diff --git a/client.cpp b/client.cpp
deleted file mode 100644
index 59cd4a685f..0000000000
--- a/client.cpp
+++ /dev/null
@@ -1,66 +0,0 @@
-#include <QtGui>
-#include <QtNetwork>
-
-#include "gui/mrview/sync/client.h"
-#include <iostream>
-
-
-namespace MR
-{
-  namespace GUI
-  {
-	namespace MRView
-	{
-		namespace Sync
-		{
-			/**
-			* Sends information to other processes. See interprocesssyncer.h for use
-			*/
-Client::Client()
-{
-    socket = new QLocalSocket();
-	SetServerName("mrview_syncer");
-}
-
-QString Client::GetServerName()
-{
-	return connectToServerName;
-}
-
-void Client::SetServerName(QString connectTo)
-{
-	connectToServerName=connectTo;
-	socket->abort();
-}
-
-bool Client::TryConnect()
-{
-	socket->abort();
-    socket->connectToServer(connectToServerName);
-	socket->waitForConnected();
-	QLocalSocket::LocalSocketState state = socket->state();
-	
-	return state == QLocalSocket::ConnectedState;
-}
-
-void Client::sendUpdate()
-{
-    socket->abort();
-    socket->connectToServer(connectToServerName);
-}
-
-void Client::SendData(QByteArray dat)
-{
-	//Prefix data with how long the message is
-	QByteArray prefixedData;
-	char a[4];
-	unsigned int size=(unsigned int)dat.size();
-	memcpy(a, &size, 4);
-	prefixedData.insert(0,a,4);
-	prefixedData.insert(4,dat,dat.size());
-	
-	//send
-	socket->write(prefixedData.data(),prefixedData.size());
-}
-
-}}}}
\ No newline at end of file
diff --git a/client.h b/client.h
deleted file mode 100644
index c45fabecba..0000000000
--- a/client.h
+++ /dev/null
@@ -1,49 +0,0 @@
-#ifndef __sync_client_h__
-#define __sync_client_h__
-
-#ifdef Q_WS_MAEMO_5
-#include <QWidget>
-#else
-#include <QDialog>
-#endif
-
-#include <qlocalsocket.h>
-
-class QDialogButtonBox;
-class QLabel;
-class QLineEdit;
-class QPushButton;
-class QLocalSocket;
-
-
-namespace MR
-{
-  namespace GUI
-  {
-	namespace MRView
-	{
-		namespace Sync
-		{
-
-class Client
-{
-
-public:
-    //Client(QWidget *parent = 0);
-	Client();
-	Client(const Client&) = delete;
-	bool TryConnect();
-	void SetServerName(QString connectTo);//sets the name of the server to connect to
-	QString GetServerName();//gets the name of the server this is connected to
-	void SendData(QByteArray dat);
-	
-private slots:
-    void sendUpdate();
-
-private:
-	QString connectToServerName;//the name of the server to connect to
-    QLocalSocket *socket;
-};	
-
-}}}}
-#endif
\ No newline at end of file
diff --git a/config_file_options.rst b/config_file_options.rst
deleted file mode 100644
index ac969a6f93..0000000000
--- a/config_file_options.rst
+++ /dev/null
@@ -1,486 +0,0 @@
-.. _config_file_options:
-
-##########################################
-List of MRtrix3 configuration file options
-##########################################
-
-*  **AmbientIntensity**
-    *default: 0.5*
-
-     The default intensity for the ambient light in OpenGL renders.
-
-*  **AnalyseLeftToRight**
-    *default: 0 (false)*
-
-     A boolean value to indicate whether images in Analyse format should be assumed to be in LAS orientation (default) or RAS (when this is option is turned on).
-
-*  **BValueScaling**
-    *default: 1 (true)*
-
-     Specifies whether the b-values should be scaled by the squared norm of the gradient vectors when loading a DW gradient scheme. This is commonly required to correctly interpret images acquired on scanners that nominally only allow a single b-value, as the common workaround is to scale the gradient vectors to modulate the actual b-value.
-
-*  **BZeroThreshold**
-    *default: 10.0*
-
-     Specifies the b-value threshold for determining those image volumes that correspond to b=0.
-
-*  **BackgroundColor**
-    *default: 1.0,1.0,1.0*
-
-     The default colour to use for the background in OpenGL panels, notably the SH viewer.
-
-*  **ConnectomeEdgeAssociatedAlphaMultiplier**
-    *default: 1.0*
-
-     The multiplicative factor to apply to the transparency of edges connected to one selected node.
-
-*  **ConnectomeEdgeAssociatedColour**
-    *default: 0.0,0.0,0.0*
-
-     The colour mixed in to edges connected to one currently selected node.
-
-*  **ConnectomeEdgeAssociatedColourFade**
-    *default: 0.5*
-
-     The fraction of the colour of an edge connected to one selected node determined by the fixed colour.
-
-*  **ConnectomeEdgeAssociatedSizeMultiplier**
-    *default: 1.0*
-
-     The multiplicative factor to apply to the size of edges connected to one selected node.
-
-*  **ConnectomeEdgeOtherAlphaMultiplier**
-    *default: 1.0*
-
-     The multiplicative factor to apply to the transparency of edges not connected to any selected node.
-
-*  **ConnectomeEdgeOtherColour**
-    *default: 0.0,0.0,0.0*
-
-     The colour mixed in to edges not connected to any currently selected node.
-
-*  **ConnectomeEdgeOtherColourFade**
-    *default: 0.75*
-
-     The fraction of the colour of an edge not connected to any selected node determined by the fixed colour.
-
-*  **ConnectomeEdgeOtherSizeMultiplier**
-    *default: 1.0*
-
-     The multiplicative factor to apply to the size of edges not connected to any selected node.
-
-*  **ConnectomeEdgeOtherVisibilityOverride**
-    *default: true*
-
-     Whether or not to force invisibility of edges not connected to any selected node.
-
-*  **ConnectomeEdgeSelectedAlphaMultiplier**
-    *default: 1.0*
-
-     The multiplicative factor to apply to the transparency of edges connected to two selected nodes.
-
-*  **ConnectomeEdgeSelectedColour**
-    *default: 0.9,0.9,1.0*
-
-     The colour used to highlight the edges connected to two currently selected nodes.
-
-*  **ConnectomeEdgeSelectedColourFade**
-    *default: 0.5*
-
-     The fraction of the colour of an edge connected to two selected nodes determined by the fixed selection highlight colour.
-
-*  **ConnectomeEdgeSelectedSizeMultiplier**
-    *default: 1.0*
-
-     The multiplicative factor to apply to the size of edges connected to two selected nodes.
-
-*  **ConnectomeEdgeSelectedVisibilityOverride**
-    *default: false*
-
-     Whether or not to force visibility of edges connected to two selected nodes.
-
-*  **ConnectomeNodeAssociatedAlphaMultiplier**
-    *default: 1.0*
-
-     The multiplicative factor to apply to the transparency of nodes associated with a selected node.
-
-*  **ConnectomeNodeAssociatedColour**
-    *default: 0.0,0.0,0.0*
-
-     The colour mixed in to those nodes associated with any selected node.
-
-*  **ConnectomeNodeAssociatedColourFade**
-    *default: 0.5*
-
-     The fraction of the colour of an associated node determined by the fixed associated highlight colour.
-
-*  **ConnectomeNodeAssociatedSizeMultiplier**
-    *default: 1.0*
-
-     The multiplicative factor to apply to the size of nodes associated with a selected node.
-
-*  **ConnectomeNodeOtherAlphaMultiplier**
-    *default: 1.0*
-
-     The multiplicative factor to apply to the transparency of nodes not currently selected nor associated with a selected node.
-
-*  **ConnectomeNodeOtherColour**
-    *default: 0.0,0.0,0.0*
-
-     The colour mixed in to those nodes currently not selected nor associated with any selected node.
-
-*  **ConnectomeNodeOtherColourFade**
-    *default: 0.75*
-
-     The fraction of the colour of an unselected, non-associated node determined by the fixed not-selected highlight colour.
-
-*  **ConnectomeNodeOtherSizeMultiplier**
-    *default: 1.0*
-
-     The multiplicative factor to apply to the size of nodes not currently selected nor associated with a selected node.
-
-*  **ConnectomeNodeOtherVisibilityOverride**
-    *default: false*
-
-     Whether or not nodes are forced to be invisible when not selected or associated with any selected node.
-
-*  **ConnectomeNodeSelectedAlphaMultiplier**
-    *default: 1.0*
-
-     The multiplicative factor to apply to the transparency of selected nodes.
-
-*  **ConnectomeNodeSelectedColour**
-    *default: 1.0,1.0,1.0*
-
-     The colour used to highlight those nodes currently selected.
-
-*  **ConnectomeNodeSelectedColourFade**
-    *default: 0.75*
-
-     The fraction of the colour of a selected node determined by the fixed selection highlight colour.
-
-*  **ConnectomeNodeSelectedSizeMultiplier**
-    *default: 1.0*
-
-     The multiplicative factor to apply to the size of selected nodes.
-
-*  **ConnectomeNodeSelectedVisibilityOverride**
-    *default: true*
-
-     Whether or not nodes are forced to be visible when selected.
-
-*  **DiffuseIntensity**
-    *default: 0.5*
-
-     The default intensity for the diffuse light in OpenGL renders.
-
-*  **FailOnWarn**
-    *default: 0 (false)*
-
-     A boolean value specifying whether MRtrix applications should abort as soon as any (otherwise non-fatal) warning is issued.
-
-*  **FontSize**
-    *default: 10*
-
-     The size (in points) of the font to be used in OpenGL viewports (mrview and shview).
-
-*  **HelpCommand**
-    *default: less*
-
-     The command to use to display each command's help page (leave empty to send directly to the terminal).
-
-*  **IconSize**
-    *default: 30*
-
-     The size of the icons in the main MRView toolbar.
-
-*  **ImageInterpolation**
-    *default: true*
-
-     Define default interplation setting for image and image overlay.
-
-*  **ImageInterpolation**
-    *default: true*
-
-     Interpolation switched on in the main image.
-
-*  **InitialToolBarPosition**
-    *default: top*
-
-     The starting position of the MRView toolbar. Valid values are: top, bottom, left, right.
-
-*  **LightPosition**
-    *default: 1.0,1.0,3.0*
-
-     The default position vector to use for the light in OpenGL renders.
-
-*  **MRViewColourBarHeight**
-    *default: 100*
-
-     The height of the colourbar in MRView, in pixels.
-
-*  **MRViewColourBarInset**
-    *default: 20*
-
-     How far away from the edge of the main window to place the colourbar in MRView, in pixels.
-
-*  **MRViewColourBarPosition**
-    *default: bottomright*
-
-     The position of the colourbar within the main window in MRView. Valid values are: bottomleft, bottomright, topleft, topright.
-
-*  **MRViewColourBarTextOffset**
-    *default: 10*
-
-     How far away from the colourbar to place the associated text, in pixels.
-
-*  **MRViewColourBarWidth**
-    *default: 20*
-
-     The width of the colourbar in MRView, in pixels.
-
-*  **MRViewColourHorizontalPadding**
-    *default: 100*
-
-     The width in pixels between horizontally adjacent colour bars.
-
-*  **MRViewDefaultTractGeomType**
-    *default: Pseudotubes*
-
-     The default geometry type used to render tractograms. Options are Pseudotubes, Lines or Points
-
-*  **MRViewDockFloating**
-    *default: 0 (false)*
-
-     Whether MRView tools should start docked in the main window, or floating (detached from the main window).
-
-*  **MRViewFocusModifierKey**
-    *default: meta (cmd on MacOSX)*
-
-     Modifier key to select focus mode in MRView. Valid choices include shift, alt, ctrl, meta (on MacOSX: shift, alt, ctrl, cmd).
-
-*  **MRViewImageBackgroundColour**
-    *default: 0,0,0 (black)*
-
-     The default image background colour in the main MRView window.
-
-*  **MRViewInitWindowSize**
-    *default: 512,512*
-
-     Initial window size of MRView in pixels.
-
-*  **MRViewMaxNumColourmapRows**
-    *default: 3*
-
-     The maximal number of rows used to layout a collection of rendered colourbars Note, that all tool-specific colourbars will form a single collection.
-
-*  **MRViewMoveModifierKey**
-    *default: shift*
-
-     Modifier key to select move mode in MRView. Valid choices include shift, alt, ctrl, meta (on MacOSX: shift, alt, ctrl, cmd).
-
-*  **MRViewOdfScale**
-    *default: 1.0*
-
-     The factor by which the ODF overlay is scaled.
-
-*  **MRViewRotateModifierKey**
-    *default: ctrl*
-
-     Modifier key to select rotate mode in MRView. Valid choices include shift, alt, ctrl, meta (on MacOSX: shift, alt, ctrl, cmd).
-
-*  **MRViewShowColourbar**
-    *default: true*
-
-     Colourbar shown in main image overlay.
-
-*  **MRViewShowComments**
-    *default: true*
-
-     Comments shown in main image overlay.
-
-*  **MRViewShowFocus**
-    *default: true*
-
-     Focus cross hair shown in main image.
-
-*  **MRViewShowOrientationLabel**
-    *default: true*
-
-     Anatomical orientation information shown in main image overlay.
-
-*  **MRViewShowVoxelInformation**
-    *default: true*
-
-     Voxel information shown in main image overlay.
-
-*  **MRViewToolFontSize**
-    *default: 2 points less than the standard system font*
-
-     The point size for the font to use in MRView tools.
-
-*  **MRViewToolsColourBarPosition**
-    *default: topright*
-
-     The position of all visible tool colourbars within the main window in MRView. Valid values are: bottomleft, bottomright, topleft, topright.
-
-*  **MRViewSyncFocus**
-    *default: false*
-
-     Whether to sync the focus in mrview between other mrview processes.
-	 
-*  **MSAA**
-    *default: 0 (false)*
-
-     How many samples to use for multi-sample anti-aliasing (to improve display quality).
-
-*  **NIfTIAllowBitwise**
-    *default: 0 (false)*
-
-     A boolean value to indicate whether bitwise storage of binary data is permitted (most 3rd party software packages don't support bitwise data). If false (the default), data will be stored using more widely supported unsigned 8-bit integers.
-
-*  **NIfTIAlwaysUseVer2**
-    *default: 0 (false)*
-
-     A boolean value to indicate whether NIfTI images should always be written in the new NIfTI-2 format. If false, images will be written in the older NIfTI-1 format by default, with the exception being files where the number of voxels along any axis exceeds the maximum permissible in that format (32767), in which case the output file will automatically switch to the NIfTI-2 format.
-
-*  **NIfTIAutoLoadJSON**
-    *default: 0 (false)*
-
-     A boolean value to indicate whether, when opening NIfTI images, any corresponding JSON file should be automatically loaded.
-
-*  **NIfTIAutoSaveJSON**
-    *default: 0 (false)*
-
-     A boolean value to indicate whether, when writing NIfTI images, a corresponding JSON file should be automatically created in order to save any header entries that cannot be stored in the NIfTI header.
-
-*  **NIfTIUseSform**
-    *default: 0 (false)*
-
-     A boolean value to control whether, in cases where both the sform and qform transformations are defined in an input NIfTI image, but those transformations differ, the sform transformation should be used in preference to the qform matrix (the default behaviour).
-
-*  **NeedOpenGLCoreProfile**
-    *default: 1 (true)*
-
-     Whether the creation of an OpenGL 3.3 context requires it to be a core profile (needed on newer versions of the ATI drivers on Linux, for instance).
-
-*  **NumberOfThreads**
-    *default: number of threads provided by hardware*
-
-     Set the default number of CPU threads to use for multi-threading.
-
-*  **NumberOfUndos**
-    *default: 16*
-
-     The number of undo operations permitted in the MRView ROI editor tool.
-
-*  **ObjectColor**
-    *default: 1,1,0 (yellow)*
-
-     The default colour to use for objects (i.e. SH glyphs) when not colouring by direction.
-
-*  **RegAnalyseDescent**
-    *default: 0 (false)*
-
-     Linear registration: write comma separated gradient descent parameters and gradients to stdout and verbose gradient descent output to stderr.
-
-*  **RegCoherenceLen**
-    *default: 3.0*
-
-     Linear registration: estimated spatial coherence length in voxels.
-
-*  **RegGdConvergenceDataSmooth**
-    *default: 0.8*
-
-     Linear registration: control point trajectory smoothing value used in convergence check parameter range: [0...1].
-
-*  **RegGdConvergenceMinIter**
-    *default: 10*
-
-     Linear registration: minimum number of iterations until convergence check is activated.
-
-*  **RegGdConvergenceSlopeSmooth**
-    *default: 0.1*
-
-     Linear registration: control point trajectory slope smoothing value used in convergence check parameter range: [0...1].
-
-*  **RegGdConvergenceThresh**
-    *default: 5e-3*
-
-     Linear registration: threshold for convergence check using the smoothed control point trajectories measured in fraction of a voxel.
-
-*  **RegGdWeightMatrix**
-    *default: 0.0003*
-
-     Linear registration: weight for optimisation of linear (3x3) matrix parameters.
-
-*  **RegGdWeightTranslation**
-    *default: 1*
-
-     Linear registration: weight for optimisation of translation parameters.
-
-*  **RegStopLen**
-    *default: 0.0001*
-
-     Linear registration: smallest gradient descent step measured in fraction of a voxel at which to stop registration.
-
-*  **ScriptTmpDir**
-    *default: `.`*
-
-     The location in which to generate the temporary directories to be used by MRtrix Python scripts. By default they will be generated in the working directory. Note that this setting does not influence the location in which piped images and other temporary files are created by MRtrix3; that is determined based on config file option TmpFileDir.
-
-*  **ScriptTmpPrefix**
-    *default: `<script>-tmp-`*
-
-     The prefix to use when generating a unique name for a Python script temporary directory. By default the name of the invoked script itself will be used, followed by `-tmp-` (six random characters are then appended to produce a unique name in cases where a script may be run multiple times in parallel).
-
-*  **SparseDataInitialSize**
-    *default: 16777216*
-
-     Initial buffer size for data in MRtrix sparse image format file (in bytes).
-
-*  **SpecularExponent**
-    *default: 5.0*
-
-     The default exponent for the specular light in OpenGL renders.
-
-*  **SpecularIntensity**
-    *default: 0.5*
-
-     The default intensity for the specular light in OpenGL renders.
-
-*  **TckgenEarlyExit**
-    *default: 0 (false)*
-
-     Specifies whether tckgen should be terminated prematurely in cases where it appears as though the target number of accepted streamlines is not going to be met.
-
-*  **TerminalColor**
-    *default: 1 (true)*
-
-     A boolean value to indicate whether colours should be used in the terminal.
-
-*  **TmpFileDir**
-    *default: `/tmp` (on Unix), `.` (on Windows)*
-
-     The prefix for temporary files (as used in pipelines). By default, these files get written to the current folder on Windows machines, which may cause performance issues, particularly when operating over distributed file systems. On Unix machines, the default is /tmp/, which is typically a RAM file system and should therefore be fast; but may cause issues on machines with little RAM capacity or where write-access to this location is not permitted. Note that this setting does not influence the location in which Python scripts construct their temporary directories; that is determined based on config file option ScriptTmpDir.
-
-*  **TmpFilePrefix**
-    *default: `mrtrix-tmp-`*
-
-     The prefix to use for the basename of temporary files. This will be used to generate a unique filename for the temporary file, by adding random characters to this prefix, followed by a suitable suffix (depending on file type). Note that this prefix can also be manipulated using the `MRTRIX_TMPFILE_PREFIX` environment variable, without editing the config file.
-
-*  **ToolbarStyle**
-    *default: 2*
-
-     The style of the main toolbar buttons in MRView. See Qt's documentation for Qt::ToolButtonStyle.
-
-*  **TrackWriterBufferSize**
-    *default: 16777216*
-
-     The size of the write-back buffer (in bytes) to use when writing track files. MRtrix will store the output tracks in a relatively large buffer to limit the number of write() calls, avoid associated issues such as file fragmentation.
-
-*  **VSync**
-    *default: 0 (false)*
-
-     Whether the screen update should synchronise with the monitor's vertical refresh (to avoid tearing artefacts).
-
diff --git a/configure b/configure
index c0cdb71838..5452394000 100755
--- a/configure
+++ b/configure
@@ -1108,7 +1108,6 @@ class Foo: public QObject {
 };
 '''
       log ('\nsource file "qt.h":\n---\n' + file + '---\n')
-      print(os.path.join (qt_dir.name, 'qt.h'))
 	  
       f=open (os.path.join (qt_dir.name, 'qt.h'), 'w')
       f.write (file)
@@ -1139,7 +1138,6 @@ int main() { Foo f; }
         file += 'QMAKE_MACOSX_DEPLOYMENT_TARGET = '+macosx_version + '\n'
 
       log ('\nproject file "qt.pro":\n---\n' + file + '---\n')
-      
       f=open (os.path.join (qt_dir.name, 'qt.pro'), 'w')
       f.write (file)
       f.close();
diff --git a/docs/reference/config_file_options.rst b/docs/reference/config_file_options.rst
index 727a1467a6..88b3412089 100644
--- a/docs/reference/config_file_options.rst
+++ b/docs/reference/config_file_options.rst
@@ -324,6 +324,11 @@ List of MRtrix3 configuration file options
 
      The position of all visible tool colourbars within the main window in MRView. Valid values are: bottomleft, bottomright, topleft, topright.
 
+*  **MRViewSyncFocus**
+    *default: false*
+
+     Whether to sync the focus in mrview between other mrview processes.	 
+
 *  **MSAA**
     *default: 0 (false)*
 
diff --git a/enums.h b/enums.h
deleted file mode 100644
index 306cd3dfc2..0000000000
--- a/enums.h
+++ /dev/null
@@ -1,30 +0,0 @@
-#ifndef __sync_enums_h__
-#define __sync_enums_h__
-
-namespace MR
-{
-  namespace GUI
-  {
-	namespace MRView
-	{
-		namespace Sync
-		{
-			/**
-			* Message keys used in interprocess syncer
-			*/
-			enum class MessageKey {
-				ConnectedID=1,
-				SyncData=2 //Data to be synced
-			};
-			/**
-			* The type of data being sent
-			*/
-			enum class DataKey {
-				WindowFocus=1
-			};
-
-		}
-	}
-  }
-}
-#endif
\ No newline at end of file
diff --git a/mrview.cpp b/mrview.cpp
deleted file mode 100644
index 246f1c8d73..0000000000
--- a/mrview.cpp
+++ /dev/null
@@ -1,111 +0,0 @@
-/*
- * Copyright (c) 2008-2018 the MRtrix3 contributors.
- *
- * This Source Code Form is subject to the terms of the Mozilla Public
- * License, v. 2.0. If a copy of the MPL was not distributed with this
- * file, you can obtain one at http://mozilla.org/MPL/2.0/
- *
- * MRtrix3 is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
- *
- * For more details, see http://www.mrtrix.org/
- */
-
-
-#include "gui/gui.h"
-#include "command.h"
-#include "progressbar.h"
-#include "memory.h"
-#include "gui/mrview/icons.h"
-#include "gui/mrview/window.h"
-#include "gui/mrview/mode/list.h"
-#include "gui/mrview/tool/list.h"
-#include "gui/mrview/sync/syncmanager.h"
-
-
-using namespace MR;
-using namespace App;
-
-void usage ()
-{
-  AUTHOR =
-    "J-Donald Tournier (jdtournier@gmail.com), "
-    "Dave Raffelt (david.raffelt@florey.edu.au), "
-    "Robert E. Smith (robert.smith@florey.edu.au), "
-    "Rami Tabbara (rami.tabbara@florey.edu.au), "
-    "Max Pietsch (maximilian.pietsch@kcl.ac.uk), "
-    "Thijs Dhollander (thijs.dhollander@gmail.com)";
-
-  SYNOPSIS = "The MRtrix image viewer.";
-
-  DESCRIPTION
-  + "Any images listed as arguments will be loaded and available through the "
-    "image menu, with the first listed displayed initially. Any subsequent "
-    "command-line options will be processed as if the corresponding action had "
-    "been performed through the GUI."
-
-  + "Note that because images loaded as arguments (i.e. simply listed on the "
-    "command-line) are opened before the GUI is shown, subsequent actions to be "
-    "performed via the various command-line options must appear after the last "
-    "argument. This is to avoid confusion about which option will apply to which "
-    "image. If you need fine control over this, please use the -load or -select_image "
-    "options. For example:"
-
-  + "$ mrview -load image1.mif -interpolation 0 -load image2.mif -interpolation 0"
-
-  + "or"
-
-  + "$ mrview image1.mif image2.mif -interpolation 0 -select_image 2 -interpolation 0";
-
-  REFERENCES
-    + "Tournier, J.-D.; Calamante, F. & Connelly, A. " // Internal
-    "MRtrix: Diffusion tractography in crossing fiber regions. "
-    "Int. J. Imaging Syst. Technol., 2012, 22, 53-66";
-
-  ARGUMENTS
-    + Argument ("image", "An image to be loaded.")
-    .optional()
-    .allow_multiple()
-    .type_image_in ();
-
-  GUI::MRView::Window::add_commandline_options (OPTIONS);
-
-#define TOOL(classname, name, description) \
-  MR::GUI::MRView::Tool::classname::add_commandline_options (OPTIONS);
-  {
-    using namespace MR::GUI::MRView::Tool;
-#include "gui/mrview/tool/list.h"
-  }
-
-  REQUIRES_AT_LEAST_ONE_ARGUMENT = false;
-
-}
-
-
-
-
-void run ()
-{
-  GUI::MRView::Window window;
-  MR::GUI::MRView::Sync::SyncManager sync;//sync allows syncing between mrview windows in different processes
-  sync.SetWindow(&window);
-  window.show();
-  try {
-    window.parse_arguments();
-  }
-  catch (Exception& e) {
-    e.display();
-    return;
-  }
-
-   
-    GUI::MRView::Sync::Client client;
-  
-  if (qApp->exec())
-    throw Exception ("error running Qt application");
-}
-
-
-
-
diff --git a/src/gui/mrview/sync/processlock.h b/src/gui/mrview/sync/processlock.h
index af3508f5e8..49b8fa2152 100644
--- a/src/gui/mrview/sync/processlock.h
+++ b/src/gui/mrview/sync/processlock.h
@@ -60,4 +60,4 @@ namespace MR
     }
   }
 }
-#endif // RUNGUARD_H
\ No newline at end of file
+#endif // __sync_processlock_h__
\ No newline at end of file
diff --git a/window.cpp b/window.cpp
deleted file mode 100644
index 033b1ed03f..0000000000
--- a/window.cpp
+++ /dev/null
@@ -1,2176 +0,0 @@
-/*
- * Copyright (c) 2008-2018 the MRtrix3 contributors.
- *
- * This Source Code Form is subject to the terms of the Mozilla Public
- * License, v. 2.0. If a copy of the MPL was not distributed with this
- * file, you can obtain one at http://mozilla.org/MPL/2.0/
- *
- * MRtrix3 is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
- *
- * For more details, see http://www.mrtrix.org/
- */
-
-
-#include "app.h"
-#include "timer.h"
-#include "file/config.h"
-#include "header.h"
-#include "algo/copy.h"
-#include "gui/opengl/gl.h"
-#include "gui/opengl/lighting.h"
-#include "gui/dialog/dialog.h"
-#include "gui/dialog/file.h"
-#include "gui/dialog/opengl.h"
-#include "gui/dialog/progress.h"
-#include "gui/dialog/image_properties.h"
-#include "gui/mrview/mode/base.h"
-#include "gui/mrview/mode/list.h"
-#include "gui/mrview/tool/base.h"
-#include "gui/mrview/tool/list.h"
-
-
-namespace MR
-{
-  namespace GUI
-  {
-    namespace MRView
-    {
-      using namespace App;
-/*
-#define MODE(classname, specifier, name, description) #specifier ", "
-#define MODE_OPTION(classname, specifier, name, description) MODE(classname, specifier, name, description)
-
-      const OptionGroup Window::options = OptionGroup ("General options")
-        + Option ("mode", "select initial display mode by its short ID. Valid mode IDs are: "
-#include "gui/mrview/mode/list.h"
-            )
-        + Argument ("name");
-#undef MODE
-#undef MODE_OPTION
-*/
-
-      Window* Window::main = nullptr;
-
-      namespace {
-
-        Qt::KeyboardModifiers get_modifier (const char* key, Qt::KeyboardModifiers default_key) {
-          std::string value = lowercase (MR::File::Config::get (key));
-          if (value.empty())
-            return default_key;
-
-          if (value == "shift") return Qt::ShiftModifier;
-          if (value == "alt") return Qt::AltModifier;
-#ifdef MRTRIX_MACOSX
-          if (value == "ctrl") return Qt::MetaModifier;
-          if (value == "cmd") return Qt::ControlModifier;
-#else
-          if (value == "ctrl") return Qt::ControlModifier;
-          if (value == "meta" || value == "win") return Qt::MetaModifier;
-#endif
-
-          throw Exception ("no such modifier \"" + value + "\" (parsed from config file)");
-          return Qt::NoModifier;
-        }
-      }
-
-
-
-
-
-
-      std::string get_modifier (Qt::KeyboardModifiers key) {
-        switch (key) {
-          case Qt::ShiftModifier: return "Shift";
-          case Qt::AltModifier: return "Alt";
-#ifdef MRTRIX_MACOSX
-          case Qt::ControlModifier: return "Cmd";
-          case Qt::MetaModifier: return "Ctrl";
-#else
-          case Qt::ControlModifier: return "Ctrl";
-          case Qt::MetaModifier: return "Win";
-#endif
-          default: assert (0);
-        }
-        return "Invalid";
-      }
-
-
-      // GLArea definitions:
-
-      Window::GLArea::GLArea (Window& parent) :
-        GL::Area (&parent) {
-          setCursor (Cursor::crosshair);
-          setMouseTracking (true);
-          setAcceptDrops (true);
-          setMinimumSize (256, 256);
-          setFocusPolicy (Qt::StrongFocus);
-          grabGesture (Qt::PinchGesture);
-          grabGesture (Qt::PanGesture);
-          QFont font_ = font();
-          //CONF option: FontSize
-          //CONF The size (in points) of the font to be used in OpenGL viewports (mrview and shview).
-          //CONF default: 10
-          font_.setPointSize (MR::File::Config::get_int ("FontSize", 10));
-          setFont (font_);
-          QSizePolicy policy (QSizePolicy::MinimumExpanding, QSizePolicy::MinimumExpanding);
-          policy.setHorizontalStretch (255);
-          policy.setVerticalStretch (255);
-          setSizePolicy (policy);
-        }
-
-      QSize Window::GLArea::sizeHint () const {
-        //CONF option: MRViewInitWindowSize
-        //CONF Initial window size of MRView in pixels.
-        //CONF default: 512,512
-        std::string init_size_string = lowercase (MR::File::Config::get ("MRViewInitWindowSize"));
-        vector<int> init_window_size;
-        if (init_size_string.length())
-          init_window_size = parse_ints(init_size_string);
-        if (init_window_size.size() == 2)
-          return QSize (init_window_size[0], init_window_size[1]);
-        else
-          return QSize (512, 512);
-      }
-      void Window::GLArea::dragEnterEvent (QDragEnterEvent* event) {
-        event->acceptProposedAction();
-      }
-      void Window::GLArea::dragMoveEvent (QDragMoveEvent* event) {
-        event->acceptProposedAction();
-      }
-      void Window::GLArea::dragLeaveEvent (QDragLeaveEvent* event) {
-        event->accept();
-      }
-      void Window::GLArea::dropEvent (QDropEvent* event) {
-        const QMimeData* mimeData = event->mimeData();
-        if (mimeData->hasUrls()) {
-          vector<std::unique_ptr<MR::Header>> list;
-          QList<QUrl> urlList = mimeData->urls();
-          for (int i = 0; i < urlList.size() && i < 32; ++i) {
-            try {
-              list.push_back (make_unique<MR::Header> (MR::Header::open (urlList.at (i).path().toUtf8().constData())));
-            }
-            catch (Exception& e) {
-              e.display();
-            }
-          }
-          if (list.size())
-            main->add_images (list);
-        }
-      }
-
-      void Window::GLArea::initializeGL () {
-        main->initGL();
-      }
-      void Window::GLArea::paintGL () {
-        main->paintGL();
-      }
-      void Window::GLArea::mousePressEvent (QMouseEvent* event) {
-        main->mousePressEventGL (event);
-      }
-      void Window::GLArea::mouseMoveEvent (QMouseEvent* event) {
-        main->mouseMoveEventGL (event);
-      }
-      void Window::GLArea::mouseReleaseEvent (QMouseEvent* event) {
-        main->mouseReleaseEventGL (event);
-      }
-      void Window::GLArea::wheelEvent (QWheelEvent* event) {
-        main->wheelEventGL (event);
-      }
-
-      bool Window::GLArea::event (QEvent* event) {
-        if (event->type() == QEvent::Gesture)
-          return main->gestureEventGL (static_cast<QGestureEvent*>(event));
-        return QWidget::event(event);
-      }
-
-
-
-
-
-
-
-
-
-
-      //CONF option: MRViewFocusModifierKey
-      //CONF default: meta (cmd on MacOSX)
-      //CONF Modifier key to select focus mode in MRView. Valid
-      //CONF choices include shift, alt, ctrl, meta (on MacOSX: shift, alt,
-      //CONF ctrl, cmd).
-
-      //CONF option: MRViewMoveModifierKey
-      //CONF default: shift
-      //CONF Modifier key to select move mode in MRView. Valid
-      //CONF choices include shift, alt, ctrl, meta (on MacOSX: shift, alt,
-      //CONF ctrl, cmd).
-
-      //CONF option: MRViewRotateModifierKey
-      //CONF default: ctrl
-      //CONF Modifier key to select rotate mode in MRView. Valid
-      //CONF choices include shift, alt, ctrl, meta (on MacOSX: shift, alt,
-      //CONF ctrl, cmd).
-
-
-      // Main Window class:
-
-      Window::Window() :
-        glarea (new GLArea (*this)),
-        mode (nullptr),
-        font (glarea->font()),
-#ifdef MRTRIX_MACOSX
-        FocusModifier (get_modifier ("MRViewFocusModifierKey", Qt::AltModifier)),
-#else
-        FocusModifier (get_modifier ("MRViewFocusModifierKey", Qt::MetaModifier)),
-#endif
-        MoveModifier (get_modifier ("MRViewMoveModifierKey", Qt::ShiftModifier)),
-        RotateModifier (get_modifier ("MRViewRotateModifierKey", Qt::ControlModifier)),
-        mouse_action (NoAction),
-        focal_point { NAN, NAN, NAN },
-        camera_target { NAN, NAN, NAN },
-        orient (),
-        field_of_view (100.0),
-        anatomical_plane (2),
-        colourbar_position (ColourMap::Position::BottomRight),
-        tools_colourbar_position (ColourMap::Position::TopRight),
-        snap_to_image_axes_and_voxel (true),
-        tool_has_focus (nullptr),
-        best_FPS (NAN),
-        show_FPS (false),
-        current_option (0) {
-          main = this;
-          GUI::App::set_main_window (this);
-          GUI::Dialog::init();
-
-          setDockOptions (AllowTabbedDocks | VerticalTabs);
-          setDocumentMode (true);
-
-          //CONF option: IconSize
-          //CONF default: 30
-          //CONF The size of the icons in the main MRView toolbar.
-          setWindowTitle (tr ("MRView"));
-          setWindowIcon (QPixmap (":/mrtrix.png"));
-          {
-            int iconsize = MR::File::Config::get_int ("IconSize", 30);
-            setIconSize (QSize (iconsize, iconsize));
-          }
-          setCentralWidget (glarea);
-          QToolBar* toolbar;
-          QAction* action;
-          QMenu* menu;
-          QToolButton* button;
-
-          setTabPosition (Qt::AllDockWidgetAreas, QTabWidget::East);
-
-          // Main toolbar:
-
-          //CONF option: InitialToolBarPosition
-          //CONF default: top
-          //CONF The starting position of the MRView toolbar. Valid values are:
-          //CONF top, bottom, left, right.
-          Qt::ToolBarArea toolbar_position = Qt::TopToolBarArea;
-          {
-            std::string toolbar_pos_spec = lowercase (MR::File::Config::get ("InitialToolBarPosition"));
-            if (toolbar_pos_spec.size()) {
-              if (toolbar_pos_spec == "bottom") toolbar_position = Qt::BottomToolBarArea;
-              else if (toolbar_pos_spec == "left") toolbar_position = Qt::LeftToolBarArea;
-              else if (toolbar_pos_spec == "right") toolbar_position = Qt::RightToolBarArea;
-              else if (toolbar_pos_spec != "top")
-                WARN ("invalid value for configuration entry \"InitialToolBarPosition\"");
-            }
-          }
-
-          //CONF option: ToolbarStyle
-          //CONF default: 2
-          //CONF The style of the main toolbar buttons in MRView. See Qt's
-          //CONF documentation for Qt::ToolButtonStyle.
-          Qt::ToolButtonStyle button_style = static_cast<Qt::ToolButtonStyle> (MR::File::Config::get_int ("ToolbarStyle", 2));
-
-          toolbar = new QToolBar ("Main toolbar", this);
-          addToolBar (toolbar_position, toolbar);
-          action = toolbar->toggleViewAction ();
-          action->setShortcut (tr ("Ctrl+M"));
-          addAction (action);
-
-
-          // File menu:
-          menu = new QMenu (tr ("File menu"), this);
-
-          action = menu->addAction (tr ("Open..."), this, SLOT (image_open_slot()));
-          action->setShortcut (tr ("Ctrl+O"));
-          addAction (action);
-
-          save_action = menu->addAction (tr ("Save..."), this, SLOT (image_save_slot()));
-          save_action->setShortcut (tr ("Ctrl+S"));
-          addAction (save_action);
-
-          close_action = menu->addAction (tr ("Close"), this, SLOT (image_close_slot()));
-          close_action->setShortcut (tr ("Ctrl+W"));
-          addAction (close_action);
-
-          menu->addSeparator();
-
-          action = menu->addAction (tr ("DICOM import..."), this, SLOT (image_import_DICOM_slot()));
-          action->setShortcut (tr ("Ctrl+D"));
-          addAction (action);
-
-          menu->addSeparator();
-
-          action = menu->addAction (tr ("Quit"), this, SLOT (close()));
-          action->setShortcut (tr ("Ctrl+Q"));
-          addAction (action);
-
-
-          button = new QToolButton (this);
-          button->setText ("File");
-          button->setToolButtonStyle (button_style);
-          button->setToolTip (tr ("Load and save images"));
-          button->setIcon (QIcon (":/file.svg"));
-          button->setPopupMode (QToolButton::InstantPopup);
-          button->setMenu (menu);
-          toolbar->addWidget (button);
-
-
-          // Image menu:
-          image_menu = new QMenu (tr ("Image menu"), this);
-
-          image_group = new QActionGroup (this);
-          image_group->setExclusive (true);
-          connect (image_group, SIGNAL (triggered (QAction*)), this, SLOT (image_select_slot (QAction*)));
-
-          properties_action = image_menu->addAction (tr ("Properties..."), this, SLOT (image_properties_slot()));
-          properties_action->setToolTip (tr ("Display the properties of the current image\n\nShortcut: Ctrl+P"));
-          addAction (properties_action);
-
-          image_menu->addSeparator();
-
-          next_slice_action = image_menu->addAction (tr ("Next slice"), this, SLOT (slice_next_slot()));
-          next_slice_action->setShortcut (tr ("Up"));
-          addAction (next_slice_action);
-
-          prev_slice_action = image_menu->addAction (tr ("Previous slice"), this, SLOT (slice_previous_slot()));
-          prev_slice_action->setShortcut (tr ("Down"));
-          addAction (prev_slice_action);
-
-          next_image_volume_action = image_menu->addAction (tr ("Next volume"), this, SLOT (image_next_volume_slot()));
-          next_image_volume_action->setShortcut (tr ("Right"));
-          addAction (next_image_volume_action);
-
-          prev_image_volume_action = image_menu->addAction (tr ("Previous volume"), this, SLOT (image_previous_volume_slot()));
-          prev_image_volume_action->setShortcut (tr ("Left"));
-          addAction (prev_image_volume_action);
-
-          goto_image_volume_action = image_menu->addAction (tr ("Go to volume..."), this, SLOT (image_goto_volume_slot()));
-          goto_image_volume_action->setShortcut (tr ("g"));
-          addAction (goto_image_volume_action);
-
-          next_image_volume_group_action = image_menu->addAction (tr ("Next volume group"), this, SLOT (image_next_volume_group_slot()));
-          next_image_volume_group_action->setShortcut (tr ("Shift+Right"));
-          addAction (next_image_volume_group_action);
-
-          prev_image_volume_group_action = image_menu->addAction (tr("Previous volume group"), this, SLOT (image_previous_volume_group_slot()));
-          prev_image_volume_group_action->setShortcut (tr ("Shift+Left"));
-          addAction (prev_image_volume_group_action);
-
-          goto_image_volume_group_action = image_menu->addAction (tr ("Go to volume group..."), this, SLOT (image_goto_volume_group_slot()));
-          goto_image_volume_group_action->setShortcut (tr ("Shift+g"));
-          addAction (goto_image_volume_group_action);
-
-          image_menu->addSeparator();
-
-          next_image_action = image_menu->addAction (tr ("Next image"), this, SLOT (image_next_slot()));
-          next_image_action->setShortcut (tr ("PgDown"));
-          addAction (next_image_action);
-
-          prev_image_action = image_menu->addAction (tr ("Previous image"), this, SLOT (image_previous_slot()));
-          prev_image_action->setShortcut (tr ("PgUp"));
-          addAction (prev_image_action);
-
-          image_list_area = image_menu->addSeparator();
-
-          button = new QToolButton (this);
-          button->setText ("Image");
-          button->setToolButtonStyle (button_style);
-          button->setToolTip (tr ("Navigate the image"));
-          button->setIcon (QIcon (":/image.svg"));
-          button->setPopupMode (QToolButton::InstantPopup);
-          button->setMenu (image_menu);
-          toolbar->addWidget (button);
-
-
-          // Colourmap menu:
-          colourmap_button = new ColourMapButton (this, *this, true, true, false);
-          colourmap_button->setText ("Colourmap");
-          colourmap_button->setToolButtonStyle (button_style);
-          colourmap_button->setToolTip (tr ("Change the colourmap"));
-          colourmap_button->setPopupMode (QToolButton::InstantPopup);
-
-          QMenu* colourmap_menu = colourmap_button->menu();
-
-          invert_scale_action = colourmap_menu->addAction (tr ("Invert"), this, SLOT (invert_scaling_slot()));
-          invert_scale_action->setCheckable (true);
-          invert_scale_action->setShortcut (tr("U"));
-          addAction (invert_scale_action);
-
-          colourmap_menu->addSeparator();
-
-          reset_windowing_action = colourmap_menu->addAction (tr ("Reset brightness/contrast"), this, SLOT (image_reset_slot()));
-          reset_windowing_action->setShortcut (tr ("Esc"));
-          addAction (reset_windowing_action);
-
-          //CONF option: ImageInterpolation
-          //CONF default: true
-          //CONF Interpolation switched on in the main image.
-          image_interpolate_action = colourmap_menu->addAction (tr ("Interpolate"), this, SLOT (image_interpolate_slot()));
-          image_interpolate_action->setShortcut (tr ("I"));
-          image_interpolate_action->setCheckable (true);
-          image_interpolate_action->setChecked (File::Config::get_bool("ImageInterpolation", true));
-          addAction (image_interpolate_action);
-
-          toolbar->addWidget (colourmap_button);
-
-
-          // Mode menu:
-          mode_group = new QActionGroup (this);
-          mode_group->setExclusive (true);
-          connect (mode_group, SIGNAL (triggered (QAction*)), this, SLOT (select_mode_slot (QAction*)));
-
-          menu = new QMenu ("Display mode", this);
-#define MODE(classname, specifier, name, description) \
-          menu->addAction (new Mode::Action<Mode::classname> (mode_group, #name, #description, n++));
-#define MODE_OPTION(classname, specifier, name, description) MODE(classname, specifier, name, description)
-          {
-            size_t n = 1;
-#include "gui/mrview/mode/list.h"
-          }
-#undef MODE
-#undef MODE_OPTION
-          mode_group->actions()[0]->setChecked (true);
-          for (int n = 0; n < mode_group->actions().size(); ++n)
-            addAction (mode_group->actions()[n]);
-
-
-          menu->addSeparator();
-
-          plane_group = new QActionGroup (this);
-          plane_group->setExclusive (true);
-          connect (plane_group, SIGNAL (triggered (QAction*)), this, SLOT (select_plane_slot (QAction*)));
-
-          axial_action = menu->addAction (tr ("Axial"));
-          axial_action->setShortcut (tr ("A"));
-          axial_action->setCheckable (true);
-          plane_group->addAction (axial_action);
-          addAction (axial_action);
-
-          sagittal_action = menu->addAction (tr ("Sagittal"));
-          sagittal_action->setShortcut (tr ("S"));
-          sagittal_action->setCheckable (true);
-          plane_group->addAction (sagittal_action);
-          addAction (sagittal_action);
-
-          coronal_action = menu->addAction (tr ("Coronal"));
-          coronal_action->setShortcut (tr ("C"));
-          coronal_action->setCheckable (true);
-          plane_group->addAction (coronal_action);
-          addAction (coronal_action);
-
-          menu->addSeparator();
-
-          action = menu->addAction (tr ("Zoom in"), this, SLOT (zoom_in_slot()));
-          action->setShortcut (tr("Ctrl++"));
-          addAction (action);
-
-          action = menu->addAction (tr ("Zoom out"), this, SLOT (zoom_out_slot()));
-          action->setShortcut (tr("Ctrl+-"));
-          addAction (action);
-
-          menu->addSeparator();
-
-          action = menu->addAction (tr ("Toggle all annotations"), this, SLOT (toggle_annotations_slot()));
-          action->setShortcut (tr("Space"));
-          addAction (action);
-
-          //CONF option: MRViewShowFocus
-          //CONF default: true
-          //CONF Focus cross hair shown in main image.
-          show_crosshairs_action = menu->addAction (tr ("Show focus"), glarea, SLOT (update()));
-          show_crosshairs_action->setShortcut (tr("F"));
-          show_crosshairs_action->setCheckable (true);
-          show_crosshairs_action->setChecked (File::Config::get_bool("MRViewShowFocus",true));
-          addAction (show_crosshairs_action);
-
-          //CONF option: MRViewShowComments
-          //CONF default: true
-          //CONF Comments shown in main image overlay.
-          show_comments_action = menu->addAction (tr ("Show comments"), glarea, SLOT (update()));
-          show_comments_action->setToolTip (tr ("Show/hide image comments\n\nShortcut: H"));
-          show_comments_action->setShortcut (tr("H"));
-          show_comments_action->setCheckable (true);
-          show_comments_action->setChecked (File::Config::get_bool("MRViewShowComments",true));
-          addAction (show_comments_action);
-
-          //CONF option: MRViewShowVoxelInformation
-          //CONF default: true
-          //CONF Voxel information shown in main image overlay.
-          show_voxel_info_action = menu->addAction (tr ("Show voxel information"), glarea, SLOT (update()));
-          show_voxel_info_action->setShortcut (tr("V"));
-          show_voxel_info_action->setCheckable (true);
-          show_voxel_info_action->setChecked (File::Config::get_bool("MRViewShowVoxelInformation",true));
-          addAction (show_voxel_info_action);
-
-          //CONF option: MRViewShowOrientationLabel
-          //CONF default: true
-          //CONF Anatomical orientation information shown in main image overlay.
-          show_orientation_labels_action = menu->addAction (tr ("Show orientation labels"), glarea, SLOT (update()));
-          show_orientation_labels_action->setShortcut (tr("O"));
-          show_orientation_labels_action->setCheckable (true);
-          show_orientation_labels_action->setChecked (File::Config::get_bool("MRViewShowOrientationLabel",true));
-          addAction (show_orientation_labels_action);
-
-          //CONF option: MRViewShowColourbar
-          //CONF default: true
-          //CONF Colourbar shown in main image overlay.
-          show_colourbar_action = menu->addAction (tr ("Show colour bar"), glarea, SLOT (update()));
-          show_colourbar_action->setShortcut (tr("B"));
-          show_colourbar_action->setCheckable (true);
-          show_colourbar_action->setChecked (File::Config::get_bool("MRViewShowColourbar",true));
-          addAction (show_colourbar_action);
-
-          menu->addSeparator();
-
-          action = menu->addAction (tr ("Background colour..."), this, SLOT (background_colour_slot()));
-          action->setCheckable (false);
-          addAction (action);
-
-          image_hide_action = menu->addAction (tr ("Hide main image"), this, SLOT (hide_image_slot()));
-          image_hide_action->setShortcut (tr ("M"));
-          image_hide_action->setCheckable (true);
-          image_hide_action->setChecked (false);
-          addAction (image_hide_action);
-
-		  menu->addSeparator();
-		  //CONF option: MRViewSyncFocus
-          //CONF default: false
-          //CONF Whether to sync the focus in mrview between other mrview processes.
-          sync_focus_action = menu->addAction (tr ("Sync focus with other windows"), this, SLOT (sync_slot()));
-          sync_focus_action->setCheckable (true);
-          sync_focus_action->setChecked (File::Config::get_bool("MRViewSyncFocus",false));
-          addAction (sync_focus_action);
-          menu->addSeparator();
-
-          full_screen_action = menu->addAction (tr ("Full screen"), this, SLOT (full_screen_slot()));
-          full_screen_action->setShortcut (tr ("F11"));
-          full_screen_action->setCheckable (true);
-          full_screen_action->setChecked (false);
-          addAction (full_screen_action);
-
-          action = menu->addAction (tr ("Reset view"), this, SLOT(reset_view_slot()));
-          action->setShortcut (tr ("R"));
-          addAction (action);
-
-          button = new QToolButton (this);
-          button->setText ("View");
-          button->setToolButtonStyle (button_style);
-          button->setToolTip (tr ("View modes and options"));
-          button->setIcon (QIcon (":/view.svg"));
-          button->setMenu (menu);
-          button->setPopupMode (QToolButton::InstantPopup);
-          toolbar->addWidget (button);
-
-          toolbar->addSeparator();
-
-
-          // Mouse mode actions:
-          mode_action_group = new QActionGroup (this);
-          mode_action_group->setExclusive (true);
-          connect (mode_action_group, SIGNAL (triggered (QAction*)), this, SLOT (select_mouse_mode_slot (QAction*)));
-
-          std::string modifier;
-          action = toolbar->addAction (QIcon (":/select_contrast.svg"), tr ("Change focus / contrast"));
-          action->setToolTip (tr ((
-                  "Left-click: set focus\n"
-                  "Right-click: change brightness/constrast\n\n"
-                  "Shortcut: 1\n\n"
-                  "Hold down " + get_modifier (FocusModifier) + " key to use this mode\n"
-                  "regardless of currently selected mode").c_str()));
-          action->setShortcut (tr("1"));
-          action->setCheckable (true);
-          action->setChecked (true);
-          mode_action_group->addAction (action);
-
-          action = toolbar->addAction (QIcon (":/move.svg"), tr ("Move viewport"));
-          action->setToolTip (tr ((
-                  "Left-click: move in-plane\n"
-                  "Right-click: move through-plane\n\n"
-                  "Shortcut: 2\n\n"
-                  "Hold down " + get_modifier (MoveModifier) + " key to use this mode\n"
-                  "regardless of currently selected mode").c_str()));
-          action->setShortcut (tr("2"));
-          action->setCheckable (true);
-          mode_action_group->addAction (action);
-
-          action = toolbar->addAction (QIcon (":/rotate.svg"), tr ("Move camera"));
-          action->setToolTip (tr ((
-                  "Left-click: move camera in-plane\n"
-                  "Right-click: rotate camera about view axis\n\n"
-                  "Shortcut: 3\n\n"
-                  "Hold down " + get_modifier (RotateModifier) + " key to use this mode\n"
-                  "regardless of currently selected mode").c_str()));
-          action->setShortcut (tr("3"));
-          action->setCheckable (true);
-          mode_action_group->addAction (action);
-
-          for (int n = 0; n < mode_action_group->actions().size(); ++n)
-            addAction (mode_action_group->actions()[n]);
-
-          toolbar->addSeparator();
-
-          snap_to_image_action = toolbar->addAction (QIcon (":/lock.svg"),
-              tr ("Snap to image"), this, SLOT (snap_to_image_slot()));
-          snap_to_image_action->setToolTip (tr (
-                "Snap focus and view orientation to\n"
-                "image voxel grid and axes respectively\n\n"
-                "Shortcut: L"));
-          snap_to_image_action->setShortcut (tr("L"));
-          snap_to_image_action->setCheckable (true);
-          snap_to_image_action->setChecked (snap_to_image_axes_and_voxel);
-          addAction (snap_to_image_action);
-
-          toolbar->addSeparator();
-
-
-          // Dynamic spacer:
-          QWidget* spacer = new QWidget();
-          spacer->setSizePolicy(QSizePolicy::Expanding, QSizePolicy::Preferred);
-          toolbar->addWidget (spacer);
-
-
-          // Tool menu:
-          tool_group = new QActionGroup (this);
-          tool_group->setExclusive (false);
-          connect (tool_group, SIGNAL (triggered (QAction*)), this, SLOT (select_tool_slot (QAction*)));
-
-          menu = new QMenu (tr ("Tools"), this);
-#undef TOOL
-#define TOOL(classname, name, description) \
-          menu->addAction (new Action<Tool::classname> (tool_group, #name, #description, n++));
-          {
-            using namespace Tool;
-            size_t n = 1;
-#include "gui/mrview/tool/list.h"
-          }
-          for (int n = 0; n < tool_group->actions().size(); ++n)
-            addAction (tool_group->actions()[n]);
-
-          button = new QToolButton (this);
-          button->setText ("Tool");
-          button->setToolButtonStyle (button_style);
-          button->setToolTip (tr ("Open different tools"));
-          button->setIcon (QIcon (":/tools.svg"));
-          button->setMenu (menu);
-          button->setPopupMode (QToolButton::InstantPopup);
-          toolbar->addWidget (button);
-
-          toolbar->addSeparator();
-
-
-          // Information menu:
-
-          menu = new QMenu (tr ("Info"), this);
-
-          menu->addAction (tr ("About MRView"), this, SLOT (about_slot()));
-          menu->addAction (tr ("About Qt"), this, SLOT (aboutQt_slot()));
-          menu->addAction (tr ("OpenGL information"), this, SLOT (OpenGL_slot()));
-
-
-          button = new QToolButton (this);
-          button->setToolButtonStyle (button_style);
-          button->setToolTip (tr ("Information"));
-          button->setIcon (QIcon (":/info.svg"));
-          button->setPopupMode (QToolButton::InstantPopup);
-          button->setMenu (menu);
-          toolbar->addWidget (button);
-
-
-
-          lighting_ = new GL::Lighting (this);
-          connect (lighting_, SIGNAL (changed()), glarea, SLOT (update()));
-
-          set_image_menu ();
-
-          //CONF option: MRViewColourBarPosition
-          //CONF default: bottomright
-          //CONF The position of the colourbar within the main window in MRView.
-          //CONF Valid values are: bottomleft, bottomright, topleft, topright.
-          std::string cbar_pos = lowercase (MR::File::Config::get ("MRViewColourBarPosition", "bottomright"));
-          colourbar_position = parse_colourmap_position_str(cbar_pos);
-          if(!colourbar_position)
-            WARN ("invalid specifier \"" + cbar_pos + "\" for config file entry \"MRViewColourBarPosition\"");
-
-          //CONF option: MRViewToolsColourBarPosition
-          //CONF default: topright
-          //CONF The position of all visible tool colourbars within the main window in MRView.
-          //CONF Valid values are: bottomleft, bottomright, topleft, topright.
