diff --git a/.DS_Store b/.DS_Store
index dc62a7f..3fc6363 100644
Binary files a/.DS_Store and b/.DS_Store differ
diff --git a/CoRegStandAlone/CoReg.m b/CoRegStandAlone/CoReg.m
new file mode 100755
index 0000000..dfbcd87
--- /dev/null
+++ b/CoRegStandAlone/CoReg.m
@@ -0,0 +1,214 @@
+function MRS_struct = CoReg(MRS_struct, nii_name)
+
+%Coregistration of MRS voxel volumes to imaging datasets, based on headers.
+
+MRS_struct.version.coreg = '180718';
+
+% First check if SPM12 is installed and on the search path
+spmversion = fileparts(which('spm'));
+if isempty(spmversion)
+    error('SPM not found! Please install SPM12 (https://www.fil.ion.ucl.ac.uk/spm/software/spm12) and make sure it is on your search path.');
+elseif strcmpi(spmversion(end-3:end),'spm8')
+    error(['SPM8 detected! Gannet 3.0 no longer supports SPM8. ' ...
+           'Please install SPM12 (https://www.fil.ion.ucl.ac.uk/spm/software/spm12) and make sure it is on your search path.']);
+end
+
+if MRS_struct.ii ~= length(nii_name)
+    error('The number of nifti files does not match the number of MRS files processed by CoRegStandAlone.');
+end
+
+numscans = numel(MRS_struct.metabfile);
+vox = {MRS_struct.p.Vox{1}};
+
+for ii = 1:numscans
+    % Loop over voxels if PRIAM
+    for kk = 1:length(vox)
+
+        %Ultimately this switch will not be necessary...
+        switch MRS_struct.p.vendor
+
+            case 'Philips'
+                fname = MRS_struct.metabfile{ii};
+                sparname = [fname(1:(end-4)) MRS_struct.p.spar_string];
+                MRS_struct = GannetMask_Philips(sparname, nii_name{ii}, MRS_struct, ii, vox, kk);
+
+            case 'Philips_data'
+                if exist(MRS_struct.metabfile_sdat,'file') % MM (170720)
+                    MRS_struct.p.vendor = 'Philips';
+                    MRS_struct.metabfile_data = MRS_struct.metabfile;
+                    MRS_struct.metabfile = MRS_struct.metabfile_sdat;
+                    MRS_struct = GannetCoRegister(MRS_struct,nii_name);
+                    MRS_struct.metabfile = MRS_struct.metabfile_data;
+                    MRS_struct.p.vendor = 'Philips_data';
+                else
+                    error([MRS_struct.p.vendor ' format does not include voxel location information in the header. See notes in GannetCoRegister.']);
+                    %If this comes up, once GannetLoad has been read:
+                    %1. Switch vendor to Philips
+                    %       MRS_struct.p.vendor = 'Philips';
+                    %2. Copy .data filenames.
+                    %       MRS_struct.metabfile_data = MRS_struct.metabfile;
+                    %3. Replace the list with the corrsponding SDAT files (in correct order)
+                    %        MRS_struct.metabfile = {'SDATfile1.sdat' 'SDATfile2.SDAT'};
+                    %4. Rerun GannetCoRegister
+                    %
+                    %5.  Copy .sdat filenames and replace .data ones. Tidy up.
+                    %       MRS_struct.metabfile_sdat = MRS_struct.metabfile;
+                    %       MRS_struct.metabfile = MRS_struct.metabfile_data;
+                    %       MRS_struct.p.vendor = 'Philips_data'
+                end
+
+            case 'Siemens_rda'
+                fname = MRS_struct.metabfile{ii};
+                MRS_struct = GannetMask_SiemensRDA(fname, nii_name{ii}, MRS_struct, ii, vox, kk);
+
+            case {'Siemens_twix', 'Siemens_dicom'} 
+                fname = MRS_struct.metabfile{ii};
+                MRS_struct = GannetMask_SiemensTWIX(fname, nii_name{ii}, MRS_struct, ii, vox, kk);
+
+            case 'GE'
+                fname = MRS_struct.metabfile{ii};
+                MRS_struct = GannetMask_GE(fname, nii_name{ii}, MRS_struct, ii, vox, kk);
+
+        end
+
+        % Build output figure
+        if ishandle(103)
+            clf(103); % MM (170720)
+        end
+        h = figure(103);
+        % MM (170629): Open figure in center of screen
+        scr_sz = get(0, 'ScreenSize');
+        fig_w = 1000;
+        fig_h = 707;
+        set(h, 'Position', [(scr_sz(3)-fig_w)/2, (scr_sz(4)-fig_h)/2, fig_w, fig_h]);
+        set(h,'Color',[1 1 1]);
+        figTitle = 'GannetCoRegister Output';
+        set(gcf,'Name',figTitle,'Tag',figTitle,'NumberTitle','off');
+
+        subplot(2,3,4:6)
+        axis off;
+
+        tmp = 'Mask output: ';
+        text(0.5, 0.75, tmp,'HorizontalAlignment','right', ...
