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This document contains the fsleyes release history in reverse chronological order.

1.8.2 (Tuesday 22nd August 2023)

Fixed

  • Fixed an issue with loading built-in plugins - the atlas panel (amongst others) was not being loaded (!400).

1.8.1 (Thursday 17th August 2023)

Fixed

  • Filtered some irrelevant warning messages from underlying libraries (!395).

1.8.0 (Wednesday 16th August 2023)

Added

  • New features in the lightbox view, allowing slices to be overlapping, and the order in which slices are displayed to be reversed. These features are available on the command-line via the --sliceOverlap and --reverseSlices flags (!379).
  • FSLeyes plugin libraries can now provide custom layouts (!386).

Changed

  • The _Nudge_ panel now applies scaling parameters such that the centre-of-volume or the current cursor location are preserved. The previous behaviour was such that location (0, 0, 0) was preserved by the scaling parameters (!378).
  • The FEAT cluster panel now remembers which contrast for a FEAT analysis was selected when switching between different analyses (!380).
  • Updated the FSLeyes plugin architecture to use importlib instead of the deprecated pkg_resources. FSLeyes plugin libraries no longer need to have a name beginning with fsleyes-plugin (!385).
  • FSLeyes plugins provided by third-party libraries are now hidden by default, but are shown when a custom layout defined in the library is applied. All plugins can be shown via the --showAllPlugins command-line option (which can be saved as a :ref:`default argument <command_line_default_arguments>` to be permanently applied) (!386).

Fixed

  • Updates to the Jupyter Notebook integration to work with Notebook 7.x (!383).
  • Fixed a transparency issue in the ortho panel (!384).

1.7.0 (Tuesday 13th June 2023)

Added

  • New colour range option (available via the --colourRange command-line option) which can be used on vector overlays when colouring them by a secondary image, to specify the mapping between the voxel intensities and the colour map (!371).
  • New Show slice location option, allowing the location of each slice to be displayed in the lightbox view (!375).

Changed

  • Changed the --initialDisplayRange command-line option to have the same behaviour as the --displayRange option - by default, the values will now be interpreted as raw intensities. Values can be specified as percentiles by appending a % to the high value (!366).
  • Colour map and lookup table files may now have a .txt suffix instead of .cmap / .lut (!368).
  • Colour map interpolation will now be applied to the colour bar shown in the ortho/lightbox/3D views (!368).
  • Changed the behaviour of the Clip by and Modulate by settings for volume overlays - when clipping/modulating by a secondary image, and a negative colour map is in use, the absolute values of the secondary image are now used for clipping/modulation (!370).
  • Changes to the mechanism used to save screenshots/movies, which should make the process more robust (!371).

Fixed

  • Fixed some issues with parsing command line arguments for RGB vector and complex images (!363, !364).
  • Fixed an issue with plotting the MELODIC power spectrum for data with an odd number of timepoints (!365).
  • Fixed an issue when passing a colour map file path to the --negativeCmap option (!368).
  • Fixed an issue related to loading NIfTI qform matrices which arose with nibabel >= 5.1.0 (!369).
  • Fixed an edit mode issue where a drawn line would have gaps in it (!369).
  • Some minor fixes which allow the overlay type of a NIfTI image to be changed whilst it is being edited (!369).
  • Fixed a small issue with volume overlays sometimes not being refreshed (!372).

1.6.1 (Thursday 23rd February 2023)

Changed

  • Internal changes to avoid having to overwrite built-in matplotlib colour maps (!360).

1.6.0 (Tuesday 20th February 2023)

Added

  • Added an outline button to the overlay display toolbar for mask overlays (!342).
  • New --no3DInterp / -ni option, which prevents interpolation from being enabled for volume overlays when a 3D view is opened (!344).
  • FSLeyes will now read "default" command-line arguments from a file called default_arguments.txt, stored in the FSLeyes settings directory (!347).
  • New --numSlices command-line option for use with lightbox views, which is an inverted alias for the --sliceSpacing option (!350).

Changed

  • DICOM directories are now only scanned once, instead of each time they are opened via the Add from DICOM menu option (!345).
  • The --useNegativeCmap / -un option is now automatically enabled when --negativeCmap / -nc is specified (!350).