-          cbar_pos = lowercase (MR::File::Config::get ("MRViewToolsColourBarPosition", "topright"));
-          tools_colourbar_position = parse_colourmap_position_str(cbar_pos);
-          if(!tools_colourbar_position)
-            WARN ("invalid specifier \"" + cbar_pos + "\" for config file entry \"MRViewToolsColourBarPosition\"");
-
-
-        }
-
-
-
-
-
-      void Window::parse_arguments ()
-      {
-        if (MR::App::argument.size()) {
-          if (MR::App::option.size())  {
-            // check that first non-standard option appears after last argument:
-            size_t last_arg_pos = 1;
-            for (; MR::App::argv[last_arg_pos] != MR::App::argument.back().c_str(); ++last_arg_pos)
-              if (MR::App::argv[last_arg_pos] == nullptr)
-                throw Exception ("FIXME: error determining position of last argument!");
-
-            // identify first non-standard option:
-            size_t first_option = 0;
-            for (; first_option < MR::App::option.size(); ++first_option) {
-              if (size_t (MR::App::option[first_option].opt - &MR::App::__standard_options[0]) >= MR::App::__standard_options.size())
-                break;
-            }
-            if (MR::App::option.size() > first_option) {
-              first_option = MR::App::option[first_option].args - MR::App::argv;
-              if (first_option < last_arg_pos)
-                throw Exception ("options must appear after the last argument - see help page for details");
-            }
-          }
-
-          vector<std::unique_ptr<MR::Header>> list;
-          for (size_t n = 0; n < MR::App::argument.size(); ++n) {
-            try { list.push_back (make_unique<MR::Header> (MR::Header::open (MR::App::argument[n]))); }
-            catch (Exception& e) { e.display(); }
-          }
-          add_images (list);
-        }
-
-        QTimer::singleShot (10, this, SLOT(process_commandline_option_slot()));
-      }
-
-
-
-
-
-
-      ColourMap::Position Window::parse_colourmap_position_str (const std::string& position_str) {
-
-        ColourMap::Position pos(ColourMap::Position::None);
-
-        if(position_str == "bottomleft")
-          pos = ColourMap::Position::BottomLeft;
-        else if(position_str == "bottomright")
-          pos = ColourMap::Position::BottomRight;
-        else if(position_str == "topleft")
-          pos = ColourMap::Position::TopLeft;
-        else if(position_str == "topright")
-          pos = ColourMap::Position::TopRight;
-
-        return pos;
-      }
-
-
-
-      Window::~Window ()
-      {
-        glarea->makeCurrent();
-        QList<QAction*> tools = tool_group->actions();
-        for (QAction* action : tools)
-          delete action;
-        mode.reset();
-        QList<QAction*> images = image_group->actions();
-        for (QAction* action : images)
-          delete action;
-      }
-
-
-
-
-      void Window::sync_slot ()
-	  {
-		  emit syncChanged();
-	  }
-
-
-      void Window::image_open_slot ()
-      {
-        vector<std::string> image_list = Dialog::File::get_images (this, "Select images to open");
-        if (image_list.empty())
-          return;
-
-        vector<std::unique_ptr<MR::Header>> list;
-        for (size_t n = 0; n < image_list.size(); ++n) {
-          try {
-            list.push_back (make_unique<MR::Header> (MR::Header::open (image_list[n])));
-          }
-          catch (Exception& E) {
-            E.display();
-          }
-        }
-        add_images (list);
-      }
-
-
-
-      void Window::image_import_DICOM_slot ()
-      {
-        std::string folder = Dialog::File::get_folder (this, "Select DICOM folder to import");
-        if (folder.empty())
-          return;
-
-
-        try {
-          vector<std::unique_ptr<MR::Header>> list;
-          list.push_back (make_unique<MR::Header> (MR::Header::open (folder)));
-          add_images (list);
-        }
-        catch (Exception& E) {
-          E.display();
-        }
-      }
-
-
-
-
-      void Window::add_images (vector<std::unique_ptr<MR::Header>>& list)
-      {
-        for (size_t i = 0; i < list.size(); ++i) {
-          const std::string name = list[i]->name(); // Gets move-constructed out
-          QAction* action = new Image (std::move (*list[i]));
-          action->setText (shorten (name, 20, 0).c_str());
-          action->setParent (Window::main);
-          action->setCheckable (true);
-          action->setToolTip (name.c_str());
-          action->setStatusTip (name.c_str());
-          image_group->addAction (action);
-          image_menu->addAction (action);
-          connect (action, SIGNAL(scalingChanged()), this, SLOT(on_scaling_changed()));
-
-          if (!i) image_select_slot (action);
-        }
-        set_image_menu();
-      }
-
-
-
-      void Window::image_save_slot ()
-      {
-        std::string image_name = Dialog::File::get_save_image_name (this, "Select image destination");
-        if (image_name.empty())
-          return;
-
-        try {
-          auto dest = MR::Image<cfloat>::create (image_name, image()->header());
-          MR::copy_with_progress (image()->image, dest);
-        }
-        catch (Exception& E) {
-          E.display();
-        }
-      }
-
-
-
-
-      void Window::image_close_slot ()
-      {
-        Image* imagep = image();
-        assert (imagep);
-        QList<QAction*> list = image_group->actions();
-        if (list.size() > 1) {
-          for (int n = 0; n < list.size(); ++n) {
-            if (imagep == list[n]) {
-              image_select_slot (list[ (n+1) %list.size()]);
-              break;
-            }
-          }
-        }
-        image_group->removeAction (imagep);
-        delete imagep;
-        set_image_menu();
-      }
-
-
-
-
-      void Window::image_properties_slot ()
-      {
-        assert (image());
-        Dialog::ImageProperties props (this, image()->header());
-        props.exec();
-      }
-
-
-
-      void Window::select_mode_slot (QAction* action)
-      {
-        glarea->makeCurrent();
-        mode.reset (dynamic_cast<GUI::MRView::Mode::__Action__*> (action)->create());
-        mode->set_visible(! image_hide_action->isChecked());
-        set_mode_features();
-        emit modeChanged();
-        glarea->update();
-      }
-
-
-      void Window::select_mouse_mode_slot (QAction* action)
-      {
-        bool rotate_button_checked = mode_action_group->actions().indexOf (action) == 2;
-        if (rotate_button_checked)
-          set_snap_to_image (false);
-        snap_to_image_action->setEnabled (!rotate_button_checked);
-        set_cursor();
-      }
-
-
-
-      void Window::select_tool_slot (QAction* action)
-      {
-        Tool::Dock* tool = dynamic_cast<Tool::__Action__*>(action)->dock;
-        if (!tool) {
-          create_tool (action, true);
-          return;
-        }
-
-        if (action->isChecked()) {
-          if (!tool->isVisible())
-            tool->show();
-          tool->raise();
-        } else {
-          tool->close();
-        }
-      }
-
-
-
-
-
-      void Window::create_tool (QAction* action, bool show)
-      {
-        if (dynamic_cast<Tool::__Action__*>(action)->dock)
-          return;
-
-        Tool::Dock* tool = dynamic_cast<Tool::__Action__*>(action)->create();
-        connect (tool, SIGNAL (visibilityChanged (bool)), action, SLOT (setChecked (bool)));
-
-        //CONF option: MRViewDockFloating
-        //CONF default: 0 (false)
-        //CONF Whether MRView tools should start docked in the main window, or
-        //CONF floating (detached from the main window).
-        bool floating = MR::File::Config::get_int ("MRViewDockFloating", 0);
-
-        if (!floating) {
-
-          for (int i = 0; i < tool_group->actions().size(); ++i) {
-            Tool::Dock* other_tool = dynamic_cast<Tool::__Action__*>(tool_group->actions()[i])->dock;
-            if (other_tool && other_tool != tool) {
-              QList<QDockWidget*> list = QMainWindow::tabifiedDockWidgets (other_tool);
-              if (list.size())
-                QMainWindow::tabifyDockWidget (list.last(), tool);
-              else
-                QMainWindow::tabifyDockWidget (other_tool, tool);
-              break;
-            }
-          }
-
-        }
-
-        tool->setFloating (floating);
-        if (show) {
-          tool->show();
-          tool->raise();
-        }
-        else {
-          tool->close();
-        }
-      }
-
-
-      void Window::selected_colourmap (size_t colourmap, const ColourMapButton&)
-      {
-        Image* imagep = image();
-        if (imagep) {
-          imagep->set_colourmap (colourmap);
-          glarea->update();
-        }
-      }
-
-
-
-      void Window::selected_custom_colour (const QColor& colour, const ColourMapButton&)
-      {
-        Image* imagep = image();
-        if (imagep) {
-          std::array<GLubyte, 3> c_colour{{GLubyte(colour.red()), GLubyte(colour.green()), GLubyte(colour.blue())}};
-          imagep->set_colour(c_colour);
-          glarea->update();
-        }
-      }
-
-
-
-      void Window::invert_scaling_slot ()
-      {
-        if (image()) {
-          image()->set_invert_scale (invert_scale_action->isChecked());
-          glarea->update();
-        }
-      }
-
-
-
-      void Window::snap_to_image_slot ()
-      {
-        if (image()) {
-          snap_to_image_axes_and_voxel = snap_to_image_action->isChecked();
-          if (snap_to_image_axes_and_voxel)
-            mode->reset_orientation();
-          glarea->update();
-        }
-      }
-
-
-
-
-      void Window::on_scaling_changed ()
-      {
-        emit scalingChanged();
-      }
-
-
-
-
-      void Window::updateGL ()
-      {
-        glarea->update();
-      }
-
-      void Window::drawGL ()
-      {
-        glarea->repaint();
-      }
-
-
-
-      void Window::image_reset_slot ()
-      {
-        if (image())
-          mode->reset_windowing ();
-      }
-
-
-
-      void Window::image_interpolate_slot ()
-      {
-        Image* imagep = image();
-        if (imagep) {
-          imagep->set_interpolate (image_interpolate_action->isChecked());
-          glarea->update();
-        }
-      }
-
-
-      void Window::full_screen_slot ()
-      {
-        if (full_screen_action->isChecked())
-          showFullScreen();
-        else
-          showNormal();
-      }
-
-      void Window::select_plane_slot (QAction* action)
-      {
-        if (action == axial_action) set_plane (2);
-        else if (action == sagittal_action) set_plane (0);
-        else if (action == coronal_action) set_plane (1);
-        else assert (0);
-        glarea->update();
-      }
-
-
-
-
-
-      void Window::zoom_in_slot ()
-      {
-        set_FOV (FOV() * std::exp (-0.1));
-        glarea->update();
-      }
-
-      void Window::zoom_out_slot ()
-      {
-        set_FOV (FOV() * std::exp (0.1));
-        glarea->update();
-      }
-
-
-
-
-      void Window::reset_view_slot ()
-      {
-        if (image()) {
-          mode->reset_event();
-          QList<QAction*> tools = tool_group->actions();
-          for (QAction* action : tools) {
-            Tool::Dock* dock = dynamic_cast<Tool::__Action__*>(action)->dock;
-            if (dock)
-              dock->tool->reset_event();
-          }
-        }
-      }
-
-
-
-      void Window::background_colour_slot ()
-      {
-        QColor colour = QColorDialog::getColor(Qt::black, this, "Select background colour", QColorDialog::DontUseNativeDialog);
-
-        if (colour.isValid()) {
-          background_colour[0] = GLubyte(colour.red()) / 255.0f;
-          background_colour[1] = GLubyte(colour.green()) / 255.0f;
-          background_colour[2] = GLubyte(colour.blue()) / 255.0f;
-          glarea->update();
-        }
-
-      }
-
-
-      void Window::set_image_volume (size_t axis, ssize_t index)
-      {
-        assert (image());
-        image()->image.index (axis) = index;
-        set_image_navigation_menu();
-        emit volumeChanged (index);
-        updateGL();
-      }
-
-
-
-
-      void Window::set_image_visibility (bool flag) {
-        image_hide_action->setChecked(! flag);
-        mode->set_visible(flag);
-      }
-
-
-
-      void Window::hide_image_slot ()
-      {
-        bool visible = ! image_hide_action->isChecked();
-        mode->set_visible(visible);
-        emit imageVisibilityChanged(visible);
-      }
-
-
-
-      void Window::slice_next_slot ()
-      {
-        assert (mode);
-        if (image())
-          mode->slice_move_event (1);
-      }
-
-      void Window::slice_previous_slot ()
-      {
-        assert (mode);
-        if (image())
-          mode->slice_move_event (-1);
-      }
-
-
-      void Window::image_next_slot ()
-      {
-        QAction* action = image_group->checkedAction();
-        int N = image_group->actions().size();
-        int n = image_group->actions().indexOf (action);
-        image_select_slot (image_group->actions()[(n+1)%N]);
-      }
-
-
-
-
-      void Window::image_previous_slot ()
-      {
-        QAction* action = image_group->checkedAction();
-        int N = image_group->actions().size();
-        int n = image_group->actions().indexOf (action);
-        image_select_slot (image_group->actions()[(n+N-1)%N]);
-      }
-
-
-
-
-      void Window::image_next_volume_slot ()
-      {
-        size_t vol = image()->image.index(3)+1;
-        set_image_volume (3, vol);
-        emit volumeChanged(vol);
-      }
-
-
-
-
-      void Window::image_previous_volume_slot ()
-      {
-        size_t vol = image()->image.index(3)-1;
-        set_image_volume (3, vol);
-        emit volumeChanged(vol);
-      }
-
-
-      void Window::image_goto_volume_slot ()
-      {
-        size_t maxvol = image()->image.size(3) - 1;
-        auto label = std::string ("volume (0...") + str(maxvol) + std::string (")");
-        bool ok;
-        size_t vol = QInputDialog::getInt (this, tr("Go to..."),
-          label.c_str(), image()->image.index(3), 0, maxvol, 1, &ok);
-        if (ok) {
-          set_image_volume (3, vol);
-          emit volumeChanged(vol);
-        }
-      }
-
-      void Window::image_goto_volume_group_slot ()
-      {
-        size_t maxvolgroup = image()->image.size(4) - 1;
-        auto label = std::string ("volume group (0...") + str(maxvolgroup) + std::string (")");
-        bool ok;
-        size_t grp = QInputDialog::getInt (this, tr("Go to..."),
-          label.c_str(), image()->image.index(4), 0, maxvolgroup, 1, &ok);
-        if (ok) {
-          set_image_volume (4, grp);
-          emit volumeGroupChanged(grp);
-        }
-      }
-
-
-      void Window::image_next_volume_group_slot ()
-      {
-        size_t vol = image()->image.index(4)+1;
-        set_image_volume (4, vol);
-        emit volumeGroupChanged(vol);
-      }
-
-
-
-
-      void Window::image_previous_volume_group_slot ()
-      {
-        size_t vol = image()->image.index(4)-1;
-        set_image_volume (4, vol);
-        emit volumeGroupChanged(vol);
-      }
-
-
-
-
-      void Window::image_select_slot (QAction* action)
-      {
-        action->setChecked (true);
-        image_interpolate_action->setChecked (image()->interpolate());
-        size_t cmap_index = image()->colourmap;
-        colourmap_button->colourmap_actions[cmap_index]->setChecked (true);
-        invert_scale_action->setChecked (image()->scale_inverted());
-        mode->image_changed_event();
-        setWindowTitle (image()->image.name().c_str());
-        set_image_navigation_menu();
-        image()->set_allowed_features (
-            mode->features & Mode::ShaderThreshold,
-            mode->features & Mode::ShaderTransparency,
-            mode->features & Mode::ShaderLighting);
-        emit imageChanged();
-        glarea->update();
-      }
-
-
-      void Window::toggle_annotations_slot ()
-      {
-        int current_annotations = 0x00000000;
-        if (show_crosshairs()) current_annotations |= 0x00000001;
-        if (show_comments()) current_annotations |= 0x00000002;
-        if (show_voxel_info()) current_annotations |= 0x00000004;
-        if (show_orientation_labels()) current_annotations |= 0x00000008;
-        if (show_colourbar()) current_annotations |= 0x00000010;
-
-        if (current_annotations) {
-          annotations = current_annotations;
-          show_crosshairs_action->setChecked (false);
-          show_comments_action->setChecked (false);
-          show_voxel_info_action->setChecked (false);
-          show_orientation_labels_action->setChecked (false);
-          show_colourbar_action->setChecked (false);
-        }
-        else {
-          if (!annotations)
-            annotations = 0xFFFFFFFF;
-          show_crosshairs_action->setChecked (annotations & 0x00000001);
-          show_comments_action->setChecked (annotations & 0x00000002);
-          show_voxel_info_action->setChecked (annotations & 0x00000004);
-          show_orientation_labels_action->setChecked (annotations & 0x00000008);
-          show_colourbar_action->setChecked (annotations & 0x00000010);
-        }
-        glarea->update();
-      }
-
-
-      void Window::set_image_menu ()
-      {
-        int N = image_group->actions().size();
-        next_image_action->setEnabled (N>1);
-        prev_image_action->setEnabled (N>1);
-        reset_windowing_action->setEnabled (N>0);
-        colourmap_button->setEnabled (N>0);
-        save_action->setEnabled (N>0);
-        close_action->setEnabled (N>0);
-        properties_action->setEnabled (N>0);
-        set_image_navigation_menu();
-        glarea->update();
-      }
-
-      int Window::get_mouse_mode ()
-      {
-        if (mouse_action == NoAction && modifiers_ != Qt::NoModifier) {
-          if (modifiers_ == FocusModifier && ( mode->features & Mode::FocusContrast ))
-            return 1;
-          else if (modifiers_ == MoveModifier && ( mode->features & Mode::MoveTarget ))
-            return 2;
-          else if (modifiers_ == RotateModifier && ( mode->features & Mode::TiltRotate ))
-            return 3;
-        }
-
-        if (mouse_action == NoAction)
-          return mode_action_group->actions().indexOf (mode_action_group->checkedAction()) + 1;
-
-        return 0;
-      }
-
-
-      void Window::set_cursor ()
-      {
-        MouseAction cursor = mouse_action;
-
-        if (cursor == NoAction) {
-          switch (get_mouse_mode()) {
-            case 1: cursor = SetFocus; break;
-            case 2: cursor = Pan; break;
-            case 3: cursor = Tilt; break;
-            default: assert (0);
-          }
-        }
-
-        if (tool_has_focus && modifiers_ == Qt::NoModifier) {
-          QCursor* ptr = tool_has_focus->get_cursor();
-          if (ptr) {
-            glarea->setCursor (*ptr);
-            return;
-          }
-        }
-
-        switch (cursor) {
-          case SetFocus: glarea->setCursor (Cursor::crosshair); break;
-          case Contrast: glarea->setCursor (Cursor::window); break;
-          case Pan: glarea->setCursor (Cursor::pan_crosshair); break;
-          case PanThrough: glarea->setCursor (Cursor::forward_backward); break;
-          case Tilt: glarea->setCursor (Cursor::throughplane_rotate); break;
-          case Rotate: glarea->setCursor (Cursor::inplane_rotate); break;
-          default: assert (0);
-        }
-      }
-
-
-
-      void Window::set_mode_features ()
-      {
-        mode_action_group->actions()[0]->setEnabled (mode->features & Mode::FocusContrast);
-        mode_action_group->actions()[1]->setEnabled (mode->features & Mode::MoveTarget);
-        mode_action_group->actions()[2]->setEnabled (mode->features & Mode::TiltRotate);
-        if (!mode_action_group->checkedAction()->isEnabled())
-          mode_action_group->actions()[0]->setChecked (true);
-        if (image())
-          image()->set_allowed_features (
-              mode->features & Mode::ShaderThreshold,
-              mode->features & Mode::ShaderTransparency,
-              mode->features & Mode::ShaderLighting);
-      }
-
-
-      void Window::set_image_navigation_menu ()
-      {
-        bool show_next_volume (false), show_goto_volume (false), show_prev_volume (false);
-        bool show_next_volume_group (false), show_goto_volume_group (false), show_prev_volume_group (false);
-        Image* imagep = image();
-        if (imagep) {
-          if (imagep->image.ndim() > 3) {
-            if (imagep->image.size(3) > 1)
-              show_goto_volume = true;
-            if (imagep->image.index(3) > 0)
-              show_prev_volume = true;
-            if (imagep->image.index(3) < imagep->image.size(3)-1)
-              show_next_volume = true;
-
-            if (imagep->image.ndim() > 4) {
-              if (imagep->image.size(4) > 1)
-                show_goto_volume_group = true;
-              if (imagep->image.index(4) > 0)
-                show_prev_volume_group = true;
-              if (imagep->image.index(4) < imagep->image.size(4)-1)
-                show_next_volume_group = true;
-            }
-          }
-        }
-        prev_image_volume_action->setEnabled (show_prev_volume);
-        next_image_volume_action->setEnabled (show_next_volume);
-        goto_image_volume_action->setEnabled (show_goto_volume);
-        prev_image_volume_group_action->setEnabled (show_prev_volume_group);
-        next_image_volume_group_action->setEnabled (show_next_volume_group);
-        goto_image_volume_group_action->setEnabled (show_goto_volume_group);
-      }
-
-
-
-
-
-      void Window::OpenGL_slot ()
-      {
-        Dialog::OpenGL glinfo (this, glarea->format());
-        glinfo.exec();
-      }
-
-
-
-
-      void Window::about_slot ()
-      {
-        std::string message =
-          std::string ("<h1>MRView</h1>The MRtrix viewer, version ") + MR::App::mrtrix_version + "<br>"
-          "<em>" + str (8*sizeof (size_t)) + " bit "
-#ifdef NDEBUG
-          "release"
-#else
-          "debug"
-#endif
-          " version, built " + MR::App::build_date +  "</em><p>"
-          "<h4>Authors:</h4>" + MR::join (MR::split (MR::App::AUTHOR, ",;&\n", true), "<br>") +
-          "<p><em>" + MR::App::COPYRIGHT + "</em>";
-
-        QMessageBox::about (this, tr ("About MRView"), message.c_str());
-      }
-
-
-
-
-      void Window::aboutQt_slot ()
-      {
-        QMessageBox::aboutQt (this);
-      }
-
-
-      void Window::paintGL ()
-      {
-        ASSERT_GL_MRVIEW_CONTEXT_IS_CURRENT;
-        GL_CHECK_ERROR;
-        gl::ClearColor (background_colour[0], background_colour[1], background_colour[2], 1.0);
-
-        if (glarea->format().samples() > 1)
-          gl::Enable (gl::MULTISAMPLE);
-
-        GL_CHECK_ERROR;
-
-        ASSERT_GL_MRVIEW_CONTEXT_IS_CURRENT;
-        mode->paintGL();
-        ASSERT_GL_MRVIEW_CONTEXT_IS_CURRENT;
-        GL_CHECK_ERROR;
-
-        if (show_FPS) {
-          render_times.push_back (Timer::current_time());
-          while (render_times.size() > 10)
-            render_times.erase (render_times.begin());
-          double FPS = NAN;
-          std::string FPS_string = "-";
-          std::string FPS_best_string = "-";
-
-          if (render_times.back() - best_FPS_time > 3.0)
-            best_FPS = NAN;
-
-          if (render_times.size() == 10) {
-            FPS = (render_times.size()-1.0) / (render_times.back()-render_times.front());
-            FPS_string = str (FPS, 4);
-            if (!std::isfinite (best_FPS) || FPS > best_FPS) {
-              best_FPS = FPS;
-              best_FPS_time = render_times.back();
-            }
-          }
-          else
-            best_FPS = NAN;
-
-          if (std::isfinite (best_FPS))
-            FPS_best_string = str (best_FPS, 4);
-          mode->projection.setup_render_text (0.0, 1.0, 0.0);
-          mode->projection.render_text ("max FPS: " + FPS_best_string, RightEdge | TopEdge);
-          mode->projection.render_text ("FPS: " + FPS_string, RightEdge | TopEdge, 1);
-          mode->projection.done_render_text();
-        }
-
-        // need to clear alpha channel when using QOpenGLWidget (Qt >= 5.4)
-        // otherwise we get transparent windows...
-#if QT_VERSION >= 0x050400
-        gl::ColorMask (false, false, false, true);
-        gl::Clear (gl::COLOR_BUFFER_BIT);
-        glColorMask (true, true, true, true);
-#endif
-        GL_CHECK_ERROR;
-        ASSERT_GL_MRVIEW_CONTEXT_IS_CURRENT;
-      }
-
-
-      void Window::initGL ()
-      {
-        ASSERT_GL_MRVIEW_CONTEXT_IS_CURRENT;
-        GL::init ();
-
-        font.initGL();
-        gl::Enable (gl::DEPTH_TEST);
-        //CONF option: MRViewImageBackgroundColour
-        //CONF default: 0,0,0 (black)
-        //CONF The default image background colour in the main MRView window.
-        File::Config::get_RGB ("MRViewImageBackgroundColour", background_colour, 0.0f, 0.0f, 0.0f);
-        gl::ClearColor (background_colour[0], background_colour[1], background_colour[2], 1.0);
-        mode.reset (dynamic_cast<Mode::__Action__*> (mode_group->actions()[0])->create());
-        set_mode_features();
-
-        ASSERT_GL_MRVIEW_CONTEXT_IS_CURRENT;
-      }
-
-
-      template <class Event> void Window::grab_mouse_state (Event* event)
-      {
-        buttons_ = event->buttons();
-        modifiers_ = event->modifiers() & ( FocusModifier | MoveModifier | RotateModifier );
-        mouse_displacement_ = QPoint (0,0);
-        mouse_position_ = event->pos();
-        mouse_position_.setY (glarea->height() - mouse_position_.y());
-      }
-
-
-      template <class Event> void Window::update_mouse_state (Event* event)
-      {
-        mouse_displacement_ = mouse_position_;
-        mouse_position_ = event->pos();
-        mouse_position_.setY (glarea->height() - mouse_position_.y());
-        mouse_displacement_ = mouse_position_ - mouse_displacement_;
-      }
-
-
-      void Window::keyPressEvent (QKeyEvent* event)
-      {
-        modifiers_ = event->modifiers() & ( FocusModifier | MoveModifier | RotateModifier );
-        set_cursor();
-      }
-
-
-      void Window::keyReleaseEvent (QKeyEvent* event)
-      {
-        modifiers_ = event->modifiers() & ( FocusModifier | MoveModifier | RotateModifier );
-        set_cursor();
-      }
-
-
-      void Window::mousePressEventGL (QMouseEvent* event)
-      {
-        assert (mode);
-
-        grab_mouse_state (event);
-        if (image())
-          mode->mouse_press_event();
-
-        if (tool_has_focus && modifiers_ == Qt::NoModifier) {
-          if (tool_has_focus->mouse_press_event()) {
-            mouse_action = NoAction;
-            event->accept();
-            return;
-          }
-        }
-
-        int group = get_mouse_mode();
-
-        if (buttons_ == Qt::MidButton)
-          mouse_action = Pan;
-        else if (group == 1) {
-          if (buttons_ == Qt::LeftButton) {
-            mouse_action = SetFocus;
-            if (image())
-              mode->set_focus_event();
-          }
-          else if (buttons_ == Qt::RightButton)
-            mouse_action = Contrast;
-        }
-        else if (group == 2) {
-          if (buttons_ == Qt::LeftButton)
-            mouse_action = Pan;
-          else if (buttons_ == Qt::RightButton)
-            mouse_action = PanThrough;
-        }
-        else if (group == 3) {
-          if (buttons_ == Qt::LeftButton)
-            mouse_action = Tilt;
-          else if (buttons_ == Qt::RightButton)
-            mouse_action = Rotate;
-        }
-
-        set_cursor();
-        event->accept();
-      }
-
-
-      void Window::mouseMoveEventGL (QMouseEvent* event)
-      {
-        assert (mode);
-        if (!image())
-          return;
-
-        update_mouse_state (event);
-
-        if (mouse_action == NoAction) {
-          if (tool_has_focus)
-            if (tool_has_focus->mouse_move_event())
-              event->accept();
-          return;
-        }
-
-
-        switch (mouse_action) {
-          case SetFocus: mode->set_focus_event(); break;
-          case Contrast: mode->contrast_event(); break;
-          case Pan: mode->pan_event(); break;
-          case PanThrough: mode->panthrough_event(); break;
-          case Tilt: mode->tilt_event(); break;
-          case Rotate: mode->rotate_event(); break;
-          default: return;
-        }
-        event->accept();
-        glarea->update();
-      }
-
-
-      void Window::mouseReleaseEventGL (QMouseEvent*)
-      {
-        assert (mode);
-        mode->mouse_release_event();
-
-        if (tool_has_focus && mouse_action == NoAction)
-          if (tool_has_focus->mouse_release_event())
-            return;
-
-        mouse_action = NoAction;
-        set_cursor();
-      }
-
-
-      void Window::wheelEventGL (QWheelEvent* event)
-      {
-        assert (mode);
-#if QT_VERSION >= 0x050500
-        QPoint delta;
-        if (event->source() == Qt::MouseEventNotSynthesized)
-          delta = event->angleDelta();
-        else
-          delta = 30 * event->pixelDelta();
-#else
-        QPoint delta = event->orientation() == Qt::Vertical ? QPoint (0, event->delta()) : QPoint (event->delta(), 0);
-#endif
-        if (delta.isNull())
-          return;
-
-        if (delta.y()) {
-
-          if (image()) {
-            grab_mouse_state (event);
-            mode->mouse_press_event();
-
-            if (buttons_ == Qt::NoButton) {
-
-              if (modifiers_ == Qt::ControlModifier) {
-                set_FOV (FOV() * std::exp (-delta.y()/1200.0));
-                glarea->update();
-                event->accept();
-                return;
-              }
-
-              float dx = delta.y()/120.0;
-              if (modifiers_ == Qt::ShiftModifier) dx *= 10.0;
-              else if (modifiers_ != Qt::NoModifier)
-                return;
-
-              mode->slice_move_event (dx);
-              event->accept();
-              return;
-            }
-          }
-
-          if (buttons_ == Qt::RightButton && modifiers_ == Qt::NoModifier) {
-            if (image_group->actions().size() > 1) {
-              QAction* action = image_group->checkedAction();
-              int N = image_group->actions().size();
-              int n = image_group->actions().indexOf (action);
-              image_select_slot (image_group->actions()[(n+N+int(std::round(delta.y()/120.0)))%N]);
-            }
-          }
-        }
-
-      }
-
-
-
-
-      bool Window::gestureEventGL (QGestureEvent* event)
-      {
-        assert (mode);
-
-        if (QGesture* pan = event->gesture(Qt::PanGesture)) {
-          QPanGesture* e = static_cast<QPanGesture*> (pan);
-          mouse_displacement_ = QPoint (e->delta().x(), -e->delta().y());
-          mode->pan_event();
-        }
-
-        if (QGesture* pinch = event->gesture(Qt::PinchGesture)) {
-          QPinchGesture* e = static_cast<QPinchGesture*> (pinch);
-          QPinchGesture::ChangeFlags changeFlags = e->changeFlags();
-          if (changeFlags & QPinchGesture::RotationAngleChanged) {
-            // TODO
-          }
-          if (changeFlags & QPinchGesture::ScaleFactorChanged) {
-            set_FOV (FOV() / e->scaleFactor());
-            glarea->update();
-          }
-        }
-        return true;
-      }
-
-
-
-      void Window::closeEvent (QCloseEvent* event)
-      {
-        qApp->quit();
-        event->accept();
-      }
-
-
-      void Window::process_commandline_option_slot ()
-      {
-        if (current_option >= MR::App::option.size())
-          return;
-
-        process_commandline_option();
-        ++current_option;
-
-        QTimer::singleShot (10, this, SLOT(process_commandline_option_slot()));
-        glarea->update();
-      }
-
-
-
-
-
-      void Window::process_commandline_option ()
-      {
-        auto& opt (MR::App::option[current_option]);
-
-#undef TOOL
-#define TOOL(classname, name, description) \
-        stub = lowercase (#classname "."); \
-        if (stub.compare (0, stub.size(), std::string (opt.opt->id), 0, stub.size()) == 0) { \
-          create_tool (tool_group->actions()[tool_id], false); \
-          if (dynamic_cast<Tool::__Action__*>(tool_group->actions()[tool_id])->dock->tool->process_commandline_option (opt)) \
-          return; \
-        } \
-        ++tool_id;
-
-        try {
-
-          // see whether option is claimed by any tools:
-          size_t tool_id = 0;
-          std::string stub;
-#include "gui/mrview/tool/list.h"
-
-
-          // process general options:
-          if (opt.opt->is ("mode")) {
-            int n = int(opt[0]) - 1;
-            if (n < 0 || n >= mode_group->actions().size())
-              throw Exception ("invalid mode index \"" + str(n) + "\" in batch command");
-            select_mode_slot (mode_group->actions()[n]);
-            return;
-          }
-
-          if (opt.opt->is ("size")) {
-            vector<int> glsize = parse_ints (opt[0]);
-            if (glsize.size() != 2)
-              throw Exception ("invalid argument \"" + std::string(opt.args[0]) + "\" to -size batch command");
-            if (glsize[0] < 1 || glsize[1] < 1)
-              throw Exception ("values provided to -size option must be positive");
-            QSize oldsize = glarea->size();
-            QSize winsize = size();
-            resize (winsize.width() - oldsize.width() + glsize[0], winsize.height() - oldsize.height() + glsize[1]);
-            return;
-          }
-
-          if (opt.opt->is ("reset")) {
-            reset_view_slot();
-            return;
-          }
-
-          if (opt.opt->is ("fov")) {
-            float fov = opt[0];
-            set_FOV (fov);
-            glarea->update();
-            return;
-          }
-
-          if (opt.opt->is ("focus")) {
-            try {
-              auto pos = parse_floats (opt[0]);
-              if (pos.size() != 3)
-                throw Exception ("-focus option expects a comma-separated list of 3 floating-point values");
-              set_focus (Eigen::Vector3f { float(pos[0]), float(pos[1]), float(pos[2]) });
-            }
-            catch (Exception& E) {
-              try {
-                show_crosshairs_action->setChecked (to<bool> (opt[0]));
-              }
-              catch (Exception& E2) {
-                throw Exception ("-focus option expects a boolean or a comma-separated list of 3 floating-point values");
-              }
-            }
-            glarea->update();
-            return;
-          }
-
-          if (opt.opt->is ("target")) {
-            if (image()) {
-              vector<default_type> pos = parse_floats (opt[0]);
-              if (pos.size() != 3)
-                throw Exception ("-target option expects a comma-separated list of 3 floating-point values");
-              set_target (Eigen::Vector3f { float(pos[0]), float(pos[1]), float(pos[2]) });
-              glarea->update();
-            }
-            return;
-          }
-
-          if (opt.opt->is ("voxel")) {
-            if (image()) {
-              vector<default_type> pos = parse_floats (opt[0]);
-              if (pos.size() != 3)
-                throw Exception ("-voxel option expects a comma-separated list of 3 floating-point values");
-              set_focus (image()->transform().voxel2scanner.cast<float>() *  Eigen::Vector3f { float(pos[0]), float(pos[1]), float(pos[2]) });
-              glarea->update();
-            }
-            return;
-          }
-
-          if (opt.opt->is ("volume")) {
-            if (image()) {
-              auto pos = parse_ints (opt[0]);
-              for (size_t n = 0; n < std::min (pos.size(), image()->image.ndim()); ++n) {
-                if (pos[n] < 0 || pos[n] >= image()->image.size(n+3))
-                  throw Exception ("volume index outside of image dimensions");
-                set_image_volume (n+3, pos[n]);
-                set_image_navigation_menu();
-              }
-              glarea->update();
-            }
-            return;
-          }
-
-          if (opt.opt->is ("fov")) {
-            float fov = opt[0];
-            set_FOV (fov);
-            glarea->update();
-            return;
-          }
-
-          if (opt.opt->is ("plane")) {
-            int n = opt[0];
-            set_plane (n);
-            glarea->update();
-            return;
-          }
-
-          if (opt.opt->is ("lock")) {
-            bool n = opt[0];
-            snap_to_image_action->setChecked (n);
-            snap_to_image_slot();
-            return;
-          }
-
-          if (opt.opt->is ("select_image")) {
-            int n = int(opt[0]) - 1;
-            if (n < 0 || n >= image_group->actions().size())
-              throw Exception ("invalid image index requested for option -select_image");
-            image_select_slot (image_group->actions()[n]);
-            return;
-          }
-
-          if (opt.opt->is ("load")) {
-            vector<std::unique_ptr<MR::Header>> list;
-            try { list.push_back (make_unique<MR::Header> (MR::Header::open (opt[0]))); }
-            catch (Exception& e) { e.display(); }
-            add_images (list);
-            return;
-          }
-
-          if (opt.opt->is ("autoscale")) {
-            image_reset_slot();
-            return;
-          }
-
-          if (opt.opt->is ("colourmap")) {
-            int n = int(opt[0]) - 1;
-            if (n < 0 || n >= static_cast<int>(colourmap_button->colourmap_actions.size()))
-              throw Exception ("invalid image colourmap index \"" + str(n+1) + "\" requested in batch command");
-            colourmap_button->set_colourmap_index(n);
-            return;
-          }
-
-          if (opt.opt->is ("interpolation")) {
-            try {
-              image_interpolate_action->setChecked (to<bool> (opt[0]));
-            }
-            catch (Exception& E) {
-              throw Exception ("-interpolation option expects a boolean");
-            }
-            image_interpolate_slot();
-            return;
-          }
-
-          if (opt.opt->is ("intensity_range")) {
-            if (image()) {
-              vector<default_type> param = parse_floats (opt[0]);
-              if (param.size() != 2)
-                throw Exception ("-intensity_range options expects comma-separated list of two floating-point values");
-              image()->set_windowing (param[0], param[1]);
-              glarea->update();
-            }
-            return;
-          }
-
-          if (opt.opt->is ("position")) {
-            vector<int> pos = opt[0];
-            if (pos.size() != 2)
-              throw Exception ("invalid argument \"" + std::string(opt[0]) + "\" to -position option");
-            move (pos[0], pos[1]);
-            return;
-          }
-
-          if (opt.opt->is ("fullscreen")) {
-            full_screen_action->setChecked (true);
-            full_screen_slot();
-            return;
-          }
-		  
-          if (opt.opt->is ("noannotations")) {
-            toggle_annotations_slot ();
-            return;
-          }
-
-          if (opt.opt->is ("comments")) {
-            try {
-              show_comments_action->setChecked (to<bool> (opt[0]));
-            }
-            catch (Exception& E) {
-              throw Exception ("-comments option expects a boolean");
-            }
-            glarea->update();
-            return;
-          }
-
-          if (opt.opt->is ("voxelinfo")) {
-            try {
-              show_voxel_info_action->setChecked (to<bool> (opt[0]));
-            }
-            catch (Exception& E) {
-              throw Exception ("-voxelinfo option expects a boolean");
-            }
-            glarea->update();
-            return;
-          }
-
-          if (opt.opt->is ("orientationlabel")) {
-            try {
-              show_orientation_labels_action->setChecked (to<bool> (opt[0]));
-            }
-            catch (Exception& E) {
-              throw Exception ("-orientationlabel option expects a boolean");
-            }
-            glarea->update();
-            return;
-          }
-
-          if (opt.opt->is ("colourbar")) {
-            try {
-              show_colourbar_action->setChecked (to<bool> (opt[0]));
-            }
-            catch (Exception& E) {
-              throw Exception ("-colourbar option expects a boolean");
-            }
-            glarea->update();
-            return;
-          }
-
-          if (opt.opt->is ("imagevisible")) {
-            bool visible;
-            try {
-              visible = to<bool> (opt[0]);
-            }
-            catch (Exception& E) {
-              throw Exception ("-imagevisible option expects a boolean");
-            }
-            if (image_hide_action->isChecked() == visible)
-              set_image_visibility (visible);
-            return;
-          }
-
-
-          if (opt.opt->is ("fps")) {
-            show_FPS = true;
-            return;
-          }
-
-          if (opt.opt->is ("exit")) {
-            qApp->processEvents();
-            qApp->quit();
-            return;
-          }
-
-		  
-		  if (opt.opt->is ("sync.focus")) {
-            sync_focus_action->setChecked (true);
-            sync_slot();
-            return;
-          }
-		  
-          assert (opt.opt->is ("info") or opt.opt->is ("debug") or ("shouldn't reach here!" && false));
-        }
-        catch (Exception& E) {
-          E.display();
-          qApp->quit();
-        }
-      }
-
-
-      void Window::add_commandline_options (MR::App::OptionList& options)
-      {
-        options
-          + OptionGroup ("View options")
-
-          + Option ("mode", "Switch to view mode specified by the integer index, as per the view menu.").allow_multiple()
-          +   Argument ("index").type_integer()
-
-          + Option ("load", "Load image specified and make it current.").allow_multiple()
-          +   Argument ("image").type_image_in()
-
-          + Option ("reset", "Reset the view according to current image. This resets the FOV, projection and focus.").allow_multiple()
-
-          + Option ("fov", "Set the field of view, in mm.").allow_multiple()
-          +   Argument ("value").type_float()
-
-          + Option ("focus", "Either set the position of the crosshairs in scanner coordinates, "
-              "with the new position supplied as a comma-separated list of floating-point values or "
-              "show or hide the focus cross hair using a boolean value as argument.").allow_multiple()
-          +   Argument ("x,y,z or boolean")
-
-          + Option ("target", "Set the target location for the viewing window (the scanner coordinate "
-              "that will appear at the centre of the viewing window")
-          +   Argument ("x,y,z").type_sequence_float()
-
-          + Option ("voxel", "Set the position of the crosshairs in voxel coordinates, "
-              "relative the image currently displayed. The new position should be supplied "
-              "as a comma-separated list of floating-point values.").allow_multiple()
-          +   Argument ("x,y,z").type_sequence_float()
-
-          + Option ("volume", "Set the volume index for the image displayed, "
-              "as a comma-separated list of integers.").allow_multiple()
-          +   Argument ("idx").type_sequence_int()
-
-          + Option ("plane", "Set the viewing plane, according to the mappping 0: sagittal; 1: coronal; 2: axial.").allow_multiple()
-          +   Argument ("index").type_integer (0,2)
-
-          + Option ("lock", "Set whether view is locked to image axes (0: no, 1: yes).").allow_multiple()
-          +   Argument ("yesno").type_bool()
-
-          + Option ("select_image", "Switch to image number specified, with reference to the list of currently loaded images.").allow_multiple()
-          +   Argument ("index").type_integer (0)
-
-          + Option ("autoscale", "Reset the image scaling to automatically determined range.").allow_multiple()
-
-          + Option ("interpolation", "Enable or disable image interpolation in main image.").allow_multiple()
-          +   Argument ("boolean").type_bool ()
-
-          + Option ("colourmap", "Switch the image colourmap to that specified, as per the colourmap menu.").allow_multiple()
-          +   Argument ("index").type_integer (0)
-
-          + Option ("noannotations", "Hide all image annotation overlays").allow_multiple()
-
-          + Option ("comments", "Show or hide image comments overlay.").allow_multiple()
-          +   Argument ("boolean").type_bool ()
-
-          + Option ("voxelinfo", "Show or hide voxel information overlay.").allow_multiple()
-          +   Argument ("boolean").type_bool ()
-
-          + Option ("orientationlabel", "Show or hide orientation label overlay.").allow_multiple()
-          +   Argument ("boolean").type_bool ()
-
-          + Option ("colourbar", "Show or hide colourbar overlay.").allow_multiple()
-          +   Argument ("boolean").type_bool ()
-
-          + Option ("imagevisible", "Show or hide the main image.").allow_multiple()
-          +   Argument ("boolean").type_bool ()
-
-          + Option ("intensity_range", "Set the image intensity range to that specified.").allow_multiple()
-          +   Argument ("min,max").type_sequence_float()
-
-          + OptionGroup ("Window management options")
-
-          + Option ("size", "Set the size of the view area, in pixel units.").allow_multiple()
-          +   Argument ("width,height").type_sequence_int()
-
-          + Option ("position", "Set the position of the main window, in pixel units.").allow_multiple()
-          +   Argument ("x,y").type_sequence_int()
-		  
-          + Option ("fullscreen", "Start fullscreen.")
-
-          + Option ("exit", "Quit MRView.")
-
-		  + OptionGroup ("Sync Options")
-		  
-		  + Option ("sync.focus", "Sync the focus with other MRViw windows that also have this turned on.")
-		  
-          + OptionGroup ("Debugging options")
-
-          + Option ("fps", "Display frames per second, averaged over the last 10 frames. "
-              "The maximum over the last 3 seconds is also displayed.")
-
-          + OptionGroup ("Other options")
-
-          + NoRealignOption;
-
-      }
-
-
-
-
-    }
-  }
-}
-
-
-
diff --git a/window.h b/window.h
deleted file mode 100644
index 4d1b2ce1c3..0000000000
--- a/window.h
+++ /dev/null
@@ -1,365 +0,0 @@
-/*
- * Copyright (c) 2008-2018 the MRtrix3 contributors.
- *
- * This Source Code Form is subject to the terms of the Mozilla Public
- * License, v. 2.0. If a copy of the MPL was not distributed with this
- * file, you can obtain one at http://mozilla.org/MPL/2.0/
- *
- * MRtrix3 is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
- *
- * For more details, see http://www.mrtrix.org/
- */
-
-
-#ifndef __gui_mrview_window_h__
-#define __gui_mrview_window_h__
-
-#include "image.h"
-#include "memory.h"
-#include "math/versor.h"
-#include "gui/cursor.h"
-#include "gui/gui.h"
-#include "gui/mrview/gui_image.h"
-#include "gui/opengl/font.h"
-#include "gui/mrview/colourmap.h"
-#include "gui/mrview/colourmap_button.h"
-
-
-namespace MR
-{
-  namespace GUI
-  {
-    namespace GL {
-      class Lighting;
-    }
-
-    namespace MRView
-    {
-
-      namespace Mode
-      {
-        class Base;
-        class __Entry__;
-      }
-      namespace Tool
-      {
-        class Base;
-        class ODF;
-      }
-
-
-      class Window : public QMainWindow, ColourMapButtonObserver
-      { MEMALIGN(Window)
-          Q_OBJECT
-
-        private:
-          Cursor cursors_do_not_use;
-
-          class GLArea : public GL::Area { MEMALIGN(GLArea)
-            public:
-              GLArea (Window& parent);
-              QSize sizeHint () const override;
-
-            protected:
-              void dragEnterEvent (QDragEnterEvent* event) override;
-              void dragMoveEvent (QDragMoveEvent* event) override;
-              void dragLeaveEvent (QDragLeaveEvent* event) override;
-              void dropEvent (QDropEvent* event) override;
-              bool event (QEvent* event) override;
-            private:
-              void initializeGL () override;
-              void paintGL () override;
-              void mousePressEvent (QMouseEvent* event) override;
-              void mouseMoveEvent (QMouseEvent* event) override;
-              void mouseReleaseEvent (QMouseEvent* event) override;
-              void wheelEvent (QWheelEvent* event) override;
-          };
-          GLArea* glarea;
-
-        public:
-          Window();
-          ~Window();
-
-          void parse_arguments ();
-          void add_images (vector<std::unique_ptr<MR::Header>>& list);
-
-          const QPoint& mouse_position () const { return mouse_position_; }
-          const QPoint& mouse_displacement () const { return mouse_displacement_; }
-          Qt::MouseButtons mouse_buttons () const { return buttons_; }
-          Qt::KeyboardModifiers modifiers () const { return modifiers_; }
-
-          void selected_colourmap(size_t colourmap, const ColourMapButton&) override;
-          void selected_custom_colour(const QColor&colour, const ColourMapButton&) override;
-
-          const Image* image () const {
-            return static_cast<const Image*> (image_group->checkedAction());
-          }
-          QActionGroup* tools () const {
-            return tool_group;
-          }
-
-          int slice () const {
-            if (!image())
-              return -1;
-            else
-              return std::round ((image()->transform().scanner2voxel.cast<float>() * focus())[anatomical_plane]);
-          }
-
-          Mode::Base* get_current_mode () const { return mode.get(); }
-          const Eigen::Vector3f& focus () const { return focal_point; }
-          const Eigen::Vector3f& target () const { return camera_target; }
-          float FOV () const { return field_of_view; }
-          int plane () const { return anatomical_plane; }
-          const Math::Versorf& orientation () const { return orient; }
-          bool snap_to_image () const { return snap_to_image_axes_and_voxel; }
-          Image* image () { return static_cast<Image*> (image_group->checkedAction()); }
-
-          void set_focus (const Eigen::Vector3f& p) { focal_point = p; emit focusChanged(); }
-          void set_target (const Eigen::Vector3f& p) { camera_target = p; emit targetChanged(); }
-          void set_FOV (float value) { field_of_view = value; emit fieldOfViewChanged(); }
-          void set_plane (int p) { anatomical_plane = p; emit planeChanged(); }
-          void set_orientation (const Math::Versorf& V) { orient = V; emit orientationChanged(); }
-          void set_scaling (float min, float max) { if (!image()) return; image()->set_windowing (min, max); }
-          void set_snap_to_image (bool onoff) { snap_to_image_axes_and_voxel = onoff; snap_to_image_action->setChecked(onoff);  emit focusChanged(); }
-
-          void set_scaling_all (float min, float max) {
-            QList<QAction*> list = image_group->actions();
-            for (int n = 0; n < list.size(); ++n)
-              static_cast<Image*> (list[n])->set_windowing (min, max);
-          }
-
-          void set_image_volume (size_t axis, ssize_t index);
-
-          bool get_image_visibility () const { return ! image_hide_action->isChecked(); }
-          void set_image_visibility (bool flag);
-
-          bool show_crosshairs () const { return show_crosshairs_action->isChecked(); }
-          bool show_comments () const { return show_comments_action->isChecked(); }
-          bool show_voxel_info () const { return show_voxel_info_action->isChecked(); }
-          bool show_orientation_labels () const { return show_orientation_labels_action->isChecked(); }
-          bool show_colourbar () const { return show_colourbar_action->isChecked(); }
-
-		  bool sync_focus_on ()  const { return sync_focus_action->isChecked(); }
-		  
-          void captureGL (std::string filename) {
-            QImage image (glarea->grabFramebuffer());
-            image.save (filename.c_str());
-          }
-
-          GL::Area* glwidget () const { return glarea; }
-          GL::Lighting& lighting () { return *lighting_; }
-          ColourMap::Renderer colourbar_renderer;
-
-          static void add_commandline_options (MR::App::OptionList& options);
-          static Window* main;
-
-        signals:
-          void focusChanged ();
-          void targetChanged ();
-          void sliceChanged ();
-          void planeChanged ();
-          void orientationChanged ();
-          void fieldOfViewChanged ();
-          void modeChanged ();
-          void imageChanged ();
-          void imageVisibilityChanged (bool);
-          void scalingChanged ();
-          void volumeChanged (size_t);
-          void volumeGroupChanged (size_t);
-		  void syncChanged();
-
-        public slots:
-          void on_scaling_changed ();
-          void updateGL ();
-          void drawGL ();
-
-        private slots:
-          void image_open_slot ();
-          void image_import_DICOM_slot ();
-          void image_save_slot ();
-          void image_close_slot ();
-          void image_properties_slot ();
-
-          void select_mode_slot (QAction* action);
-          void select_mouse_mode_slot (QAction* action);
-          void select_tool_slot (QAction* action);
-          void select_plane_slot (QAction* action);
-          void zoom_in_slot ();
-          void zoom_out_slot ();
-          void invert_scaling_slot ();
-          void full_screen_slot ();
-          void toggle_annotations_slot ();
-          void snap_to_image_slot ();
-		  
-		  void sync_slot();
-
-          void hide_image_slot ();
-          void slice_next_slot ();
-          void slice_previous_slot ();
-          void image_next_slot ();
-          void image_previous_slot ();
-          void image_next_volume_slot ();
-          void image_previous_volume_slot ();
-          void image_goto_volume_slot ();
-          void image_next_volume_group_slot ();
-          void image_goto_volume_group_slot ();
-          void image_previous_volume_group_slot ();
-          void image_reset_slot ();
-          void image_interpolate_slot ();
-          void image_select_slot (QAction* action);
-
-          void reset_view_slot ();
-          void background_colour_slot ();
-
-          void OpenGL_slot ();
-          void about_slot ();
-          void aboutQt_slot ();
-
-          void process_commandline_option_slot ();
-
-
-        private:
-          QPoint mouse_position_, mouse_displacement_;
-          Qt::MouseButtons buttons_;
-          Qt::KeyboardModifiers modifiers_;
-
-          enum MouseAction {
-            NoAction,
-            SetFocus,
-            Contrast,
-            Pan,
-            PanThrough,
-            Tilt,
-            Rotate
-          };
-
-          std::unique_ptr<Mode::Base> mode;
-          GL::Lighting* lighting_;
-          GL::Font font;
-
-          const Qt::KeyboardModifiers FocusModifier, MoveModifier, RotateModifier;
-          MouseAction mouse_action;
-
-          Eigen::Vector3f focal_point, camera_target;
-          Math::Versorf orient;
-          float field_of_view;
-          int anatomical_plane, annotations;
-          ColourMap::Position colourbar_position, tools_colourbar_position;
-          bool snap_to_image_axes_and_voxel;
-
-          float background_colour[3];
-
-          QMenu *image_menu;
-
-          ColourMapButton *colourmap_button;
-
-          QActionGroup *mode_group,
-                       *tool_group,
-                       *image_group,
-                       *mode_action_group,
-                       *plane_group;
-
-          QAction *save_action,
-                  *close_action,
-                  *properties_action,
-
-                  **tool_actions,
-                  *invert_scale_action,
-                  *extra_controls_action,
-                  *snap_to_image_action,
-                  *image_hide_action,
-                  *next_image_action,
-                  *prev_image_action,
-                  *next_image_volume_action,
-                  *prev_image_volume_action,
-                  *goto_image_volume_action,
-                  *next_slice_action,
-                  *prev_slice_action,
-                  *reset_view_action,
-                  *next_image_volume_group_action,
-                  *prev_image_volume_group_action,
-                  *goto_image_volume_group_action,
-                  *image_list_area,
-
-                  *reset_windowing_action,
-                  *axial_action,
-                  *sagittal_action,
-                  *coronal_action,
-
-                  *toggle_annotations_action,
-                  *show_comments_action,
-                  *show_voxel_info_action,
-                  *show_orientation_labels_action,
-                  *show_crosshairs_action,
-                  *show_colourbar_action,
-                  *image_interpolate_action,
-                  *full_screen_action,
-				  
-				  *sync_focus_action,
-
-                  *OpenGL_action,
-                  *about_action,
-                  *aboutQt_action;
-
-          static ColourMap::Position parse_colourmap_position_str (const std::string& position_str);
-
-          void paintGL ();
-          void initGL ();
-          void keyPressEvent (QKeyEvent* event) override;
-          void keyReleaseEvent (QKeyEvent* event) override;
-          void mousePressEventGL (QMouseEvent* event);
-          void mouseMoveEventGL (QMouseEvent* event);
-          void mouseReleaseEventGL (QMouseEvent* event);
-          void wheelEventGL (QWheelEvent* event);
-          bool gestureEventGL (QGestureEvent* event);
-
-          int get_mouse_mode ();
-          void set_cursor ();
-          void set_image_menu ();
-          void set_mode_features ();
-          void set_image_navigation_menu ();
-
-          void closeEvent (QCloseEvent* event) override;
-          void create_tool (QAction* action, bool show);
-
-          void process_commandline_option ();
-
-          template <class Event> void grab_mouse_state (Event* event);
-          template <class Event> void update_mouse_state (Event* event);
-
-          Tool::Base* tool_has_focus;
-
-          vector<double> render_times;
-          double best_FPS, best_FPS_time;
-          bool show_FPS;
-          size_t current_option;
-
-          friend class ImageBase;
-          friend class Mode::Base;
-          friend class Tool::Base;
-          friend class Tool::ODF;
-          friend class Window::GLArea;
-          friend class GrabContext;
-      };
-
-
-      class GrabContext : private Context::Grab { NOMEMALIGN
-        public:
-          GrabContext () : Context::Grab (Window::main->glarea) { }
-      };
-
-
-#ifndef NDEBUG
-# define ASSERT_GL_MRVIEW_CONTEXT_IS_CURRENT ASSERT_GL_CONTEXT_IS_CURRENT (::MR::GUI::MRView::Window::main->glwidget())
-#else
-# define ASSERT_GL_MRVIEW_CONTEXT_IS_CURRENT
-#endif
-
-
-    }
-  }
-}
-
-#endif