+            'VerticalAlignment', 'top', ...
+            'FontName', 'Helvetica','FontSize',13);
+
+        [~,tmp,tmp2] = fileparts(MRS_struct.mask.(vox{kk}).outfile{ii});
+        text(0.5, 0.75, [' ' tmp tmp2], ...
+            'VerticalAlignment', 'top', ...
+            'FontName', 'Helvetica','FontSize',13,'Interpreter','none');
+
+        tmp = 'Spatial parameters: ';
+        text(0.5, 0.63, tmp, 'HorizontalAlignment', 'right', ...
+            'VerticalAlignment', 'top', ...
+            'FontName', 'Helvetica','FontSize',13);
+        tmp = ' [LR, AP, FH]';
+        text(0.5, 0.63, tmp, ...
+            'VerticalAlignment', 'top', ...
+            'FontName', 'Helvetica','FontSize',13);
+
+        tmp = 'Dimension: ';
+        text(0.5, 0.51, tmp, 'HorizontalAlignment', 'right', ...
+            'VerticalAlignment', 'top', ...
+            'FontName', 'Helvetica','FontSize',13);
+        tmp = [' [' num2str(MRS_struct.p.voxdim(ii,1)) ', ' num2str(MRS_struct.p.voxdim(ii,2)) ', ' num2str(MRS_struct.p.voxdim(ii,3)) '] mm'];
+        text(0.5, 0.51, tmp, ...
+            'VerticalAlignment', 'top', ...
+            'FontName', 'Helvetica','FontSize',13);
+
+        tmp = 'Volume: ';
+        text(0.5, 0.39, tmp, 'HorizontalAlignment', 'right', ...
+            'VerticalAlignment', 'top', ...
+            'FontName', 'Helvetica','FontSize',13);
+        vol = MRS_struct.p.voxdim(ii,1)*MRS_struct.p.voxdim(ii,2)*MRS_struct.p.voxdim(ii,3)*.001;
+        tmp = [' ' num2str(vol) ' mL'];
+        text(0.5, 0.39, tmp, ...
+            'VerticalAlignment', 'top', ...
+            'FontName', 'Helvetica','FontSize',13);
+
+        tmp = 'Position: ';
+        text(0.5, 0.27, tmp, 'HorizontalAlignment', 'right', ...
+            'VerticalAlignment', 'top', ...
+            'FontName', 'Helvetica','FontSize',13);
+        tmp = [' [' num2str(MRS_struct.p.voxoff(ii,1), '%3.1f') ', ' num2str(MRS_struct.p.voxoff(ii,2), '%3.1f') ', ' num2str(MRS_struct.p.voxoff(ii,3), '%3.1f') '] mm'];
+        text(0.5, 0.27, tmp, ...
+            'VerticalAlignment', 'top', ...
+            'FontName', 'Helvetica','FontSize',13);
+
+        tmp = 'Angulation: ';
+        text(0.5, 0.15, tmp, 'HorizontalAlignment', 'right', ...
+            'VerticalAlignment', 'top', ...
+            'FontName', 'Helvetica','FontSize',13);
+        tmp = [' [' num2str(MRS_struct.p.voxang(ii,1), '%3.1f') ', ' num2str(MRS_struct.p.voxang(ii,2), '%3.1f') ', ' num2str(MRS_struct.p.voxang(ii,3), '%3.1f') '] deg'];
+        text(0.5, 0.15, tmp, ...
+            'VerticalAlignment', 'top', ...
+            'FontName', 'Helvetica','FontSize',13);
+
+        tmp = 'CoRegVer: ';
+        text(0.5, 0.03, tmp, 'HorizontalAlignment', 'right', ...
+            'VerticalAlignment', 'top', ...
+            'FontName', 'Helvetica','FontSize',13);
+        tmp = [' ' MRS_struct.version.coreg];
+        text(0.5, 0.03, tmp, ...
+            'VerticalAlignment', 'top', ...
