VersionCheck(0, MRS_struct.version.Gannet);
 ToolboxCheck;
 
@@ -465,10 +466,7 @@
                     AllFramesFTrealign = AllFramesFT;
                     MRS_struct.out.reject{ii} = zeros(1,size(AllFramesFT,2));
                 otherwise
-                    filepath = fullfile(fileparts(which(mfilename('fullpath'))), 'GannetPreInitialise.m');
-                    msg = 'FPC parameter in GannetPreInitialise.m not recognized. Check spelling.';
-                    msg = hyperlink(['matlab: opentoline(''' filepath ''', 22, 0)'], 'FPC parameter in GannetPreInitialise.m not recognized', msg);
-                    error(msg);
+                    error('Alignment method in GannetPreInitialise.m not recognized. Check spelling.');
             end
 
             MRS_struct.spec.AllFramesFT        = AllFramesFT;

GannetQuantify.m

@@ -1,10 +1,11 @@
 function MRS_struct = GannetQuantify(MRS_struct)
 
 if nargin == 0
-    error('MATLAB:minrhs','Not enough input arguments.');
+    fprintf('\n');
+    error('MATLAB:minrhs', 'Not enough input arguments.');
 end
 
-MRS_struct.version.quantify = '230302';
+MRS_struct.version.quantify = '230314';
 
 if MRS_struct.p.PRIAM
     vox = MRS_struct.p.vox;
@@ -16,8 +17,8 @@
 
 % Check if there are water files, otherwise exit
 if ~strcmp(MRS_struct.p.reference, 'H2O')
-    warning('No water reference files found in input structure ''%s''. GannetQuantify.m requires water references. Exiting...\n', inputname(1));
-    return
+    fprintf('\n');
+    error('No water reference files found in input structure ''%s''. GannetQuantify.m requires water references to run. Exiting...', inputname(1));
 end
 
 % ******

GannetSegment.m

@@ -8,23 +8,26 @@
 % are loaded and used for the voxel segmentation
 
 if nargin == 0
-    error('MATLAB:minrhs','Not enough input arguments.');
+    fprintf('\n');
+    error('MATLAB:minrhs', 'Not enough input arguments.');
 end
 
-MRS_struct.version.segment = '230302';
+MRS_struct.version.segment = '230314';
 
 warning('off'); % temporarily suppress warning messages
 
 % First check if SPM12 is installed and on the search path
 spm_version = fileparts(which('spm'));
 if isempty(spm_version)
     msg = 'SPM not found! Please install SPM12 and make sure it is in your search path.';
-    msg = hyperlink('https://www.fil.ion.ucl.ac.uk/spm/software/spm12', 'SPM12', msg);
+    msg = hyperlink('https://www.fil.ion.ucl.ac.uk/spm/software/spm12/', 'SPM12', msg);
+    fprintf('\n');
     error(msg);
 elseif strcmpi(spm_version(end-3:end), 'spm8')
     msg = ['SPM8 detected. Gannet no longer supports SPM8. ' ...
            'Please install SPM12 and make sure it is in your search path.'];
-    msg = hyperlink('https://www.fil.ion.ucl.ac.uk/spm/software/spm12', 'SPM12', msg);
+    msg = hyperlink('https://www.fil.ion.ucl.ac.uk/spm/software/spm12/', 'SPM12', msg);
+    fprintf('\n');
     error(msg);
 end
 

GannetVersion.m

@@ -4,7 +4,8 @@
 loadFile = which('GannetLoad');
 fileID = fopen(loadFile, 'rt');
 if fileID == -1
-    error('Can''t read %s.', loadFile);
+    fclose(fileID);
+    error('Cannot read %s.', loadFile);
 end
 str = fread(fileID, Inf, '*uchar');
 fclose(fileID);

NIfTIMRSRead.m

@@ -363,7 +363,8 @@
 
 else
 
-    error(sprintf('\nData are not single-voxel data. Exiting...'));
+    fprintf('\n');
+    error('Data are not single-voxel data. Exiting...');
 
 end
 

PRIAM/read_cpx.m

@@ -508,12 +508,13 @@
 info.filename = filename;
 % Open LAB file and read all hexadecimal labels
 labfid = fopen(labname,'r');
-if labfid==-1,
-    error( sprintf('Cannot open %s for reading', labname) );
+if labfid == -1
+    fclose(labfid);
+    error('Cannot open %s for reading', labname);
 end
 
 % Read all hexadecimal labels
-[unparsed_labels, readsize] = fread (labfid,[16 Inf], 'uint32=>uint32');
+unparsed_labels = fread (labfid, [16 Inf], 'uint32=>uint32');
 info.nLabels = size(unparsed_labels,2);
 fclose(labfid);
 

PaperPlot.m

@@ -63,6 +63,7 @@ function PaperPlot(MRS_struct, varargin)
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 if nargin == 0
+    fprintf('\n');
     error('MATLAB:minrhs','Not enough input arguments.');
 end
 

PhilipsRawRead.m

@@ -729,7 +729,8 @@
 
                         fid = fopen([rawpath filesep 'rec_spectra_txt' filesep savefile1 '.txt'],'w');
                         if fid == -1
-                            disp(['cant open file: ' savefile1])
+                            fclose(fid);
+                            disp(['Cannot open file: ' savefile1])
                             continue
                         end
                         for p=1:npoints
@@ -1601,12 +1602,12 @@
 info.filename = filename;
 % Open LAB file and read all hexadecimal labels
 labfid = fopen(labname,'r');
-if labfid==-1,
-    error( sprintf('Cannot open %s for reading', labname) );
+if labfid == -1
+    error('Cannot open %s for reading', labname);
 end
 
 % Read all hexadecimal labels
-[unparsed_labels, readsize] = fread (labfid,[16 Inf], 'uint32=>uint32');
+unparsed_labels = fread (labfid, [16 Inf], 'uint32=>uint32');
 info.nLabels = size(unparsed_labels,2);
 fclose(labfid);
 
@@ -2228,7 +2229,7 @@ function write_sdat_spar(data, fname_p, fname_out, fname_out_spar, averages, np)
 end
 
 % Check that the file has been open in ieee-le machineformat
-[filename, permission, machineformat] = fopen(fid);
+[~, ~, machineformat] = fopen(fid);
 if ~strcmp(machineformat, 'ieee-le')
     error('Use FOPEN with ieee-le precision');
 end

SDATread.m

@@ -3,8 +3,8 @@
 % Open file to read reference scan data.
 fid = fopen(filename, 'rb', 'ieee-le');
 if fid == -1
-    sprintf('Unable to locate file %s', filename);
-    return
+    fclose(fid);
+    error('Unable to locate file %s', filename);
 end
 
 % Set up a structure to take the data:

SDATreadMEGA.m

@@ -3,8 +3,8 @@
 % Open file to read reference scan data.
 fid = fopen(filename, 'rb', 'ieee-le');
 if fid == -1
-    sprintf('Unable to locate file %s', filename);
-    return
+    fclose(fid);
+    error('Unable to locate file %s', filename);
 end
 
 % Set up a structure to take the data: