diff --git a/GUI/OspreyGUI.m b/GUI/OspreyGUI.m
index 215559a8..bd2aac23 100644
--- a/GUI/OspreyGUI.m
+++ b/GUI/OspreyGUI.m
@@ -122,6 +122,8 @@
             gui.controls.Tab = 1;
             gui.controls.Number = 1;
             gui.controls.KeyPress = 0;
+        %Manual manipulation like phasing performed
+            gui.process.ManualManipulation = 0;
         %File selections for each sub function
             gui.load.Selected = 1;
             gui.process.Selected = 1;
@@ -440,7 +442,25 @@
             gui.layout.ListBox = uicontrol('Style', 'list','BackgroundColor', 'w','FontName', gui.font,'BackgroundColor',gui.colormap.Background, ...
                                     'Parent', gui.layout.controlPanel, 'String',gui.layout.RedFileList(:) , ...
                                     'Value', gui.controls.Selected, 'Interruptible', 'on', 'BusyAction', 'cancel', ...
-                                    'ForegroundColor',gui.colormap.Foreground, 'TooltipString', 'Select a file you want to inspect.','Tag','SubjectListBox');
+                                    'ForegroundColor',gui.colormap.Foreground, 'TooltipString', sprintf(['Select a file you want to inspect.\n\r\n' ...
+                                    'Other intersting key presses after clicking are:\n' ...
+                                    'left arrow - remove data\n' ...
+                                    'right arrow - add data\n\r\n' ...
+                                    'In the Processed Tab you can manipulate the averaged spectrum as follows:\n' ...
+                                    'a - Subtract 5 degree from ph0\n' ...
+                                    'd - Add 5 degree to ph0\n' ...
+                                    'q - Subtract 0.00001 s from ph1\n' ...
+                                    'e - Add 0.00001 s to ph1\n' ...
+                                    's - Subtract 1 Hz from f\n' ...
+                                    'w - Add 1 Hz to f\n' ...
+                                    'f - Add 180 degree to ph0\n\r\n' ...
+                                    'You can change the axis of the processed plot as follows:\n' ...
+                                    'r - Reset y-axis limits\n' ...
+                                    'z - Zoom out y-axis\n' ...
+                                    'x - Zoom in y-axis\n' ...
+                                    'c - Move y-axis center down\n' ...
+                                    'v - Move y-axis center up' ...
+                                    ]),'Tag','SubjectListBox');
             if MRSCont.flags.isMRSI
                 gui.layout.MRSILocPanel = uix.Panel('Parent', gui.layout.leftMenu, 'Title', 'Voxel Location','BackgroundColor',gui.colormap.Background);
                 set(gui.layout.MRSILocPanel,'Units','Normalized','Position',[0.5 0 0.66 0.1], 'FontSize', 16, 'FontName', gui.font, 'FontWeight', 'Bold',...
diff --git a/GUI/osp_WindowKeyDown.m b/GUI/osp_WindowKeyDown.m
index c97a2a61..0d87a401 100644
--- a/GUI/osp_WindowKeyDown.m
+++ b/GUI/osp_WindowKeyDown.m
@@ -30,6 +30,7 @@ function osp_WindowKeyDown(~,EventData,gui)
     % 31 downarrow
 % Get MRSCont from hidden class container
     MRSCont = getappdata(gui.figure,'MRSCont');  
+    gui.controls.PhasePress = 0;
     MRSCont.flags.exclude = 1;
     if strcmp(EventData.Key, 'uparrow') % scrolling up
         OldValue = get( gui.layout.ListBox,'value');
@@ -129,5 +130,204 @@ function osp_WindowKeyDown(~,EventData,gui)
             end
         end
     end
+    if strcmp(EventData.Key, 'f') % 180 degree flip
+        gui.controls.KeyPress = 1;
+        gui.controls.PhasePress = 1;
+        gui.controls.posPhase0Shift = 0;
+        gui.controls.negPhase0Shift = 0;
+        gui.controls.posPhase1Shift = 0;
+        gui.controls.negPhase1Shift = 0;
+        gui.controls.flipPhase = 1;
+        gui.controls.posFreqShift = 0;
+        gui.controls.negFreqShift = 0;
+        gui.controls.resetAxis = 0;
+        gui.controls.zoomOut = 0;
+        gui.controls.zoomIn = 0;
+        gui.controls.MoveUp = 0;
+        gui.controls.MoveDown = 0;
+        gui.process.ManualManipulation = 1;
+    end
+    if strcmp(EventData.Key, 'd') % positive phase
+        gui.controls.KeyPress = 1;
+        gui.controls.PhasePress = 1;
+        gui.controls.posPhase0Shift = 1;
+        gui.controls.negPhase0Shift = 0;
+        gui.controls.posPhase1Shift = 0;
+        gui.controls.negPhase1Shift = 0;
+        gui.controls.flipPhase = 0;
+        gui.controls.posFreqShift = 0;
+        gui.controls.negFreqShift = 0;
+        gui.controls.resetAxis = 0;
+        gui.controls.zoomOut = 0;
+        gui.controls.zoomIn = 0;
+        gui.controls.MoveUp = 0;
+        gui.controls.MoveDown = 0;
+        gui.process.ManualManipulation = 1;
+    end
+    if strcmp(EventData.Key, 'a') % negative phase
+        gui.controls.KeyPress = 1;
+        gui.controls.PhasePress = 1;
+        gui.controls.posPhase0Shift = 0;
+        gui.controls.negPhase0Shift = 1;
+        gui.controls.posPhase1Shift = 0;
+        gui.controls.negPhase1Shift = 0;
+        gui.controls.flipPhase = 0;
+        gui.controls.posFreqShift = 0;
+        gui.controls.negFreqShift = 0;
+        gui.controls.resetAxis = 0;
+        gui.controls.zoomOut = 0;
+        gui.controls.zoomIn = 0;
+        gui.controls.MoveUp = 0;
+        gui.controls.MoveDown = 0;
+        gui.process.ManualManipulation = 1;
+    end
+    if strcmp(EventData.Key, 'e') % positive phase1
+        gui.controls.KeyPress = 1;
+        gui.controls.PhasePress = 1;
+        gui.controls.posPhase0Shift = 0;
+        gui.controls.negPhase0Shift = 0;
+        gui.controls.posPhase1Shift = 1;
+        gui.controls.negPhase1Shift = 0;
+        gui.controls.flipPhase = 0;
+        gui.controls.posFreqShift = 0;
+        gui.controls.negFreqShift = 0;
+        gui.controls.resetAxis = 0;
+        gui.controls.zoomOut = 0;
+        gui.controls.zoomIn = 0;
+        gui.controls.MoveUp = 0;
+        gui.controls.MoveDown = 0;
+        gui.process.ManualManipulation = 1;
+    end
+    if strcmp(EventData.Key, 'q') % negative phase1
+        gui.controls.KeyPress = 1;
+        gui.controls.PhasePress = 1;
+        gui.controls.posPhase0Shift = 0;
+        gui.controls.negPhase0Shift = 0;
+        gui.controls.posPhase1Shift = 0;
+        gui.controls.negPhase1Shift = 1;
+        gui.controls.flipPhase = 0;
+        gui.controls.posFreqShift = 0;
+        gui.controls.negFreqShift = 0;
+        gui.controls.resetAxis = 0;
+        gui.controls.zoomOut = 0;
+        gui.controls.zoomIn = 0;
+        gui.controls.MoveUp = 0;
+        gui.controls.MoveDown = 0;
+        gui.process.ManualManipulation = 1;
+    end
+    if strcmp(EventData.Key, 'w') % positive freq
+        gui.controls.KeyPress = 1;
+        gui.controls.PhasePress = 1;
+        gui.controls.posPhase0Shift = 0;
+        gui.controls.negPhase0Shift = 0;
+        gui.controls.posPhase1Shift = 0;
+        gui.controls.negPhase1Shift = 0;
+        gui.controls.flipPhase = 0;
+        gui.controls.posFreqShift = 1;
+        gui.controls.negFreqShift = 0;
+        gui.controls.resetAxis = 0;
+        gui.controls.zoomOut = 0;
+        gui.controls.zoomIn = 0;
+        gui.controls.MoveUp = 0;
+        gui.controls.MoveDown = 0;
+        gui.process.ManualManipulation = 1;
+    end
+    if strcmp(EventData.Key, 's') % negative freq
+        gui.controls.KeyPress = 1;
+        gui.controls.PhasePress = 1;
+        gui.controls.posPhase0Shift = 0;
+        gui.controls.negPhase0Shift = 0;
+        gui.controls.posPhase1Shift = 0;
+        gui.controls.negPhase1Shift = 0;
+        gui.controls.flipPhase = 0;
+        gui.controls.posFreqShift = 0;
+        gui.controls.negFreqShift = 1;
+        gui.controls.resetAxis = 0;
+        gui.controls.zoomOut = 0;
+        gui.controls.zoomIn = 0;
+        gui.controls.MoveUp = 0;
+        gui.controls.MoveDown = 0;
+        gui.process.ManualManipulation = 1;
+    end
+    if strcmp(EventData.Key, 'r') % reset axis
+        gui.controls.KeyPress = 1;
+        gui.controls.PhasePress = 1;
+        gui.controls.posPhase0Shift = 0;
+        gui.controls.negPhase0Shift = 0;
+        gui.controls.posPhase1Shift = 0;
+        gui.controls.negPhase1Shift = 0;
+        gui.controls.flipPhase = 0;
+        gui.controls.posFreqShift = 0;
+        gui.controls.negFreqShift = 0;
+        gui.controls.resetAxis = 1;
+        gui.controls.zoomOut = 0;
+        gui.controls.zoomIn = 0;
+        gui.controls.MoveUp = 0;
+        gui.controls.MoveDown = 0;
+    end
+    if strcmp(EventData.Key, 'z') % zoom out
+        gui.controls.KeyPress = 1;
+        gui.controls.PhasePress = 1;
+        gui.controls.posPhase0Shift = 0;
+        gui.controls.negPhase0Shift = 0;
+        gui.controls.posPhase1Shift = 0;
+        gui.controls.negPhase1Shift = 0;
+        gui.controls.flipPhase = 0;
+        gui.controls.posFreqShift = 0;
+        gui.controls.negFreqShift = 0;
+        gui.controls.resetAxis = 0;
+        gui.controls.zoomOut = 1;
+        gui.controls.zoomIn = 0;
+        gui.controls.MoveUp = 0;
+        gui.controls.MoveDown = 0;
+    end
+    if strcmp(EventData.Key, 'x') % zoom in
+        gui.controls.KeyPress = 1;
+        gui.controls.PhasePress = 1;
+        gui.controls.posPhase0Shift = 0;
+        gui.controls.negPhase0Shift = 0;
+        gui.controls.posPhase1Shift = 0;
+        gui.controls.negPhase1Shift = 0;
+        gui.controls.flipPhase = 0;
+        gui.controls.posFreqShift = 0;
+        gui.controls.negFreqShift = 0;
+        gui.controls.resetAxis = 0;
+        gui.controls.zoomOut = 0;
+        gui.controls.zoomIn = 1;
+        gui.controls.MoveUp = 0;
+        gui.controls.MoveDown = 0;
+    end
+    if strcmp(EventData.Key, 'c') % move up
+        gui.controls.KeyPress = 1;
+        gui.controls.PhasePress = 1;
+        gui.controls.posPhase0Shift = 0;
+        gui.controls.negPhase0Shift = 0;
+        gui.controls.posPhase1Shift = 0;
+        gui.controls.negPhase1Shift = 0;
+        gui.controls.flipPhase = 0;
+        gui.controls.posFreqShift = 0;
+        gui.controls.negFreqShift = 0;
+        gui.controls.resetAxis = 0;
+        gui.controls.zoomOut = 0;
+        gui.controls.zoomIn = 0;
+        gui.controls.MoveUp = 1;
+        gui.controls.MoveDown = 0;
+    end
+    if strcmp(EventData.Key, 'v') % move down
+        gui.controls.KeyPress = 1;
+        gui.controls.PhasePress = 1;
+        gui.controls.posPhase0Shift = 0;
+        gui.controls.negPhase0Shift = 0;
+        gui.controls.posPhase1Shift = 0;
+        gui.controls.negPhase1Shift = 0;
+        gui.controls.flipPhase = 0;
+        gui.controls.posFreqShift = 0;
+        gui.controls.negFreqShift = 0;
+        gui.controls.resetAxis = 0;
+        gui.controls.zoomOut = 0;
+        gui.controls.zoomIn = 0;
+        gui.controls.MoveUp = 0;
+        gui.controls.MoveDown = 1;
+    end
     setappdata(gui.figure,'MRSCont',MRSCont); % Write MRSCont into hidden container in gui class
 end
\ No newline at end of file
diff --git a/GUI/osp_WindowKeyUp.m b/GUI/osp_WindowKeyUp.m
index 2f4ef92d..b28066b4 100644
--- a/GUI/osp_WindowKeyUp.m
+++ b/GUI/osp_WindowKeyUp.m
@@ -25,5 +25,10 @@ function osp_WindowKeyUp(~,~,gui)
 %       2020-01-16: First version of the code.
 %%% 1. GET HANDLES %%%
     gui.controls.KeyPress = 0;
-    osp_updateListBox(gui);
+    if gui.controls.PhasePress == 0
+        osp_updateListBox(gui);
+    else
+        gui.controls.PhasePress = 0;
+        osp_phaseProWindow(gui)
+    end
 end
\ No newline at end of file
diff --git a/GUI/osp_iniProcessWindow.m b/GUI/osp_iniProcessWindow.m
index 7350da98..738f635b 100644
--- a/GUI/osp_iniProcessWindow.m
+++ b/GUI/osp_iniProcessWindow.m
@@ -270,6 +270,7 @@ function osp_iniProcessWindow(gui)
             close(h(ff))
         end
     end
+    gui.controls.YLimits = [];
     gui.info.nYvoxels = MRSCont.processed.metab{1, 1}.subspecs;
     setappdata(gui.figure,'MRSCont',MRSCont); % Write MRSCont into hidden container in gui class
 end
\ No newline at end of file
diff --git a/GUI/osp_onFit.m b/GUI/osp_onFit.m
index 6823b3e0..f4a58473 100644
--- a/GUI/osp_onFit.m
+++ b/GUI/osp_onFit.m
@@ -31,6 +31,30 @@ function osp_onFit( ~, ~ ,gui)
     set(gui.layout.fitTab, 'SelectionChangedFcn','');
     gui.layout.b_fit.Enable = 'off';
     gui.layout.tabs.Selection  = 3;
+    if gui.process.ManualManipulation
+        % Optional: write edited files to LCModel .RAW files
+        if MRSCont.opts.saveLCM && ~MRSCont.flags.isPRIAM && ~MRSCont.flags.isMRSI
+            [MRSCont] = osp_saveLCM(MRSCont);
+        end
+        
+        % Optional: write edited files to jMRUI .txt files
+        if MRSCont.opts.savejMRUI && ~MRSCont.flags.isPRIAM && ~MRSCont.flags.isMRSI
+            [MRSCont] = osp_saveJMRUI(MRSCont);
+        end
+        
+        % Optional: write edited files to vendor specific format files readable to
+        % LCModel and jMRUI
+        % SPAR/SDAT if Philips
+        % RDA if Siemens
+        if MRSCont.opts.saveVendor && ~MRSCont.flags.isPRIAM && ~MRSCont.flags.isMRSI
+            [MRSCont] = osp_saveVendor(MRSCont);
+        end
+        
+        % Optional: write edited files to NIfTI-MRS format
+        if MRSCont.opts.saveNII && ~MRSCont.flags.isPRIAM && ~MRSCont.flags.isMRSI
+            [MRSCont] = osp_saveNII(MRSCont);
+        end
+    end
     [gui,MRSCont] = osp_processingWindow(gui,MRSCont);
 %%% 2. CALL OSPREYFIT %%%
     MRSCont = OspreyFit(MRSCont);
diff --git a/GUI/osp_onSave.m b/GUI/osp_onSave.m
index 8dd7d587..28bac2a1 100644
--- a/GUI/osp_onSave.m
+++ b/GUI/osp_onSave.m
@@ -43,4 +43,32 @@ function osp_onSave( ~, ~,gui)
     setappdata(gui.figure,'MRSCont',MRSCont); % Write MRSCont into hidden container in gui class
     set(gui.figure,'HandleVisibility','on');
     toc(refProcessTime);
+
+    if gui.process.ManualManipulation
+        fprintf('Rewriting MRS data after manual manipulation...\n');
+        % Optional: write edited files to LCModel .RAW files
+        if MRSCont.opts.saveLCM && ~MRSCont.flags.isPRIAM && ~MRSCont.flags.isMRSI
+            [MRSCont] = osp_saveLCM(MRSCont);
+        end
+        
+        % Optional: write edited files to jMRUI .txt files
+        if MRSCont.opts.savejMRUI && ~MRSCont.flags.isPRIAM && ~MRSCont.flags.isMRSI
+            [MRSCont] = osp_saveJMRUI(MRSCont);
+        end
+        
+        % Optional: write edited files to vendor specific format files readable to
+        % LCModel and jMRUI
+        % SPAR/SDAT if Philips
+        % RDA if Siemens
+        if MRSCont.opts.saveVendor && ~MRSCont.flags.isPRIAM && ~MRSCont.flags.isMRSI
+            [MRSCont] = osp_saveVendor(MRSCont);
+        end
+        
+        % Optional: write edited files to NIfTI-MRS format
+        if MRSCont.opts.saveNII && ~MRSCont.flags.isPRIAM && ~MRSCont.flags.isMRSI
+            [MRSCont] = osp_saveNII(MRSCont);
+        end
+        fprintf('... done.\n');
+    end
+
 end % onExit
\ No newline at end of file
diff --git a/GUI/osp_phaseProWindow.m b/GUI/osp_phaseProWindow.m
new file mode 100644
index 00000000..6e3810bb
--- /dev/null
+++ b/GUI/osp_phaseProWindow.m
@@ -0,0 +1,361 @@
+function osp_phaseProWindow(gui)
+%% osp_phaseProWindow
+%   This function updates the process tab for manual phasing.
+%
+%
+%   USAGE:
+%       osp_updateProWindow(gui);
+%
+%   INPUT:  
+%           gui      = gui class containing all handles and the MRSCont             
+%
+%
+%   AUTHORS:
+%       Dr. Helge Zoellner (Johns Hopkins University, 2020-01-16)
+%       hzoelln2@jhmi.edu
+%
+%   CREDITS:
+%       This code is based on numerous functions from the FID-A toolbox by
+%       Dr. Jamie Near (McGill University)
+%       https://github.com/CIC-methods/FID-A
+%       Simpson et al., Magn Reson Med 77:23-33 (2017)
+%
+%   HISTORY:
+%       2020-01-16: First version of the code.
+%%% 1. INITIALIZE %%%
+        MRSCont = getappdata(gui.figure,'MRSCont');  % Get MRSCont from hidden container in gui class 
+         if (isfield(MRSCont.flags,'isPRIAM') || isfield(MRSCont.flags,'isMRSI')) && (MRSCont.flags.isPRIAM || MRSCont.flags.isMRSI)
+            set(gui.layout.(gui.layout.proTabhandles{gui.process.Selected}).Children(2).Children(3).Children(1).Children.Children(4),'String',gui.controls.act_z);
+            set(gui.layout.(gui.layout.proTabhandles{gui.process.Selected}).Children(2).Children(3).Children(1).Children.Children(5),'String',gui.controls.act_y);
+            set(gui.layout.(gui.layout.proTabhandles{gui.process.Selected}).Children(2).Children(3).Children(1).Children.Children(6),'String',gui.controls.act_x);
+         else
+            set(gui.layout.(gui.layout.proTabhandles{gui.process.Selected}).Children(2).Children(3).Children(1).Children.Children(3),'String',gui.controls.act_y);
+            set(gui.layout.(gui.layout.proTabhandles{gui.process.Selected}).Children(2).Children(3).Children(1).Children.Children(4),'String',gui.controls.act_x);
+        end
+        gui.layout.EmptyProPlot = 0;
+        Selection = gui.process.TabTitles{gui.process.Selected};
+        Exp = gui.controls.act_x;
+        SubSpec = gui.controls.act_y;
+        
+        if (MRSCont.processed.(gui.process.TabTitles{gui.process.Selected}){gui.controls.Selected}.dims.extras == 0) || (Exp > MRSCont.processed.(gui.process.TabTitles{gui.process.Selected}){gui.controls.Selected}.sz(MRSCont.processed.(gui.process.TabTitles{gui.process.Selected}){gui.controls.Selected}.dims.extras))
+            Exp = 1;
+            gui.controls.act_x = 1;
+        end
+        if (MRSCont.processed.(gui.process.TabTitles{gui.process.Selected}){gui.controls.Selected}.dims.subSpecs == 0) || (SubSpec > MRSCont.processed.(gui.process.TabTitles{gui.process.Selected}){gui.controls.Selected}.sz(MRSCont.processed.(gui.process.TabTitles{gui.process.Selected}){gui.controls.Selected}.dims.subSpecs))
+            SubSpec = 1;
+            gui.controls.act_y = 1;
+        end
+  
+%%% 2. PHASING AND FREQUENCY SHIFT HAPPENS HERE %%%   
+    if isfield(MRSCont.processed.metab{gui.controls.Selected}, 'extras')
+        procData = op_takeextra(MRSCont.processed.metab{gui.controls.Selected},Exp);
+        if gui.controls.posPhase0Shift
+            procData=op_addphase(procData ,5);
+            if isfield(procData, 'manual') && isfield(procData.manual,'ph0') && Exp <= length(procData.manual.ph0)
+                procData.manual.ph0(Exp) = procData.manual.ph0(Exp) + 5;
+            else
+                procData.manual.ph0(Exp) =  5;
+            end
+        end
+        if gui.controls.negPhase0Shift
+            procData=op_addphase(procData ,-5);
+            if isfield(procData, 'manual') && isfield(procData.manual,'ph0') && Exp <= length(procData.manual.ph0)
+                procData.manual.ph0(Exp) = procData.manual.ph0(Exp) - 5;
+            else
+                procData.manual.ph0(Exp) =  -5;
+            end
+        end
+        if gui.controls.posPhase1Shift
+            procData=op_addphase(procData ,0,0.00001);
+            if isfield(procData, 'manual') && isfield(procData.manual,'ph1') && Exp <= length(procData.manual.ph1)
+                procData.manual.ph1(Exp) = procData.manual.ph1(Exp) + 0.00001;
+            else
+                procData.manual.ph1(Exp) =  0.00001;
+            end
+        end
+        if gui.controls.negPhase1Shift
+            procData=op_addphase(procData ,0,-0.00001);
+            if isfield(procData, 'manual') && isfield(procData.manual,'ph1') && Exp <= length(procData.manual.ph1)
+                procData.manual.ph1(Exp) = procData.manual.ph1(Exp) - 0.00001;
+            else
+                procData.manual.ph1(Exp) =  -0.00001;
+            end
+        end
+        if gui.controls.flipPhase
+            procData=op_addphase(procData ,180);
+            if isfield(procData, 'manual') && isfield(procData.manual,'ph0') && Exp <= length(procData.manual.ph0)
+                procData.manual.ph0(Exp) = procData.manual.ph0(Exp) + 180;
+            else
+                procData.manual.ph0(Exp) =  180;
+            end
+        end
+        if gui.controls.posFreqShift
+            procData=op_freqshift(procData ,1);
+            if isfield(procData, 'manual') && isfield(procData.manual,'f') && Exp <= length(procData.manual.f)
+                procData.manual.f(Exp) = procData.manual.f(Exp) + 1;
+            else
+                procData.manual.f(Exp) =  1;
+            end
+        end
+        if gui.controls.negFreqShift
+            procData=op_freqshift(procData ,-1);
+            if isfield(procData, 'manual') && isfield(procData.manual,'f') && Exp <= length(procData.manual.f)
+                procData.manual.f(Exp) = procData.manual.f(Exp) - 1;
+            else
+                procData.manual.f(Exp) =  -1;
+            end
+        end
+        if isfield(procData, 'manual') && isfield(procData.manual,'ph0')
+            if abs(procData.manual.ph0(Exp)) > 360
+                procData.manual.ph0(Exp) = procData.manual.ph0(Exp) + sign(procData.manual.ph0(Exp))*(-1)*360;
+            end
+        end
+        MRSCont.processed.metab{gui.controls.Selected}=op_addextra(MRSCont.processed.metab{gui.controls.Selected},procData,Exp); 
+    
+        if isfield(MRSCont, 'processed_no_align')
+            procData = op_takeextra(MRSCont.processed_no_align.metab{gui.controls.Selected},Exp);
+            if gui.controls.posPhase0Shift
+                procData=op_addphase(procData ,5);
+                if isfield(procData, 'manual') && isfield(procData.manual,'ph0') && Exp <= length(procData.manual.ph0)
+                    procData.manual.ph0(Exp) = procData.manual.ph0(Exp) + 5;
+                else
+                    procData.manual.ph0(Exp) =  5;
+                end
+            end
+            if gui.controls.negPhase0Shift
+                procData=op_addphase(procData ,-5);
+                if isfield(procData, 'manual') && isfield(procData.manual,'ph0') && Exp <= length(procData.manual.ph0)
+                    procData.manual.ph0(Exp) = procData.manual.ph0(Exp) - 5;
+                else
+                    procData.manual.ph0(Exp) =  -5;
+                end
+            end