+            'FontName', 'Helvetica','FontSize',13);
+
+        h = subplot(2,3,1:3);
+
+        % MM (180112)
+        [~,tmp,tmp2] = fileparts(MRS_struct.metabfile{ii});
+        [~,tmp3,tmp4] = fileparts(MRS_struct.mask.(vox{kk}).T1image{ii});
+        t = ['Voxel from ' tmp tmp2 ' on ' tmp3 tmp4];
+
+        imagesc(squeeze(MRS_struct.mask.(vox{kk}).img{ii}));
+        colormap('gray');
+        img = MRS_struct.mask.(vox{kk}).img{ii};
+        img = img(:);
+        caxis([0 mean(img(img>0.01)) + 3*std(img(img>0.01))]); % MM (180807)
+        axis equal;
+        axis tight;
+        axis off;
+        text(10,size(MRS_struct.mask.(vox{kk}).img{ii},1)/2,'L','Color',[1 1 1],'FontSize',20);
+        text(size(MRS_struct.mask.(vox{kk}).img{ii},2)-20,size(MRS_struct.mask.(vox{kk}).img{ii},1)/2,'R','Color',[1 1 1],'FontSize',20);
+        get(h,'pos');
+        set(h,'pos',[0.0 0.15 1 1]);
+        title(t, 'FontName', 'Helvetica', 'FontSize', 15, 'Interpreter', 'none');
+
+        script_path = which('GannetLoad');
+        Gannet_logo = [script_path(1:(end-13)) '/Gannet3_logo.png'];
+        A2 = imread(Gannet_logo,'png','BackgroundColor',[1 1 1]);
+        axes('Position',[0.80, 0.05, 0.15, 0.15]);
+        image(A2);
+        axis off;
+        axis square;
+
+        % For Philips .data
+        if strcmpi(MRS_struct.p.vendor,'Philips_data')
+            fullpath = MRS_struct.metabfile{ii};
+            fullpath = regexprep(fullpath, '.data', '_data');
+            fullpath = regexprep(fullpath, '\', '_');
+            fullpath = regexprep(fullpath, '/', '_');
+        end
+
+        % MM (180112)
+        [~,metabfile_nopath] = fileparts(MRS_struct.metabfile{ii});
+
+        % Save PDF output
+        set(gcf,'PaperUnits','inches');
+        set(gcf,'PaperSize',[11 8.5]);
+        set(gcf,'PaperPosition',[0 0 11 8.5]);
+        if strcmpi(MRS_struct.p.vendor,'Philips_data')
+            pdfname = fullfile('CoRegStandAlone_output', [fullpath '_' vox{kk} '_coreg.pdf']); % MM (180112)
+        else
+            pdfname = fullfile('CoRegStandAlone_output', [metabfile_nopath '_' vox{kk} '_coreg.pdf']); % MM (180112)
+        end
+        saveas(gcf, pdfname);
+        
+   
+    end
+    
+end
+
+
+
+
diff --git a/CoRegStandAlone/CoRegStandAlone.m b/CoRegStandAlone/CoRegStandAlone.m
new file mode 100755
index 0000000..e1f6dfe
--- /dev/null
+++ b/CoRegStandAlone/CoRegStandAlone.m
@@ -0,0 +1,128 @@
+function MRS_struct = CoRegStandAlone(metabfile,niifile)
+% CoRegStandAlone(metabfile,niifile)
+%   Reads the relevant header information from MRS files, performs 
+%   SPM-based co-registration to a 3D anatomical image in nifti (*.nii)
+%   format, and returns the tissue class fractions of gray matter, white
+%   matter, and cerebrospinal fluid in the MRS voxel. 
+%
+%   Requires:
+%       - SPM 12 (https://www.fil.ion.ucl.ac.uk/spm/software/spm12/)
+%
+%   Input:
+%       metabfile - cell containing the path to an MRS data file in one of 
+%                   the following formats:
+%                   Philips SDAT/SPAR, Siemens TWIX (*.dat), Siemens
+%                   RDA (*.rda), GE (.7), DICOM (*.ima, *.dcm)
+%       niifile   - cell containing the path to a *.nii file
+%
+%       It is possible to batch process data. In this case, the number of
+%       elements of the metabfile cell needs to match the number of
+%       elements of the niifile cell, with matching order.
+%
+%   Example:
+%       MRS_struct = CoRegStandAlone({'MRS1.dat, 'MRS2.dat'}, {'nii.dat', 'nii.dat'})
+%                                       
+%       This example will co-register and segment two Siemens MRS voxels to
+%       the same structural.
+%
+%   Author:
+%       Dr. Georg Oeltzschner (Johns Hopkins University, 2018-09-19)
+%       goeltzs1@jhmi.edu
+%   
+%   History:
+%       2018-09-19: First version of the code.
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%   1. Pre-initialise
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+MRS_struct.version.load = '180326'; % set to date when final updates have been made
+MRS_struct.ii = 0;
+MRS_struct.metabfile = metabfile;
+
+% Flags
+MRS_struct.p.mat = 1;       % Save results in *.mat output structure? (0 = NO, 1 = YES (default)).