Fixed

  • Fixed some issues related to shutting down FSLeyes cleanly, which could occasionally result in segmentation faults (!340).
  • Fixed an issue with tractogram overlays not being drawn in some circumstances (!341).
  • Fixed an issue with loading mesh vertex data (!343).
  • Fixed an issue with loading annotations when using fsleyes render (!346).

1.5.0 (Wednesday 31st August 2022)

Added

  • ViewPanel plugin classes can now implement the :meth:`~.ViewPanel.defaultLocation` static method to specify an initial location and size within the FSLeyes frame (!334).
  • New built-in defaultlb and default3d layouts, which respectively open a lightbox or 3D view with standard toolbars and control panels.
  • New --noBrowser / -nbb command-line option, which starts a Jupyter kernel without opening the Notebooks home page; this can be used when you wish to attach a terminal IPython instance to FSLeyes, instead of a Jupyter notebook (!334).

Changed

  • Redesigned the lightbox view to simplify behaviour and interaction (!334).
  • Restored low-performance settings for the ortho and lightbox views (!333).
  • The time series, power spectra and histogram panels now default to displaying data series from all compatible overlays, instead of just the currently selected overlay (!334).

Fixed

  • Fixed several issues related to mesh rendering in the lightbox view (!333).
  • Fixed an issue with the location cursor (and other annotations) not being displayed when running FSLeyes in OpenGL 1.4 compatibility mode on macOS (!334).
  • Fixed a memory leak triggered by the file tree panel (!334).

Removed

  • Removed the --highDpi command-line and interface option - as of wxPython 4.1.0, high DPI scaling should be taken care of automatically (!338).

1.4.6 (Tuesday 14th June 2022)

Fixed

  • Fixed an issue with mesh outlines not appearing in the orthographic view (!331).

1.4.5 (Friday 20th May 2022)

Fixed

  • Added support for the NIFTI_TEMPLATE_XFORM_OTHER code (!329).

1.4.4 (Tuesday 17th May 2022)

Fixed

  • Fixed an issue with removing items from the annotation panel (!327).
  • Fixed an issue with toggling ortho view canvases in VNC/SSH sessions (!327).

1.4.3 (Tuesday 17th May 2022)

Fixed

  • Changed GL initialisation logic so that it is compatible with newer GTK2/GLX versions of wxPython (!324).

1.4.2 (Friday 13th May 2022)

Fixed

  • Make sure atlas images (selected through the atlas panel) are loaded into RAM. This used to be the case, but default behaviour was changed recently in the fsl.data.image and fsl.data.atlases modules (!322).

1.4.1 (Tuesday 3rd May 2022)

Fixed

  • Fixed an issue with 2D tractogram display on macOS (!318).

1.4.0 (Monday 2nd May 2022)

Added

  • FSLeyes is now able to visualise TrackVis .trk and Mrtrix3 .tck tractogram files, containing tractography streamlines (!307, !312).
  • New Invert modulata alpha display setting (available via the --inverModulateAlpha command-line option), which can be used to make regions with high intensity more transparent (!311).
  • New --index command-line option for volume overlays, allowing the indices for all non-spatial dimensions to be specified (!304).
  • New option to display the coordinates for the current location on the canvases of an ortho view (available on the command-line via --showLocation) (!314).
  • New option to control the location cursor width on ortho/lightbox views (available on the command-line via --cursorWidth) (!314).

Changed

  • Improvements to overlay blending, and default volume quality settings, in the 3D view (!309).

Fixed

  • Fixed an issue with loading FIRST subcortical segmentation VTK meshes (!306).
  • Fixed an issue with the --updatecheck commmand line argument (!306).
  • Fixed some bugs in the File tree panel (!315).

Removed

  • The --occlusion command-line option has been rendered obsolete by the improved 3D overlay blending, and so has been removed (along with the corresponding option in the 3D view settings panel).

1.3.3 (Thursday 23rd December 2021)

Fixed

  • Fixed an issue with black screenshot images in some environments (e.g. SSH sessions in mobaxterm) (!301).
  • Removed pyobj-core and pyobjc-framework-cocoa from the list of dependencies (!302).

1.3.2 (Thursday 9th December 2021)

Fixed

  • Fixed an issue with line vector display when running FSLeyes in an environment which doesn't support floating point textures (!299).

1.3.1 (Thursday 2nd December 2021)

Fixed

  • Updated Jupyter notebook integration to work with newer versions of ipykernel (!297).
  • Various small tweaks for Python 3.10 compatibility (!297).

1.3.0 (Monday 18th October 2021)

Added

  • The 3D view now allows the display location to be set to the corresponding location under the mouse on a volume overlay, by shift+clicking (!290).
  • The display range for a volume overlay can now be adjusted interactively by ⌘ + ⇧ + right clicking (⌃ + ⇧ on Linux) and dragging to select a region - the display range will be set to the minimum/maximum voxel intensities within that region (!293).

Changed

  • The Sample along line tool now supports 2D and multi-channel (e.g. RGB) images (currently plotting the mean intensity across channels for the latter).
  • Small improvementsto the File ⇒ Add from XNAT dialog (!291).

Fixed

  • The Display space ⇒ Scaled voxel coordinates setting no longer applies a L/R flip for images with neurological data storage order (!289).
  • The high clipping range is no longer set when loading a Melodic image with the --autoDisplay / -ad option.(!293).

1.2.0 (Monday 13th September 2021)

Added

  • The Display space setting can now be set to Scaled voxel coordinates on ortho and lightbox views. This causes all images to be displayed in scaled voxels, with the origin for each image set to the centre of voxel (0, 0, 0) (!286).

Changed

  • The scale vectors to unit length option for line vector overlays now scales the vector colouring, in addition to lengths (!285).

Fixed

  • Fixed an issue on macOS / Big Sur whereby an image specified on the command-line could be loaded twice (!285).
  • Fixed some rendering issues for images stored as type NIFTI_TYPE_RGB24 (!285).

1.1.0 (Friday 6th August 2021)

Added

  • New --interpolation option for mesh overlays, which allows nearest-neighbour or linear interpolation to be selected when colouring meshes with vertex data. This replaces the --flatShading option (!278).

Changed

  • The Location panel now displays the region label associated with the current vertex for mesh overlays which are being coloured with a lookup table (!278).

Fixed

  • Fixed a bug which was preventing the same colour map or lookup table file to be specified more than once on the command line (!278).
  • Fixed the Check for updates menu item - it now queries conda-forge for the latest available FSLeyes version (!279).
  • Fixed a bug which had broken volume navigation in the time series view (!283).

Deprecated

  • The --flatShading option for mesh overlays is equivalent to using --interpolation nearest (!278).

1.0.15 (Thursday 22nd July 2021)

Fixed

  • Fixed a subtle bug affecting fsleyes render, where taking a screenshot of a large 4D image could result in an infinite loop or segmentation fault (!275).

1.0.14 (Friday 16th July 2021)

Fixed

  • Fixed an issue with image copying, which could cause pixdims to be changed slightly (!270).
  • The x-axis of the power spectrum view can can now show frequencies of ICA power spectra for for MELODIC overlays (!271).

1.0.13 (Tuesday 6th July 2021)

Fixed

  • Fixed a circular import issue, affecting programmatic use of FSLeyes (!268).

1.0.12 (Monday 28th June 2021)

Fixed

  • Fixed an issue with Jupyter Notebook integration on macOS (!266).

1.0.11 (Monday 14th June 2021)

Fixed

  • Fixed a compatibility issue with NoMachine/x2go-like remote environments (!264).

1.0.10 (Wednesday 2nd June 2021)

Fixed

  • Fixed an issue with removing data series from plot views (!262).

1.0.9 (Wednesday 2nd June 2021)

Fixed

  • Fixed an issue with opening the overlay display panel in 3D views (!260).

1.0.8 (Wednesday 26th May 2021)

Changed

  • Gamma correction is no longer disabled when log scaling is active (!256).

Fixed

  • Fixed a problem with API documentation generation (!256, !258).

1.0.7 (Monday 24th May 2021)

Added

  • New logarithmic scaling option (--logScale on the command-line) for volume overlays, which causes voxel intensities to be mapped to the colour map logarithmically, rather than linearly (!254).

1.0.6 (Monday 24th May 2021)

Changed

  • Overlay display options which refer to other overlays (e.g. Clip by) now use the display name of the other overlay, rather than their file base name (!251).
  • Restored compatibiilty with wxPython 4.0.* (!250).

Fixed

  • Fixed a bug related to positioning of line vectors, tensors and FODs for images with non-isotropic voxels (!250).

1.0.5 (Thursday 6th May 2021)

Fixed

  • Fixed some issues with shutting down cleanly (!248).
  • Fixed a bug when saving a layout with plugin-provided view panels (!248).

1.0.4 (Tuesday 4th May 2021)

Changed

  • Improved ortho edit mode performance on large images (!246).
  • Suppressed some warning messages (!246).

Fixed

  • Fixed an issue with the :attr:`.PlotCanvas.limits` becoming out of sync with the matplotlib.Axes limits (!246).
  • The file-tree library is now optional (!246).

1.0.3 (Friday 23rd April 2021)

Fixed

  • Fixed an issue with the management of built-in asset files (e.g. icons, colour maps, etc). Asset files are now located inside the fsleyes package directory (!244).

1.0.2 (Thursday 22nd April 2021)

Fixed

  • Fixed some issues with FSLeyes plugin management (!242).
  • Fixed some issues with GL initialisations on GTK2 versions of wxpython (!242).
  • New --annotations command-line option, allowing annotations to be loaded from a file into an ortho view (!242).

1.0.1 (Tuesday 20th April 2021)

Fixed

  • Fixed compatibility issues with recent versions of matplotlib (!240).

1.0.0 (Monday 19th April 2021)

Added

  • The lighting effect in the 3D view is now applied to volume overlays (OpenGL 2.1 or newer only) (!222).
  • New --lightDistance option (for 3D view), allowing the distance of the light source from the centre of the display bounding box to be set (!222).
  • New --noBlendByIntensity option, for volume overlays in the 3D view, allowing the modulation of samples by voxel intensity to be disabled (!222).
  • New -ixh, -ixv, -iyh, -iyv, -izh, and -izv options, allowing ortho canvases to be inverted vertically or horizontally (!225).
  • New --modulateMode option for rgbvector, linevector, tensor and sh overlays, allowing modulation to be applied to either brightness or transparency (!231).
  • New option to copy/paste 2D selections between slices when editing a NIFTI image (!232).
  • New annotation panel, allowing simple shapes and text to be overlaid on the canvases of an ortho view. Annotations can be saved to/loaded from file, via new options in the Tools menu (!233).
  • New Sample along line tool, allowing data from an image to be sampled along a line and plotted (!235).

Changed

  • Text labels drawn on GL canvases are now created using matplotilb rather than [Free]GLUT (!221).
  • Removed dependence on [Free]GLUT - this means that fsleyes render can now be used on headless systems without using xvfb-run, as long as OSMesa is installed (!221).
  • The --lightPos command-line option (for the 3D view) has been changed to expect three rotation values (in degrees), which specify the position of the light source with respect to the centre of the display bounding box. This can be combined with the new --lightDistance option to specify the position of the light source (!222).
  • FSLeyes no longer ignores the LIBGL_ALWAYS_INDIRECT environment variable (!222).
  • FSLeyes attempts to determine a suitable value for PYOPENGL_PLATFORM if it is not already set (!222).
  • FSLeyes should now work with both Wayland/EGL and X11/GLX builds of wxPython on Linux (!222).
  • The normalisation method used in the power spectrum panel has been adjusted so that, instead of the data being normalised to unit variance before the fourier transform, the fourier-transformed data itself is normalised to the range [-1, 1] (!224).
  • The Show command line for scene option will display a warning if any overlays are not saved (!226).
  • The :class:`.FileTreePanel` has been updated to work with the new file-tree library (!230).
  • Change to the interface for copying/pasting data between images - there is now a single button for copying, pasting, and clearing the clipboard (!232).
  • :class:`.annotations.TextAnnotation` objects can now be positioned in the display coordinate system, in addition to being positioned at pixel locations on a canvas (!232).
  • Changes to the FSLeyes plugin system to ease the development of FSLeyes controls that use custom interaction profiles, and to improve switching between different interaction proflies (!234).
  • The FSLeyes plugin system now supports tools which are bound to a specific view panel (!234).
  • Many built-in FSLeyes control panels and tools have been migrated into the FSLeyes plugin system so that they are dynamically loaded as plugins, rather than being hard-coded (!234).
  • It is now possible to save and re-load view/control panel layouts with plugin-provided views and control panels (!234).

Fixed

  • Various fixes and improvements to the lighting effect on mesh overlays in the 3D view (!222).
  • When opening a melodic_IC.nii.gz file with the --autoDisplay'`/-ad``, option, the melodic_IC file is now selected by default, instead of the mean underlay (!219).
  • Fixed a bug in image texture preparation for complex data types, when running in a limited GL environment (e.g. VNC) (!220).
  • Compatibility fixes for newer versions of Jupyter notebook (!227).
  • Fixed a problem with macOS desktop integration - it should now be possible to open a file with FSLeyes as the default application, and to drag a file onto the FSLeyes.app icon (!228).
  • Improved stability when running under macOS+XQuartz (!229).
  • Fixed an issue with screenshots generated by fsleyes render containing transparent pixels (!233).
  • Fixed a collision between the -mc and -a command-line options for mesh overlays (!233).

0.34.2 (Tuesday 14th July 2020)

Fixed

  • Added support for high-DPI scaling under macOS with wxPython >= 4.1.0 (!217).

0.34.1 (Monday 13th July 2020)

Fixed

  • Fixed an issue with Jupyter Notebook integration on conda+macOS installations (!215).
  • Fixed an issue with the high-DPI option not appearing in the view settings panel under macOS (!215).

0.34.0 (Wednesday 8th July 2020)

Added

  • New option under the Tools menu which allows data from an image overlay to be projected onto a surface overlay (!213).
  • New Flat shading display option when viewing surfaces in 3D (!213).

Changed

  • Tweaked GL initialisation to avoid errors when running via XQuartz (!211).
  • Minor adjustment to Jupyter Notebook integration (!213).
  • NaN values in mesh overlay vertex data are now handled in the same manner as clipped values - previously they would be displayed in the low colour from the selected colour map (!213).

0.33.2 (Tuesday 23rd June 2020)

Added

  • Added some more line styles to the plotting panels (!206).
  • Added a new "accessible" lookup table, courtesy of Paul Tol (https://personal.sron.nl/~pault/) (!206).

Changed

  • Increased the default plotting line width (!206).
  • The default plot colours are now from a pre-generated accessible palette, rather than being randomly generated (!206).
  • The default plot line style is also rotated, in addition the plot colour (!206).
  • Adjusted the histogram panel so that, when plotting a probability histogram, the values are normalised by bin-width (!203).
  • A minor adjustment to the default font, to improve readability on some platforms (!202).

Fixed

  • Fixed an issue with FSLeyes not shutting down cleanly (!204).

0.33.1 (Monday 8th June 2020)

Changed

  • Changed the :func:`.embed` function so that a parent wx object is not required.

0.33.0 (Tuesday 26th May 2020)

Added

  • New modulate alpha option for volume and mesh overlays, which causes opacity to be modulated by voxel/vertex intensity (!193).

Changed

  • The minimum supported Python version is now 3.7, due to reliance upon a recent version of fslpy (!190).
  • The :func:`.embed` function accepts a mkFrame argument, allowing it to be called without creating a :class:`.FSLeyesFrame` (!195).
  • A warning is now displayed in the location panel when images with different orientations, resolutions and/or fields-of-view are being displayed (!198).

Fixed

  • Fixed a bug in the Export data series action, which was causing a crash on macOS (!190).
  • Importing modules from the current directory in the Notebook/shell environments is now possible within standalone versions of FSLeyes (!189).
  • Fixed a small bug in the :func:`.embed` function (!189).
  • Fixed a bug in the Add from XNAT action (!192).
  • Adjusted the Jupyter Notebook integration so it does not rely on the existence of a command called jupyter-notebook (!191).
  • Fixed a couple of bugs in the RGB vector overlay code (!194).
  • Fixed a bug in ortho edit mode (!196).

0.32.3 (Monday 2nd March 2020)

Fixed

  • Fixed a bug which occurred when using 3D mode on platforms with limited OpenGL capabilities.
  • Fixed some minor issues in the file tree panel.

0.32.2 (Friday 21st February 2020)

Fixed

  • The animated GIF changes in 0.32.1 broke movie mode.

0.32.1 (Thursday 20th February 2020)

Changed

  • Any mesh overlay can now be displayed in the Freesurfer mesh coordinate system - not just Freesurfer meshes.
  • Internal changes to avoid using the deprecated nibabel.dataobj_images.DataobjImage.get_data method.

Fixed

  • Fixed a bug which caused mesh display to be corrupted when changing rows in the file tree panel.
  • Added support for high-DPI displays on platforms other than macOS.
  • Fixed a bug in animated GIF generation.
  • Fixed a bug which occurred when editing 4D images.

0.32.0 (Thursday 7th November 2019)

Added

  • New --notebookFile command-line option, which starts the Jupyter notebook server, and opens a specified notebook file.
  • New option to change the location of the Notes column in the file treee panel.
  • New --unitLength option for the RGB vector overlay type, which scales the vector data to unit length.
  • Metadata from JSON sidecar files (e.g. in BIDS data sets) is now displayed in the overlay information panel.

Changed

  • The :func:`.main.embed` function has been changed so that it now works in a synchronous manner, rather than using an asynchronous callback function.
  • The Jupyter notebook server is now configured so that its root directory is the current working directory.
  • Small valued regions are no longer shown in the atlas information panel. They are thresholded according to the lower threshold in the :class:`.AtlasDescription`.

Fixed

  • Fixed a bug in :class:`.MeshOpts` bounds calculation.
  • Fixed a bug in Jupyter notebook integration, where an error in the notebook would stop the kernel from executing any more commands.
  • The Robust FOV and load/export affine transformation options now work with in-memory images.

0.31.2 (Tuesday October 22nd 2019)

Changed

  • FSLeyes is now more lenient towards NIfTI images with extreme qform affines.
  • Various changes to improve GTK3 compatibility.
  • Various changes to reduce warnings and unnecessary output messages.

Fixed

  • Image texture data is now prepared off the main thread; this was the behaviour before version 0.30.0, but was accidentally disabled for that release.

0.31.1 (Tuesday October 8th 2019)

Fixed

  • Fixed a bug in edit mode where the image texture would not get updated correctly in restricted environments (e.g. VNC) with certain image data types.

0.31.0 (Thursday September 10th 2019)

Added

  • New File tree control panel, for viewing data contained in structured directories.
  • New complex overlay type, for displaying images with a complex data type.
  • Support in plot panels for complex images - data from the real, imaginary, magnitude, and/or phase components can be plotted.
  • New plot panel options to invert axes, and to apply scale/offsets.
  • New power spectrum panel options to apply phase correction to complex image data.
  • The atlas panel has basic support for more general "Statistic" atlas types.
  • New File ⇒ New image menu option, a shortcut to create a new empty image.

Changed

  • Images with a complex data type are no longer split into separate real and imaginary volume overlays - they are loaded as a single image, and displayed as complex overlays.
  • The Overlay ⇒ Copy menu option now supports complex and RGB(A) images.
  • The plugin interface for tools has changed slightly - tools provided by FSLeyes plugins are now passed references to the :class:`.OverlayList`, the :class:`.DisplayContext`, and to the main :class:`.FSLeyesFrame`, to their __init__ method.

Fixed

  • Fixed a bug in the :class:`.OverlayGroup` where old display settings were mistakenly being applied to newly added overlays.
  • Fixed a number of minor bugs in the plot panel logic.

0.30.1 (Wednesday 7th August 2019)

Changed

  • The Crop tool can now be used to expand the field-of-view of an image, in addition to cropping an image.
  • The label overlay --lut command-line option will accepts colour map files.

Fixed

  • Added support for editing 2D images.
  • Fixed a bug in the mesh vertex picking logic which would occur when multiple views were open.

0.30.0 (Thursday 27th June 2019)

Added

  • The volume overlay type now has support for NIfTI images of type RGB24 and RGBA32, via a new Channel setting.
  • New RGB(A) overlay type, for displaying the above image types.
  • FSLeyes can now load bitmap images (e.g. .jpg, .png, etc.). When a bitmap file is loaded it is internally converted into a 2D NIfTI image.
  • New alternative main function :func:`fsleyes.filtermain.main`, which filters out useless warnings that originate from underlying libraries (e.g. wx, GTK, Cocoa, etc).
  • New --cliserver option, allowing command-line arguments to be passed to a single FSLeyes instance.

Changed

  • The :mod:`fsleyes.gl.textures` package has been cleaned up and refactored without any attempt to preserve backwards compatibility. Much of the texture data handling code is now shared by the :class:`.Texture2D` and :class:`.Texture3D` classes.
  • The :class:`.NiftiOpts` class has been moved into a separate module.
  • 2D NIfTI images are now displayed with a 2D texture - this means that the maximum dimension size for 2D images is now 16384 on typical hardware.
  • The Freesurfer coordinates coordinate space option is no longer available on non-freesurfer mesh overlays.

0.29.0 (Sunday May 12th 2019)

Added

  • The Tools ⇒ Resample image option now allows an image to be resampled to the space of another image.
  • New -stdb and -std1mmb command-line options for loading brain-extracted versions of the MNI152 templtes.

Fixed

  • Fixed an issue where images with unconventional voxel storage orders were being transformed into the display coordinate system in a slightly inaccurate manner.
  • FIxed an issue with orthographic edit mode being incorrectly disabled when the selected overlay is changed.

0.28.3 (Sunday April 14th 2019)

Fixed

  • More PyOpenGL / read-only numpy array workarounds.

0.28.2 (Sunday April 14th 2019)

Changed

  • The update check option does not verify SSL certificates when downloading the latest version string.

Fixed

  • Fixed an issue with the MIP overlay on macOS.
  • Workarounds for the inability of PyOpenGL to accept read-only numpy arrays.
  • Minimum required fslpy version is now 2.1, so that "compressed" voxelwise EVs (suh as those generated by PNM) are supported.

0.28.1 (Monday April 8th 2019)

Fixed

  • Fixed a bug in drag-and-drop functionality.

0.28.0 (Friday April 5th 2019)

Added

  • Added metadata to allow better integration with Linux desktop environments.
  • Added ability to drag-and-drop files onto the FSLeyes window to open them.
  • The --vertexSet and --vertexData command-line options now cause the last vertex set/data to be selected, and also support GIFTI surface files which contain multiple vertex sets and vertex data.
  • New :meth:`.ControlMixin.defaultLayout` method, which can be overridden by control panels (including plugins) to customise the default panel positioning/layout.

Changed

  • FSLeyes no longer depends on the deprecation library.

Fixed

  • Jupyter Notebook integration has been updated to work with newer versions of the ipykernel library.
  • Fixed bug with initial directory shown in open file dialogs.
  • Fixed a bug which would sometimes cause 4D image data display to be corrupted on macOS.
  • Fixed a bug which was preventing image textures from being updated when non-3D data regions were changed.

Deprecated

0.27.3 (Friday February 8th 2019)

Fixed

  • Fixed initialisation bug on platforms with a non-English language.

0.27.2 (Friday February 8th 2019)

Changed

  • Small display range values are forced to 0 on the colour bar.

0.27.1 (Friday January 18th 2019)

Fixed

  • Updated the render command so it incoporates the recent enhancments to colour bar display.

0.27.0 (Monday December 3rd 2018)

Added

  • Complex image types are now supported - the real and imaginary components are loaded as separate overlays.
  • New Set $FSLDIR menu option, for updating the FSL installation directory.

Changed

  • FSLeyes is no longer tested against Python 2, or wxPython 3.
  • The Tools ⇒ Resample image menu option now supports images with more than three dimensions.
  • Increased range of colour bar tick labels.
  • When the negative colour map is enabled, and the display range minimum is 0.0, only a single central tick label is displayed on the colour bar.

Fixed

  • FSLeyes should fail more gracefully when unrecognised files/directories are specified on the command line.
  • Fixed a bug in the --fullhelp/-fh command line option.

0.26.6 (Monday November 26th 2018)

Fixed

  • Fixed an issue with Zenodo DOI registration.

0.26.5 (Monday November 26th 2018)

Added

  • New option to change the colour bar width/height - this is available in the ortho/lightbox/3D settings panel (the spanner_icon button).
  • The Label size option now adjusts the colour bar font size, in addition to the orientation label font size.

Fixed

  • Fixed a bug in the time series panel when viewing a FEAT analysis with voxelwise confound EVs.
  • Fixed a bug in the FEAT cluster panel when viewing a FEAT analysis which had not used cluster-based thresholding.

0.26.4 (Tuesday October 23rd 2018)

Changed

  • Renamed the File ⇒ Add atlas menu item to Import new atlas.