+            if gui.controls.posPhase1Shift
+                procData=op_addphase(procData ,0,0.00001);
+                if isfield(procData, 'manual') && isfield(procData.manual,'ph1') && Exp <= length(procData.manual.ph1)
+                    procData.manual.ph1(Exp) = procData.manual.ph1(Exp) + 0.00001;
+                else
+                    procData.manual.ph1(Exp) =  0.00001;
+                end
+            end
+            if gui.controls.negPhase1Shift
+                procData=op_addphase(procData ,0,-0.00001);
+                if isfield(procData, 'manual') && isfield(procData.manual,'ph1') && Exp <= length(procData.manual.ph1)
+                    procData.manual.ph1(Exp) = procData.manual.ph1(Exp) - 0.00001;
+                else
+                    procData.manual.ph1(Exp) =  -0.00001;
+                end
+            end
+            if gui.controls.flipPhase
+                procData=op_addphase(procData ,180);
+                if isfield(procData, 'manual') && isfield(procData.manual,'ph0') && Exp <= length(procData.manual.ph0)
+                    procData.manual.ph0(Exp) = procData.manual.ph0(Exp) + 180;
+                else
+                    procData.manual.ph0(Exp) =  180;
+                end
+            end
+            if gui.controls.posFreqShift
+                procData=op_freqshift(procData ,1);
+                if isfield(procData, 'manual') && isfield(procData.manual,'f') && Exp <= length(procData.manual.f)
+                    procData.manual.f(Exp) = procData.manual.f(Exp) + 1;
+                else
+                    procData.manual.f(Exp) =  1;
+                end
+            end
+            if gui.controls.negFreqShift
+                procData=op_freqshift(procData ,-1);
+                if isfield(procData, 'manual') && isfield(procData.manual,'f') && Exp <= length(procData.manual.f)
+                    procData.manual.f(Exp) = procData.manual.f(Exp) - 1;
+                else
+                    procData.manual.f(Exp) =  -1;
+                end
+            end
+            if isfield(procData, 'manual') && isfield(procData.manual,'ph0')
+                if abs(procData.manual.ph0(Exp)) > 360
+                    procData.manual.ph0(Exp) = procData.manual.ph0(Exp) + sign(procData.manual.ph0(Exp))*(-1)*360;
+                end
+            end
+            MRSCont.processed_no_align.metab{gui.controls.Selected}=op_addextra(MRSCont.processed_no_align,procData,Exp);
+        end
+    else
+        if gui.controls.posPhase0Shift
+            MRSCont.processed.metab{gui.controls.Selected}=op_addphase(MRSCont.processed.metab{gui.controls.Selected} ,5);
+            if isfield(MRSCont.processed.metab{gui.controls.Selected}, 'manual') && isfield(MRSCont.processed.metab{gui.controls.Selected}.manual,'ph0')
+                MRSCont.processed.metab{gui.controls.Selected}.manual.ph0 = MRSCont.processed.metab{gui.controls.Selected}.manual.ph0 + 5;
+            else
+                MRSCont.processed.metab{gui.controls.Selected}.manual.ph0 =  5;
+            end
+        end
+        if gui.controls.negPhase0Shift
+            MRSCont.processed.metab{gui.controls.Selected}=op_addphase(MRSCont.processed.metab{gui.controls.Selected} ,-5);
+            if isfield(MRSCont.processed.metab{gui.controls.Selected}, 'manual') && isfield(MRSCont.processed.metab{gui.controls.Selected}.manual,'ph0')
+                MRSCont.processed.metab{gui.controls.Selected}.manual.ph0 = MRSCont.processed.metab{gui.controls.Selected}.manual.ph0 - 5;
+            else
+                MRSCont.processed.metab{gui.controls.Selected}.manual.ph0 =  -5;
+            end
+        end
+        if gui.controls.posPhase1Shift
+            MRSCont.processed.metab{gui.controls.Selected}=op_addphase(MRSCont.processed.metab{gui.controls.Selected} ,0,0.00001);
+            if isfield(MRSCont.processed.metab{gui.controls.Selected}, 'manual') && isfield(MRSCont.processed.metab{gui.controls.Selected}.manual,'ph1')
+                MRSCont.processed.metab{gui.controls.Selected}.manual.ph1 = MRSCont.processed.metab{gui.controls.Selected}.manual.ph1 + 0.00001;
+            else
+                MRSCont.processed.metab{gui.controls.Selected}.manual.ph1 =  0.00001;
+            end
+        end
+        if gui.controls.negPhase1Shift
+            MRSCont.processed.metab{gui.controls.Selected}=op_addphase(MRSCont.processed.metab{gui.controls.Selected} ,0,-0.00001);
+            if isfield(MRSCont.processed.metab{gui.controls.Selected}, 'manual') && isfield(MRSCont.processed.metab{gui.controls.Selected}.manual,'ph1')
+                MRSCont.processed.metab{gui.controls.Selected}.manual.ph1 = MRSCont.processed.metab{gui.controls.Selected}.manual.ph1 -0.00001;
+            else
+                MRSCont.processed.metab{gui.controls.Selected}.manual.ph1 =  -0.00001;
+            end
+        end
+        if gui.controls.flipPhase
+            MRSCont.processed.metab{gui.controls.Selected}=op_addphase(MRSCont.processed.metab{gui.controls.Selected} ,180);
+            if isfield(MRSCont.processed.metab{gui.controls.Selected}, 'manual') && isfield(MRSCont.processed.metab{gui.controls.Selected}.manual,'ph0')
+                MRSCont.processed.metab{gui.controls.Selected}.manual.ph0 = MRSCont.processed.metab{gui.controls.Selected}.manual.ph0 + 180;
+            else
+                MRSCont.processed.metab{gui.controls.Selected}.manual.ph0 =  180;
+            end
+        end
+        if gui.controls.posFreqShift
+            MRSCont.processed.metab{gui.controls.Selected}=op_freqshift(MRSCont.processed.metab{gui.controls.Selected} ,1);
+            if isfield(MRSCont.processed.metab{gui.controls.Selected}, 'manual') && isfield(MRSCont.processed.metab{gui.controls.Selected}.manual,'f')
+                MRSCont.processed.metab{gui.controls.Selected}.manual.f = MRSCont.processed.metab{gui.controls.Selected}.manual.f + 1;
+            else
+                MRSCont.processed.metab{gui.controls.Selected}.manual.f =  1;
+            end
+        end
+        if gui.controls.negFreqShift
+            MRSCont.processed.metab{gui.controls.Selected}=op_freqshift(MRSCont.processed.metab{gui.controls.Selected} ,-1);
+            if isfield(MRSCont.processed.metab{gui.controls.Selected}, 'manual') && isfield(MRSCont.processed.metab{gui.controls.Selected}.manual,'f')
+                MRSCont.processed.metab{gui.controls.Selected}.manual.f = MRSCont.processed.metab{gui.controls.Selected}.manual.f - 1;
+            else
+                MRSCont.processed.metab{gui.controls.Selected}.manual.f =  -1;
+            end
+        end
+        if isfield(MRSCont.processed.metab{gui.controls.Selected}, 'manual') && isfield(MRSCont.processed.metab{gui.controls.Selected}.manual,'ph0')
+            if abs(MRSCont.processed.metab{gui.controls.Selected}.manual.ph0) > 360
+                MRSCont.processed.metab{gui.controls.Selected}.manual.ph0 = MRSCont.processed.metab{gui.controls.Selected}.manual.ph0 + sign(MRSCont.processed.metab{gui.controls.Selected}.manual.ph0)*(-1)*360;
+            end
+        end
+        
+        if isfield(MRSCont, 'processed_no_align')
+            if gui.controls.posPhase0Shift
+                MRSCont.processed_no_align.metab{gui.controls.Selected}=op_addphase(MRSCont.processed_no_align.metab{gui.controls.Selected} ,5);
+                if isfield(MRSCont.processed_no_align.metab{gui.controls.Selected}, 'manual') && isfield(MRSCont.processed_no_align.metab{gui.controls.Selected}.manual,'ph0')
+                    MRSCont.processed_no_align.metab{gui.controls.Selected}.manual.ph0 = MRSCont.processed_no_align.metab{gui.controls.Selected}.manual.ph0 + 5;
+                else
+                    MRSCont.processed_no_align.metab{gui.controls.Selected}.manual.ph0 =  5;
+                end
+            end
+            if gui.controls.negPhase0Shift
+                MRSCont.processed_no_align.metab{gui.controls.Selected}=op_addphase(MRSCont.processed_no_align.metab{gui.controls.Selected} ,-5);
+                if isfield(MRSCont.processed_no_align.metab{gui.controls.Selected}, 'manual') && isfield(MRSCont.processed_no_align.metab{gui.controls.Selected}.manual,'ph0')
+                    MRSCont.processed_no_align.metab{gui.controls.Selected}.manual.ph0 = MRSCont.processed_no_align.metab{gui.controls.Selected}.manual.ph0 - 5;
+                else
+                    MRSCont.processed_no_align.metab{gui.controls.Selected}.manual.ph0 =  -5;
+                end
+            end
+            if gui.controls.posPhase1Shift
+                MRSCont.processed_no_align.metab{gui.controls.Selected}=op_addphase(MRSCont.processed_no_align.metab{gui.controls.Selected} ,0,0.00001);
+                if isfield(MRSCont.processed_no_align.metab{gui.controls.Selected}, 'manual') && isfield(MRSCont.processed_no_align.metab{gui.controls.Selected}.manual,'ph1')
+                    MRSCont.processed_no_align.metab{gui.controls.Selected}.manual.ph1 = MRSCont.processed_no_align.metab{gui.controls.Selected}.manual.ph1 + 0.00001;
+                else
+                    MRSCont.processed_no_align.metab{gui.controls.Selected}.manual.ph1 =  0.00001;
+                end
+            end
+            if gui.controls.negPhase1Shift
+                MRSCont.processed_no_align.metab{gui.controls.Selected}=op_addphase(MRSCont.processed_no_align.metab{gui.controls.Selected} ,0,-0.00001);
+                if isfield(MRSCont.processed_no_align.metab{gui.controls.Selected}, 'manual') && isfield(MRSCont.processed_no_align.metab{gui.controls.Selected}.manual,'ph1')
+                    MRSCont.processed_no_align.metab{gui.controls.Selected}.manual.ph1 = MRSCont.processed_no_align.metab{gui.controls.Selected}.manual.ph1 -0.00001;
+                else
+                    MRSCont.processed_no_align.metab{gui.controls.Selected}.manual.ph1 =  -0.00001;
+                end
+            end
+            if gui.controls.flipPhase
+                MRSCont.processed_no_align.metab{gui.controls.Selected}=op_addphase(MRSCont.processed_no_align.metab{gui.controls.Selected} ,180);
+                if isfield(MRSCont.processed_no_align.metab{gui.controls.Selected}, 'manual') && isfield(MRSCont.processed_no_align.metab{gui.controls.Selected}.manual,'ph0')
+                    MRSCont.processed_no_align.metab{gui.controls.Selected}.manual.ph0 = MRSCont.processed_no_align.metab{gui.controls.Selected}.manual.ph0 + 180;
+                else
+                    MRSCont.processed_no_align.metab{gui.controls.Selected}.manual.ph0 =  180;
+                end
+            end
+            if gui.controls.posFreqShift
+                MRSCont.processed_no_align.metab{gui.controls.Selected}=op_freqshift(MRSCont.processed_no_align.metab{gui.controls.Selected} ,1);
+                if isfield(MRSCont.processed_no_align.metab{gui.controls.Selected}, 'manual') && isfield(MRSCont.processed_no_align.metab{gui.controls.Selected}.manual,'f')
+                    MRSCont.processed_no_align.metab{gui.controls.Selected}.manual.f = MRSCont.processed_no_align.metab{gui.controls.Selected}.manual.f + 1;
+                else
+                    MRSCont.processed_no_align.metab{gui.controls.Selected}.manual.f =  1;
+                end
+            end
+            if gui.controls.negFreqShift
+                MRSCont.processed_no_align.metab{gui.controls.Selected}=op_freqshift(MRSCont.processed_no_align.metab{gui.controls.Selected} ,-1);
+                if isfield(MRSCont.processed_no_align.metab{gui.controls.Selected}, 'manual') && isfield(MRSCont.processed_no_align.metab{gui.controls.Selected}.manual,'f')
+                    MRSCont.processed_no_align.metab{gui.controls.Selected}.manual.f = MRSCont.processed_no_align.metab{gui.controls.Selected}.manual.f - 1;
+                else
+                    MRSCont.processed_no_align.metab{gui.controls.Selected}.manual.f =  -1;
+                end
+            end
+            if isfield(MRSCont.processed_no_align.metab{gui.controls.Selected}, 'manual') && isfield(MRSCont.processed_no_align.metab{gui.controls.Selected}.manual,'ph0')
+                if abs(MRSCont.processed_no_align.metab{gui.controls.Selected}.manual.ph0) > 360
+                    MRSCont.processed_no_align.metab{gui.controls.Selected}.manual.ph0 = MRSCont.processed_no_align.metab{gui.controls.Selected}.manual.ph0 + sign(MRSCont.processed_no_align.metab{gui.controls.Selected}.manual.ph0)*(-1)*360;
+                end
+            end
+
+        end
+    end
+        
+%%% 3. VISUALIZATION PART OF THIS TAB %%%
+    temp_match = MRSCont.plot.processed.match;
+    MRSCont.plot.processed.match = 2;
+    if ~(isfield(MRSCont.flags,'isPRIAM') || isfield(MRSCont.flags,'isMRSI')) || ~(MRSCont.flags.isPRIAM || MRSCont.flags.isMRSI)
+        temp = osp_plotProcess(MRSCont, gui.controls.Selected,Selection,SubSpec,Exp); %Create figure
+    elseif isfield(MRSCont.flags,'isPRIAM')  && MRSCont.flags.isPRIAM
+        temp = osp_plotProcess(MRSCont, gui.controls.Selected,Selection,SubSpec,Exp,gui.controls.act_x); %Create figure
+    else
+        temp = osp_plotProcess(MRSCont, gui.controls.Selected,Selection,SubSpec,Exp,[gui.controls.act_x gui.controls.act_y gui.controls.act_z]); %Create figure
+    end
+    MRSCont.plot.processed.match = temp_match;
+    %Delete old content
+    delete(gui.layout.proAlgn.Children.Children)
+    %Fill window with new content        
+    set( flipud(temp.Children(2).Children), 'Parent', gui.layout.proAlgn.Children ); % Update aligned and averaged plot
+    set(  gui.layout.proAlgn.Children, 'XLim', temp.Children(2).XLim);
+    set(  gui.layout.proAlgn.Children, 'YLimMode', 'auto');
+    if isempty(gui.controls.YLimits)
+        gui.controls.YLimits = gui.layout.proAlgn.Children.YLim;
+    end
+
+    if gui.controls.resetAxis
+        set(  gui.layout.proAlgn.Children, 'YLimMode', 'auto');
+        gui.controls.YLimits = gui.layout.proAlgn.Children.YLim;
+    end
+
+    range = abs(gui.controls.YLimits(1)) + abs(gui.controls.YLimits(2));
+    if gui.controls.zoomOut
+        gui.controls.YLimits = [gui.controls.YLimits(1)+sign(gui.controls.YLimits(1))*range*0.05 gui.controls.YLimits(2)+sign(gui.controls.YLimits(2))*range*0.05];
+    end
+    if gui.controls.zoomIn
+        gui.controls.YLimits = [gui.controls.YLimits(1)-sign(gui.controls.YLimits(1))*range*0.05 gui.controls.YLimits(2)-sign(gui.controls.YLimits(2))*range*0.05];
+    end
+    if gui.controls.MoveUp
+        gui.controls.YLimits = [gui.controls.YLimits(1)+range*0.01 gui.controls.YLimits(2)+range*0.01];
+    end
+    if gui.controls.MoveDown
+        gui.controls.YLimits = [gui.controls.YLimits(1)-range*0.01 gui.controls.YLimits(2)-range*0.01];
+    end
+
+    % For debugging purposes
+    % if isfield(MRSCont.processed.metab{gui.controls.Selected},'manual')
+    %     MRSCont.processed.metab{gui.controls.Selected}.manual
+    % end
+    % gui.controls.YLimits
+    
+    set(gui.layout.proAlgn.Children, 'YLim', gui.controls.YLimits);
+    set(  gui.layout.proAlgn.Children, 'XTick', temp.Children(2).XTick);
+    close( temp );
+
+    set(gui.controls.b_save_proTab{gui.process.Selected},'Callback',{@osp_onPrint,gui});
+    setappdata(gui.figure,'MRSCont',MRSCont); % Write MRSCont into hidden container in gui class 
+end
\ No newline at end of file
diff --git a/GUI/osp_updateProWindow.m b/GUI/osp_updateProWindow.m
index 25499131..1977091a 100644
--- a/GUI/osp_updateProWindow.m
+++ b/GUI/osp_updateProWindow.m
@@ -127,5 +127,6 @@ function osp_updateProWindow(gui)
         end
         set(gui.upperBox.pro.Info{gui.process.Selected},'Title', ['Actual file: ' MRSCont.files{gui.controls.Selected}]);
         set(gui.controls.b_save_proTab{gui.process.Selected},'Callback',{@osp_onPrint,gui});
+        gui.controls.YLimits = [];
         setappdata(gui.figure,'MRSCont',MRSCont); % Write MRSCont into hidden container in gui class 
 end
\ No newline at end of file
diff --git a/libraries/FID-A/processingTools/op_add_analysis_provenance.m b/libraries/FID-A/processingTools/op_add_analysis_provenance.m
index 8ad9e646..306fbb67 100644
--- a/libraries/FID-A/processingTools/op_add_analysis_provenance.m
+++ b/libraries/FID-A/processingTools/op_add_analysis_provenance.m
@@ -42,7 +42,11 @@
         % Add shared fields
         fields.Time     = datestr(now,30);
         fields.Program  = 'Osprey';
-        fields.Version  = hdr_ext.ProcessingSoftwareVersion.Value;
+        try
+            fields.Version  = hdr_ext.ProcessingSoftwareVersion.Value;
+        catch
+            fields.Version  = hdr_ext.ProcessingSoftwareVersion;
+        end
     
         fields = orderfields(fields,{'Time','Program','Version','Method', 'Details'});
         field_names = {'Time','Program','Version','Method', 'Details'};
diff --git a/libraries/FID-A/processingTools/op_addextra.m b/libraries/FID-A/processingTools/op_addextra.m
new file mode 100644
index 00000000..f45ed872
--- /dev/null
+++ b/libraries/FID-A/processingTools/op_addextra.m
@@ -0,0 +1,59 @@
+% op_addextra.m
+% Jamie Near, McGill University 2014.
+% 
+% USAGE:
+% out=op_takesubspec(in,index);
+% 
+% DESCRIPTION:
+% Add the subspectra with indices corresponding to the 'index' input
+% array. 
+% 
+% INPUTS:
+% in     = input data in matlab structure format.
+% index  = vector indicating the indices of the subspectra you would like 
+%          to extract.
+%
+% OUTPUTS:
+% out    = Output dataset consisting of subspectra indices extracted from 
+%          the input.
+
+function out=op_addextra(in,in2,index);
+
+if in.dims.extras>0
+in.fids = squeeze(in.fids);        
+    if in.dims.extras==1
+        %SHOULD NEVER HAPPEN (Time dimension should always be dim=1)
+        error('ERROR:  dims.extras==1.  This should never happen!  Aborting!');
+    elseif in.dims.extras==2
+        in.fids(:,index,:,:,:) = in2.fids(:,1,:,:,:);
+    elseif in.dims.extras==3;
+        in.fids(:,:,index,:,:,:) =  in2.fids(:,:,1,:,:,:);
+    elseif in.dims.extras==4;
+        in.fids(:,:,:,index,:,:,:) =  in2.fids(:,:,:,1,:,:,:);
+    elseif in.dims.extras==5
+        in.fids(:,:,:,:,index,:,:,:) =  in2.fids(:,:,:,:,1,:,:,:);
+    end
+
+    %re-calculate Specs using fft
+    in.specs=fftshift(fft(in.fids,[],in.dims.t),in.dims.t);
+
+    %re-calculate the sz variable
+    sz=size(in.fids);
+
+    %add manual phasing entries
+    if isfield(in2, 'manual')
+        in.manual = in2.manual;
+    end
+
+    %FILLING IN DATA STRUCTURE
+    out=in;
+    out.sz=sz;
+    
+    
+    %FILLING IN THE FLAGS
+    out.flags=in.flags;
+    out.flags.writtentostruct=1;
+    out.flags.isISIS=0;
+else
+    out = in;
+end
diff --git a/plot/osp_plotProcess.m b/plot/osp_plotProcess.m
index 8c237bf4..13214bd7 100755
--- a/plot/osp_plotProcess.m
+++ b/plot/osp_plotProcess.m
@@ -916,7 +916,12 @@
             plot(ax_proc, NoAlignProcDataToPlot.ppm, real(NoAlignProcDataToPlot.specs(:,1)), 'Color',MRSCont.colormap.LightAccent, 'LineWidth', 1);       
         end
     else
-        plot(ax_proc, NoAlignProcDataToPlot.ppm, real(NoAlignProcDataToPlot.specs(:,1))/max(real(NoAlignProcDataToPlot.specs(NoAlignProcDataToPlot.ppm>ppmmin&NoAlignProcDataToPlot.ppm<ppmmax))), 'Color',MRSCont.colormap.LightAccent, 'LineWidth', 1);
+        if MRSCont.plot.processed.match == 0
+            plot(ax_proc, NoAlignProcDataToPlot.ppm, real(NoAlignProcDataToPlot.specs(:,1))/max(real(NoAlignProcDataToPlot.specs(NoAlignProcDataToPlot.ppm>ppmmin&NoAlignProcDataToPlot.ppm<ppmmax))), 'Color',MRSCont.colormap.LightAccent, 'LineWidth', 1);
+        else
+            range = abs(min(abs(NoAlignProcDataToPlot.specs(NoAlignProcDataToPlot.ppm>ppmmin&NoAlignProcDataToPlot.ppm<ppmmax)))) + abs(max(abs(NoAlignProcDataToPlot.specs(NoAlignProcDataToPlot.ppm>ppmmin&NoAlignProcDataToPlot.ppm<ppmmax))));
+            plot(ax_proc, NoAlignProcDataToPlot.ppm, real(NoAlignProcDataToPlot.specs(:,1))/range, 'Color',MRSCont.colormap.LightAccent, 'LineWidth', 1);
+        end      
     end
     text(ax_proc, ppmmin+1.5, 1, 'pre alignment', 'Color', colormap.LightAccent);
     text(ax_proc, ppmmin+1.5, 0.9, 'post alignment', 'Color', colormap.Foreground); 
@@ -975,34 +980,45 @@
         end        
     end
 else
-    plot(ax_proc, procDataToPlot.ppm, real(procDataToPlot.specs(:,1))/max(real(procDataToPlot.specs(procDataToPlot.ppm>ppmmin&procDataToPlot.ppm<ppmmax))), 'Color',MRSCont.colormap.Foreground, 'LineWidth', 1.5);
-    if strcmp(which_sub_spec,'diff2')
-        y = [-1.2, 1.2];
-    else if strcmp(which_sub_spec,'diff1')
-            if strcmp(which_spec,'metab')
-                y = [-2, 1.2];   
-            else
-                y = [-1.5, 1.2];   
-            end
-        else
-            if strcmp(which_spec,'metab')
-                y = [-0.2, 1.2];
+    if MRSCont.plot.processed.match == 0
+        plot(ax_proc, procDataToPlot.ppm, real(procDataToPlot.specs(:,1))/max(real(procDataToPlot.specs(procDataToPlot.ppm>ppmmin&procDataToPlot.ppm<ppmmax))), 'Color',MRSCont.colormap.Foreground, 'LineWidth', 1.5);
+    else
+        range = abs(min(abs(procDataToPlot.specs(procDataToPlot.ppm>ppmmin&procDataToPlot.ppm<ppmmax)))) + abs(max(abs(procDataToPlot.specs(procDataToPlot.ppm>ppmmin&procDataToPlot.ppm<ppmmax))));
+        plot(ax_proc, procDataToPlot.ppm, real(procDataToPlot.specs(:,1))/range, 'Color',MRSCont.colormap.Foreground, 'LineWidth', 1.5);
+    end
+        if strcmp(which_sub_spec,'diff2')
+            y = [-1.2, 1.2];
+        else if strcmp(which_sub_spec,'diff1')
+                if strcmp(which_spec,'metab')
+                    y = [-2, 1.2];   
+                else
+                    y = [-1.5, 1.2];   
+                end
             else
-                y = [-1.5, 1.2];   
+                if strcmp(which_spec,'metab')
+                    y = [-0.2, 1.2];
+                else
+                    y = [-1.5, 1.2];   
+                end
+    
             end
-
         end
-    end
+       
 end
 set(ax_proc, 'XDir', 'reverse', 'XLim', [ppmmin, ppmmax], 'YLim', y);
 if ~(strcmp(which_sub_spec,'w') || strcmp(which_sub_spec,'ref')|| strcmp(which_sub_spec,'MM_ref'))
-    plot(ax_proc, [2.008 2.008], [y(1)-y(2) y(2)],'LineStyle', ':', 'Color', colormap.Foreground,  'LineWidth', 0.5);
-    plot(ax_proc, [3.027 3.027], [y(1)-y(2) y(2)],'LineStyle', ':', 'Color', colormap.Foreground,  'LineWidth', 0.5);
+    % plot(ax_proc, [2.008 2.008], [y(1)-y(2) y(2)],'LineStyle', ':', 'Color', colormap.Foreground,  'LineWidth', 0.5);   
+    % plot(ax_proc, [3.027 3.027], [y(1)-y(2) y(2)],'LineStyle', ':', 'Color', colormap.Foreground,  'LineWidth', 0.5);
+    xline(ax_proc,2.008,'LineStyle', ':', 'Color', colormap.Foreground,  'LineWidth', 0.5)
+    xline(ax_proc,3.027,'LineStyle', ':', 'Color', colormap.Foreground,  'LineWidth', 0.5)
     if ~strcmp(which_sub_spec, 'mm')
-        plot(ax_proc, [3.200 3.200], [y(1)-y(2) y(2)],'LineStyle', ':', 'Color', colormap.Foreground,  'LineWidth', 0.5); 
+        % plot(ax_proc, [3.200 3.200], [y(1)-y(2) y(2)],'LineStyle', ':', 'Color', colormap.Foreground,  'LineWidth', 0.5); 
+        xline(ax_proc,3.200,'LineStyle', ':', 'Color', colormap.Foreground,  'LineWidth', 0.5)
     else
-        plot(ax_proc, [3.9 3.9], [y(1)-y(2) y(2)],'LineStyle', ':', 'Color', colormap.Foreground,  'LineWidth', 0.5);
+        % plot(ax_proc, [3.9 3.9], [y(1)-y(2) y(2)],'LineStyle', ':', 'Color', colormap.Foreground,  'LineWidth', 0.5);
+        xline(ax_proc,3.9,'LineStyle', ':', 'Color', colormap.Foreground,  'LineWidth', 0.5)
     end
+    yline(ax_proc,0,'LineStyle', ':', 'Color', colormap.LightAccent,  'LineWidth', 1)
 end
 hold(ax_proc, 'off');
 if MRSCont.plot.processed.match == 0
diff --git a/process/osp_saveJMRUI.m b/process/osp_saveJMRUI.m
index 434cca94..05b9ddcf 100644
--- a/process/osp_saveJMRUI.m
+++ b/process/osp_saveJMRUI.m
@@ -34,8 +34,6 @@
 %   HISTORY:
 %       2019-07-23: First version of the code.
 
-% Close any remaining open figures
-close all;
 
 % Set up saving location
 saveDestination = fullfile(MRSCont.outputFolder, 'jMRUIFiles');
diff --git a/process/osp_saveLCM.m b/process/osp_saveLCM.m
index 1c80791b..70bc91ee 100644
--- a/process/osp_saveLCM.m
+++ b/process/osp_saveLCM.m
@@ -31,10 +31,6 @@
 %       https://github.com/CIC-methods/FID-A
 %       Simpson et al., Magn Reson Med 77:23-33 (2017)
 
-
-% Close any remaining open figures
-close all;
-
 % Set up saving location
 saveDestination = fullfile(MRSCont.outputFolder, 'LCModelFiles');
 if ~exist(fullfile(saveDestination,'metabs'),'dir')
diff --git a/process/osp_saveNII.m b/process/osp_saveNII.m
index e89f715c..c7cdeed0 100644
--- a/process/osp_saveNII.m
+++ b/process/osp_saveNII.m
@@ -30,8 +30,6 @@
 %       https://github.com/CIC-methods/FID-A
 %       Simpson et al., Magn Reson Med 77:23-33 (2017)
 
-% Close any remaining open figures
-close all;
 
 % Set up saving location
 saveDestination = fullfile(MRSCont.outputFolder, 'NIfTIMRS');
diff --git a/process/osp_saveVendor.m b/process/osp_saveVendor.m
index a6e4be60..6304a43d 100644
--- a/process/osp_saveVendor.m
+++ b/process/osp_saveVendor.m
@@ -39,9 +39,6 @@
 %   HISTORY:
 %       2019-08-06: First version of the code.
 
-% Close any remaining open figures
-close all;
-
 % Set up saving location
 switch MRSCont.vendor
     case 'Philips'