+MRS_struct.p.Vox = {'vox1'};  % Name of the voxel
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%   2. Determine data parameters from header
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+% Discern input data format
+MRS_struct = GannetDiscernDatatype(metabfile{1}, MRS_struct);
+
+% Create output folder
+if ~exist('CoRegStandAlone_output','dir')
+    mkdir CoRegStandAlone_output;
+end
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%   3. Load data from files
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+for ii = 1:length(metabfile) % Loop over all files in the batch (from metabfile)
+    
+    MRS_struct.ii = ii;
+    
+    switch MRS_struct.p.vendor
+        
+        case 'GE'
+            MRS_struct = GERead(MRS_struct, metabfile{ii});
+            
+        case 'Siemens_twix'
+            MRS_struct = SiemensTwixRead(MRS_struct, metabfile{ii});
+            
+        case 'Siemens_dicom' % GO 11/01/2016
+            MRS_struct = SiemensDICOMRead(MRS_struct,metabfile{ii}); % GO 11/01/2016
+            
+        case 'dicom' % GO 11/30/2016
+            MRS_struct = DICOMRead(MRS_struct,metabfile{ii}); % GO 11/01/2016
+            
+        case 'Siemens_rda'
+            MRS_struct = SiemensRead(MRS_struct, metabfile{ii}, metabfile{ii});
+            
+        case 'Philips'
+            MRS_struct = PhilipsRead(MRS_struct, metabfile{ii});
+            
+        case 'Philips_data'
+            MRS_struct = PhilipsRead_data(MRS_struct, metabfile{ii});
+        
+        case 'Philips_raw'
+            MRS_struct = PhilipsRawLoad(MRS_struct,metabfile{ii},3,0); % GO 11/02/2016 
+    
+    end % end of vendor switch loop for data load
+        
+end % end of load-and-processing loop over datasets
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%   4. Call coregister function
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+for ii = 1:length(metabfile) % Loop over all files in the batch (from metabfile)
+    MRS_struct = CoReg(MRS_struct, niifile);
+end
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%   5. Call segment function
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+for ii = 1:length(metabfile) % Loop over all files in the batch (from metabfile)
+    MRS_struct = Seg(MRS_struct);
+end
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%   6. Clean up, save data
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+    
+% Save MRS_struct as mat file
+MRS_struct = rmfield(MRS_struct,'fids');
+if ii == length(metabfile) && MRS_struct.p.mat
+    % Set up filename
+    mat_name = ['CoRegStandAlone_output/MRS_struct_CoRegStandAlone.mat'];
+    save(mat_name,'MRS_struct');
+end
+           
+end
+
+
+
diff --git a/CoRegStandAlone/Seg.m b/CoRegStandAlone/Seg.m
new file mode 100644
index 0000000..1cf1d28
--- /dev/null
+++ b/CoRegStandAlone/Seg.m
@@ -0,0 +1,218 @@
+function MRS_struct = Seg(MRS_struct)
+
+% Relies on SPM being installed
+%
+% Runs segmentation script if segmented images not present according to
+% file convention of c1, c2 and c3 as prefixes on the anatomical image name
+% for the GM, WM and CSF segmentations. If these files are present, they
+% are loaded and used for the voxel segmentation
+%
+% This script does not require any information from the fit.
+% This is useful if only the tissue segmentation information is supposed to
+% be obtained.
+
+MRS_struct.version.segment = '180403';
+vox = {MRS_struct.p.Vox{1}};
+
+% Set up SPM for batch processing
+spm('defaults','fmri');
+spm_jobman('initcfg');
+kk = 1;
+for ii = 1:length(MRS_struct.metabfile)
+    
+    % 1 - Take nifti from GannetCoRegister and segment it in SPM
+    
+    [T1dir, T1name, T1ext] = fileparts(MRS_struct.mask.(vox{kk}).T1image{ii});
+    anatimage = MRS_struct.mask.(vox{kk}).T1image{ii};
+    
+    % Check to see if segmentation already done - if not, do it
+    % Check which SPM version is installed and segment accordingly
+    tmp = [T1dir '/c1' T1name T1ext];
+    if ~exist(tmp,'file')
+        spmversion = fileparts(which('spm'));
+        if strcmpi(spmversion(end-4:end),'spm12')
+            CallSPM12segmentation(anatimage);
+        else
+            CallSPM8segmentation(anatimage);
+        end
+    end
+    
+    % 2 - Determine GM, WM and CSF fractions for each voxel
+    
+    if strcmp(T1dir,'')
+        T1dir='.';
+    end
+    
+    GM  = [T1dir '/c1' T1name T1ext];
+    WM  = [T1dir '/c2' T1name T1ext];
+    CSF = [T1dir '/c3' T1name T1ext];
+    
+    GMvol  = spm_vol(GM);
+    WMvol  = spm_vol(WM);
+    CSFvol = spm_vol(CSF);
+    
+    % Loop over voxels if PRIAM
+    for kk = 1:length(vox)
+        
+        voxmaskvol = spm_vol(cell2mat(MRS_struct.mask.(vox{kk}).outfile(ii)));
+        
+        % GM
+        O_GMvox.fname = [T1dir '/c1' T1name '_GM_mask.nii'];
+        O_GMvox.descrip = 'GMmasked_MRS_Voxel_Mask';
+        O_GMvox.dim = voxmaskvol.dim;
+        O_GMvox.dt = voxmaskvol.dt;
+        O_GMvox.mat = voxmaskvol.mat;
+        GM_voxmask_vol = GMvol.private.dat(:,:,:) .* voxmaskvol.private.dat(:,:,:);
+        O_GMvox = spm_write_vol(O_GMvox, GM_voxmask_vol);
+        
+        % WM
+        O_WMvox.fname = [T1dir '/c2' T1name '_WM_mask.nii'];
+        O_WMvox.descrip = 'WMmasked_MRS_Voxel_Mask';
+        O_WMvox.dim = voxmaskvol.dim;
+        O_WMvox.dt = voxmaskvol.dt;
+        O_WMvox.mat = voxmaskvol.mat;
+        WM_voxmask_vol = WMvol.private.dat(:,:,:) .* voxmaskvol.private.dat(:,:,:);
+        O_WMvox = spm_write_vol(O_WMvox, WM_voxmask_vol);
+        
+        % CSF
+        O_CSFvox.fname = [T1dir '/c3' T1name '_CSF_mask.nii'];
+        O_CSFvox.descrip = 'CSFmasked_MRS_Voxel_Mask';
+        O_CSFvox.dim = voxmaskvol.dim;
+        O_CSFvox.dt = voxmaskvol.dt;
+        O_CSFvox.mat = voxmaskvol.mat;
+        CSF_voxmask_vol = CSFvol.private.dat(:,:,:) .* voxmaskvol.private.dat(:,:,:);
+        O_CSFvox = spm_write_vol(O_CSFvox, CSF_voxmask_vol);
+        
+        % ***NB***
+        % For a subject with multiple voxels, the segmented voxels will
+        % get overwritten
+        
+        % 3 - Calculate an adjusted gabaiu and output it to the structure
+        
+        gmsum = sum(sum(sum(O_GMvox.private.dat(:,:,:))));
+        wmsum = sum(sum(sum(O_WMvox.private.dat(:,:,:))));
+        csfsum = sum(sum(sum(O_CSFvox.private.dat(:,:,:))));
+        
+        gmfra = gmsum/(gmsum+wmsum+csfsum);
+        wmfra = wmsum/(gmsum+wmsum+csfsum);
+        csffra = csfsum/(gmsum+wmsum+csfsum);
+        
+        tissuefra = gmfra+wmfra;
+        
+        MRS_struct.out.(vox{kk}).tissue.GMfra(ii) = gmfra;
+        MRS_struct.out.(vox{kk}).tissue.WMfra(ii) = wmfra;
+        MRS_struct.out.(vox{kk}).tissue.CSFfra(ii) = csffra;
+        
+        % 4 - Build output
+        if ishandle(104)
+            clf(104); % MM (170831)
+        end
+        h = figure(104);
+        % MM (170831): Open figure in center of screen
+        scr_sz = get(0, 'ScreenSize');
+        fig_w = 1000;
+        fig_h = 707;
+        set(h,'Position',[(scr_sz(3)-fig_w)/2, (scr_sz(4)-fig_h)/2, fig_w, fig_h]);
+        set(h,'Color',[1 1 1]);
+        figTitle = 'GannetSegment Output';
+        set(gcf,'Name',figTitle,'Tag',figTitle,'NumberTitle','off');
+        
+        % Voxel co-registration
+        subplot(2,2,1);
+        size_max = size(MRS_struct.mask.(vox{kk}).img{ii},1);
+        imagesc(MRS_struct.mask.(vox{kk}).img{ii}(:,size_max+(1:size_max)));
+        colormap('gray');
+        caxis([0 0.5]);
+        axis equal;
+        axis tight;
+        axis off;
+        
+        % MM (180112)
+        [~,tmp,tmp2] = fileparts(MRS_struct.metabfile{ii});
+        [~,tmp3,tmp4] = fileparts(MRS_struct.mask.(vox{kk}).T1image{ii});
+        t = ['Voxel from ' tmp tmp2 ' on ' tmp3 tmp4];
+        title(t, 'Interpreter', 'none');
+        
+        % Output results
+        subplot(2,2,2);
+        axis off;
+        
+        text_pos = 1;
+        
+        tmp1 = 'GM voxel fraction';
+        tmp2 = sprintf(': %.3g', MRS_struct.out.(vox{kk}).tissue.GMfra(ii));
+        text(0, text_pos-0.1, tmp1, 'FontName', 'Helvetica', 'FontSize', 10);
+        text(0.5, text_pos-0.1, tmp2, 'FontName', 'Helvetica', 'FontSize', 10);
+        
+        tmp1 = 'WM voxel fraction';
+        tmp2 = sprintf(': %.3g', MRS_struct.out.(vox{kk}).tissue.WMfra(ii));
+        text(0, text_pos-0.2, tmp1, 'FontName', 'Helvetica', 'FontSize', 10);
+        text(0.5, text_pos-0.2, tmp2, 'FontName', 'Helvetica', 'FontSize', 10);
+        
+        tmp1 = 'CSF voxel fraction';
+        tmp2 = sprintf(': %.3g', MRS_struct.out.(vox{kk}).tissue.CSFfra(ii));
+        text(0, text_pos-0.3, tmp1, 'FontName', 'Helvetica', 'FontSize', 10);
+        text(0.5, text_pos-0.3, tmp2, 'FontName', 'Helvetica', 'FontSize', 10);
+        
+        % MM (180112)
+        tmp1 = 'Filename';
+        if strcmp(MRS_struct.p.vendor,'Siemens_rda')
+            [~,tmp2,tmp3] = fileparts(MRS_struct.metabfile{ii*2-1});
+        else
+            [~,tmp2,tmp3] = fileparts(MRS_struct.metabfile{ii});
+        end
+        text(0, text_pos-0.4, tmp1, 'FontName', 'Helvetica', 'FontSize', 10);
+        text(0.5, text_pos-0.4, [': ' tmp2 tmp3], 'FontName', 'Helvetica', 'FontSize', 10, 'Interpreter', 'none');
+        
+        tmp1 = 'Anatomical image';
+        [~,tmp2,tmp3] = fileparts(MRS_struct.mask.(vox{kk}).T1image{ii}); % MM (180112)
+        text(0, text_pos-0.5, tmp1, 'FontName', 'Helvetica', 'FontSize', 10);
+        text(0.5, text_pos-0.5, [': ' tmp2 tmp3], 'FontName', 'Helvetica', 'FontSize', 10, 'Interpreter', 'none');
+        
+        tmp1 = 'SegmentVer';
+        tmp2 = [': ' MRS_struct.version.segment];
+        text(0, text_pos-0.6, tmp1, 'FontName', 'Helvetica', 'FontSize', 10);
+        text(0.5, text_pos-0.6, tmp2, 'FontName', 'Helvetica', 'FontSize', 10);
+        
+        % Gannet logo
+        subplot(2,2,4);
+        axis off;
+        script_path = which('GannetFit');
+        Gannet_logo = [script_path(1:(end-12)) '/Gannet3_logo.png'];
+        A2 = imread(Gannet_logo,'png','BackgroundColor',[1 1 1]);
+        axes('Position',[0.80, 0.05, 0.15, 0.15]);
+        image(A2);
+        axis off;
+        axis square;
+        
+        % For Philips .data
+        if strcmpi(MRS_struct.p.vendor,'Philips_data')
+            fullpath = MRS_struct.metabfile{ii};
+            fullpath = regexprep(fullpath, '.data', '_data');
+            fullpath = regexprep(fullpath, '\', '_');
+            fullpath = regexprep(fullpath, '/', '_');
+        end
+        
+        % MM (180112)
+        [~,metabfile_nopath] = fileparts(MRS_struct.metabfile{ii});
+        
+        % Save PDF output
+        set(gcf,'PaperUnits','inches');
+        set(gcf,'PaperSize',[11 8.5]);
+        set(gcf,'PaperPosition',[0 0 11 8.5]);
+        if strcmpi(MRS_struct.p.vendor,'Philips_data')
+            pdfname = fullfile('CoRegStandAlone_output', [fullpath '_segment.pdf']); % MM (180112)
+        else
+            pdfname = fullfile('CoRegStandAlone_output', [metabfile_nopath '_segment.pdf']); % MM (180112)
+        end        
+        saveas(gcf, pdfname);
+        
+     
+    end
+    
+end
+
+end
+
+
+
diff --git a/DICOMRead.m b/DICOMRead.m
index 8985e31..01a1a44 100644
--- a/DICOMRead.m
+++ b/DICOMRead.m
@@ -1,19 +1,17 @@
-function MRS_struct = DICOMRead(MRS_struct,folder,waterfolder)
-%% MRS_struct = DICOMRead(MRS_struct,folder,waterfolder)
+function MRS_struct = DICOMRead(MRS_struct,metabfile,waterfile)
+%% MRS_struct = DICOMRead(MRS_struct,metabfile,waterfile)
 %   This function is designed to load edited MR spectroscopy data in the 
 %   general form of DICOM data into a Gannet file structure. Files usually
 %   have the extension '.DCM' or '.dcm', and contain exactly 1 FID per
-%   file, i.e. an acquisition of 320 averages will yield 320 IMA files.
+%   file, i.e. an acquisition of 320 averages will yield 320 DCM files.
 %   
-%   The user must specify the folder containing all of these averages. It
-%   is assumed that they are ordered in the order of acquisition.
+%   It is assumed that they are ordered in the order of acquisition.
 %   Water-suppressed and water-unsuppressed files need to be stored in
-%   separate folders, which need to be defined accordingly:
+%   separate folders, e.g. '/user/data/subject01/dcm_gaba/' and 
+%   '/user/data/subject01/dcm_water/', respectively.
 %
 %   Example:
-%       folder = '/user/data/subject01/dcm_gaba/';
-%       waterfolder = '/user/data/subject01/dcm_water/'; (optional)
-%       MRS_struct = DICOMRead(MRS_struct,folder,waterfolder);
+%       MRS_struct = DICOMRead(MRS_struct,'/user/data/subject01/dcm_gaba/metab.dcm','/user/data/subject01/dcm_water/water.dcm');
 %
 %   Author:
 %       Dr. Georg Oeltzschner (Johns Hopkins University, 2016-11-10)
@@ -32,7 +30,9 @@
 %           of Minnesota) (2017-11-20). Thanks to Jim Lagopoulos.
 %   0.95: Fills missing voxel geometry parameters in DICOM header with zero
 %           values. Thanks to Alen Tersakyan.
-%   
+%   0.96: Fixed to accomodate batch processing of coregister/segmentation.
+%           (2018-09-19)
+%
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 
@@ -46,6 +46,7 @@
 % no overlap.
 % dcm_file_list = [dir([folder,'/*.DCM']); dir([folder,'/*.dcm'])]; % may
 % cause problems on win/unix systems, take out for now % GO 11/16/2016
+[folder,~,~] = fileparts(metabfile); % GO 11/01/2016
 dcm_file_list = dir([folder,'/*.dcm']); % GO 11/16/2016
 fprintf('%d water-suppressed DCM files detected in %s.\n',length(dcm_file_list),folder);
 
@@ -60,7 +61,7 @@
 %%% /PREPARATION %%%
 
 %%% HEADER INFO PARSING %%%
-DicomHeader = read_dcm_header(dcm_file_names{1});
+DicomHeader = read_dcm_header(metabfile);
 MRS_struct.p.seq = DicomHeader.sequenceFileName;
 MRS_struct.p.TR(ii) = DicomHeader.TR;
 MRS_struct.p.TE(ii) = DicomHeader.TE;
@@ -100,12 +101,14 @@
 
 % It appears that IMA stores the transients weirdly, 1-n/2 are all ONs, and
 % n/2-n are all OFFS. Shuffle them below.
-a = MRS_struct.fids.data(:,1:end/2);
-b = MRS_struct.fids.data(:,1+end/2:end);
-c = zeros(size(MRS_struct.fids.data));
-c(:,1:2:end) = a;
-c(:,2:2:end) = b;
-MRS_struct.fids.data = c;
+if size(MRS_struct.fids.data,2) > 1
+    a = MRS_struct.fids.data(:,1:end/2);
+    b = MRS_struct.fids.data(:,1+end/2:end);
+    c = zeros(size(MRS_struct.fids.data));
+    c(:,1:2:end) = a;
+    c(:,2:2:end) = b;
+    MRS_struct.fids.data = c;
+end
 %%% /DATA LOADING %%%
 
 
@@ -117,6 +120,7 @@
 
 % Set up the file name array.
 if nargin == 3
+    [waterfolder,~,~] = fileparts(waterfile);
     water_file_list = dir([waterfolder,'/*.DCM']);
     fprintf('%d water-unsuppressed DCM files detected in %s.\n',length(water_file_list),waterfolder);
     disp('Reading water-unsuppressed files...')
diff --git a/GannetLoad.m b/GannetLoad.m
index 7c9ab23..c36bb3e 100755
--- a/GannetLoad.m
+++ b/GannetLoad.m
@@ -47,7 +47,7 @@
 %   1. Pre-initialise
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
-MRS_struct.version.load = '180326'; % set to date when final updates have been made
+MRS_struct.version.load = '180919'; % set to date when final updates have been made
 MRS_struct.ii = 0;
 MRS_struct.metabfile = metabfile;
 MRS_struct = GannetPreInitialise(MRS_struct);
@@ -136,17 +136,10 @@
             
         case 'Siemens_dicom' % GO 11/01/2016
             if exist('waterfile','var')
-                % Load the data. GannetLoad specifies a file in the first
-                % place, so take apart that filename, and feed the containing
-                % folder into the SiemensDICOMRead function. % GO 11/01/2016
-                [imafolder,~,~] = fileparts(metabfile{ii}); % GO 02/05/2017
-                [waterfolder,~,~] = fileparts(waterfile{ii}); % GO 02/05/2017
-                MRS_struct = SiemensDICOMRead(MRS_struct,imafolder,waterfolder); % GO 02/05/2017
+                MRS_struct = SiemensDICOMRead(MRS_struct,metabfile{ii},waterfile{ii}); % GO 02/05/2017
                 WaterData = MRS_struct.fids.data_water;
             else
-                % Same as above, but without parsing the waterfolder. % GO 02/05/2017
-                [imafolder,~,~] = fileparts(metabfile{ii}); % GO 11/01/2016
-                MRS_struct = SiemensDICOMRead(MRS_struct,imafolder); % GO 11/01/2016
+                MRS_struct = SiemensDICOMRead(MRS_struct,metabfile{ii}); % GO 11/01/2016
             end
             FullData = MRS_struct.fids.data;
             % Determine order of ON and OFF acquisitions
@@ -154,17 +147,10 @@
             
         case 'dicom' % GO 11/30/2016
             if exist('waterfile','var')
-                % Load the data. GannetLoad specifies a file in the first
-                % place, so take apart that filename, and feed the containing
-                % folder into the DICOMRead function. % GO 11/01/2016
-                [dcmfolder,~,~] = fileparts(metabfile{ii}); % GO 02/05/2017
-                [waterfolder,~,~] = fileparts(waterfile{ii}); % GO 02/05/2017
-                MRS_struct = DICOMRead(MRS_struct,dcmfolder,waterfolder); % GO 02/05/2017
+                MRS_struct = DICOMRead(MRS_struct,metabfile{ii},waterfile{ii}); % GO 02/05/2017
                 WaterData = MRS_struct.fids.data_water;
             else
-                % Same as above, but without parsing the waterfolder. % GO 02/05/2017
-                [dcmfolder,~,~] = fileparts(metabfile{ii}); % GO 11/01/2016
-                MRS_struct = DICOMRead(MRS_struct,dcmfolder); % GO 11/01/2016
+                MRS_struct = DICOMRead(MRS_struct,metabfile{ii}); % GO 11/01/2016
             end
             FullData = MRS_struct.fids.data;
             
diff --git a/SiemensDICOMRead.m b/SiemensDICOMRead.m
index 67a986a..95e46e8 100644
--- a/SiemensDICOMRead.m
+++ b/SiemensDICOMRead.m
@@ -1,19 +1,17 @@
-function MRS_struct = SiemensDICOMRead(MRS_struct,folder,waterfolder)
-%% MRS_struct = SiemensDICOMRead(MRS_struct,folder,waterfolder)
+function MRS_struct = SiemensDICOMRead(MRS_struct,metabfile,waterfile)
+%% MRS_struct = SiemensDICOMRead(MRS_struct,metabfile,waterfile)
 %   This function is designed to load edited MR spectroscopy data in the 
 %   Siemens flavour of DICOM data into a Gannet file structure. Files usually
 %   have the extension '.IMA' or '.ima', and contain exactly 1 FID per
 %   file, i.e. an acquisition of 320 averages will yield 320 IMA files.
 %   
-%   The user must specify the folder containing all of these averages. It
-%   is assumed that they are ordered in the order of acquisition.
+%   It is assumed that they are ordered in the order of acquisition.
 %   Water-suppressed and water-unsuppressed files need to be stored in
-%   separate folders, which need to be defined accordingly:
+%   separate folders, e.g. '/user/data/subject01/ima_gaba/' and 
+%   '/user/data/subject01/ima_water/', respectively.
 %
 %   Example:
-%       folder = '/user/data/subject01/ima_gaba/';
-%       waterfolder = '/user/data/subject01/ima_water/'; (optional)
-%       MRS_struct = SiemensDICOMRead(MRS_struct,folder,waterfolder);
+%       MRS_struct = SiemensDICOMRead(MRS_struct,'/user/data/subject01/ima_gaba/metab.ima','/user/data/subject01/ima_water/water.ima');
 %
 %   Author:
 %       Dr. Georg Oeltzschner (Johns Hopkins University, 2016-11-10)
@@ -32,6 +30,8 @@
 %           of Minnesota) (2017-11-20). Thanks to Jim Lagopoulos.
 %   0.95: Fills missing voxel geometry parameters in DICOM header with zero
 %           values. Thanks to Alen Tersakyan.
+%   0.96: Fixed to accomodate batch processing of coregister/segmentation.
+%           (2018-09-19)
 %   
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
@@ -46,6 +46,7 @@
 % no overlap.
 % ima_file_list = [dir([folder,'/*.IMA']); dir([folder,'/*.ima'])]; % may
 % cause problems on win/unix systems, take out for now % GO 11/16/2016
+[folder,~,~] = fileparts(metabfile); % GO 11/01/2016
 ima_file_list = dir([folder,'/*.IMA']); % GO 11/16/2016
 fprintf('%d water-suppressed IMA files detected in %s.\n',length(ima_file_list),folder);
 
@@ -60,7 +61,7 @@
 %%% /PREPARATION %%%
 
 %%% HEADER INFO PARSING %%%
-DicomHeader = read_dcm_header(ima_file_names{1});
+DicomHeader = read_dcm_header(metabfile);
 MRS_struct.p.seq = DicomHeader.sequenceFileName;
 MRS_struct.p.TR(ii) = DicomHeader.TR;
 MRS_struct.p.TE(ii) = DicomHeader.TE;
@@ -106,12 +107,14 @@
 
 % It appears that IMA stores the transients weirdly, 1-n/2 are all ONs, and
 % n/2-n are all OFFS. Shuffle them below.
-a = MRS_struct.fids.data(:,1:end/2);
-b = MRS_struct.fids.data(:,1+end/2:end);
-c = zeros(size(MRS_struct.fids.data));
-c(:,1:2:end) = a;
-c(:,2:2:end) = b;
-MRS_struct.fids.data = c;
+if size(MRS_struct.fids.data,2) > 1
+    a = MRS_struct.fids.data(:,1:end/2);
+    b = MRS_struct.fids.data(:,1+end/2:end);
+    c = zeros(size(MRS_struct.fids.data));
+    c(:,1:2:end) = a;
+    c(:,2:2:end) = b;
+    MRS_struct.fids.data = c;
+end
 %%% /DATA LOADING %%%
 
 
@@ -123,6 +126,7 @@
 
 % Set up the file name array.
 if nargin == 3
+    [waterfolder,~,~] = fileparts(waterfile);
     water_file_list = dir([waterfolder,'/*.IMA']);
     fprintf('%d water-unsuppressed IMA files detected in %s.\n',length(water_file_list),waterfolder);
     disp('Reading water-unsuppressed files...')