Removed

  • Test data is not included in the FSLeyes source distribution, as it is too large for PyPi.

0.26.3 (Tuesday October 23rd 2018)

Fixed

  • Fixed a bug in edit mode where the selection overlay would sometimes not be displayed.
  • Fixed a bug in the :class:`.DiagnosticReportAction` (the FSLeyes ⇒ Diagnostic Report menu item).

0.26.2 (Friday October 5th 2018)

Changed

  • Development (test and documentation dependencies) are no longer listed in setup.py - they now need to be installed manually.
  • Removed conda build infrastructure.

0.26.1 (Sunday September 16th 2018)

Changed

  • Reduced user documentation image sizes.

0.26.0 (Sunday September 16th 2018)

Added

  • New :mod:`.plugins` architecture, for adding custom panels and tools to FSLeyes.
  • The render tool has a new --crop option, to auto-crop screenshots.
  • The :attr:`.VolumeOpts.overrideDataRange` is now automatically enabled for images with an extreme data range, on platforms that do not support floating point textures.
  • New brain_colour colour maps provided by MRICron and Cyril Pernet.

Changed

  • User-added and built-in colour map/lookup table names and display order can now be customised by adding a file called order.txt to the FSLeyes user configuration directory.

Fixed

0.25.0 (Tuesday August 28th 2018)

Added

  • New MIP overlay type, for displaying 2D maximum intensity projections (not available over SSH/X11).
  • A new movie mode option to change the canvas refresh regime between synchronised and unsynchronised, as the default synchronised regime does not work in some environments/platforms.
  • New :func:`fsleyes.main.embed` function, allowing a FSLeyes frame to be opened from within an existing application.

0.24.6 (Monday August 6th 2018)

Fixed

  • Fixed a small bug in detection of image/analysis types from command line arguments.
  • Fixed deprecation warning suppression in standalone versions of FSLeyes.

0.24.5 (Wednesday August 1st 2018)

Added

  • New command line flag --notebook/-nb, which starts the Jupyter notebook server automatically.

Changed

  • Overlays loaded from fslpy wrapper functions are now named accordingly.

Fixed

0.24.4 (Thursday July 19th 2018)

Fixed

  • Fixed an error caused when loading a Melodic IC label file containing unrecognised labels.

Changed

  • fslpy wrapper functions now return a value (e.g. if output files are marked for loading) when called from a Jupyter notebook or the FSLeyes python shell.
  • The appnope library is only a dependency on macOS.

0.24.3 (Monday June 11th 2018)

Fixed

  • Further fixes to Jupyter notebook server and kernel management for running within frozen versions of FSLeyes.
  • Fixed a sizing issue in the FSLeyes about dialog.

0.24.2 (Friday June 8th 2018)

Changed

  • Changed the Jupyter notebook server management so it can be easily run within a frozen version of FSLeyes.

0.24.1 (Wednesday June 6th 2018)

Changed

  • Reduced the size of the PyPi source distribution files.

0.24.0 (Tuesday June 5th 2018)

Added

  • Integration with Jupyter Notebook is now available via the File ⇒ Open notebooks menu option.
  • Support for high-resolution (e.g. retina) displays under macOS.
  • fslpy FSL wrapper functions are now available in the Python shell and Jupyter notebooks.
  • A colour bar preview is now shown in the overlay display panel.

Changed

Deprecated

Fixed

  • Regression in handling 3D textures from on-disk image files.

0.23.0 (Friday May 4th 2018)

Added

  • The Nudge tool now allows users to change the centre of rotation.
  • New gamma correction display setting for volume and mesh overlays.
  • New smoothing display setting for 3D volume rendering.
  • New normalise display setting for SH FODs, to normalise individual FODs to voxel size.
  • New fill tool in orthographic edit mode, which allows a bounded region to be filled or selected.

Changed

  • Plot view interaction changed - left click to pan, right click to zoom, and hold down ⌃ (⌘ under macOS) and click for secondary behaviour (e.g. changing the current volume on a time series panel).
  • In edit mode, when a new image is created, it is now selected.

Fixed

  • Freesurfer surface files could not be selectd in macOS open file dialogs.
  • Freesurfer surfaces were causing an error in overlay information panel.
  • Fixed issue where edit mode selection overlay could become out of date when display space was changed.
  • Show/hide button in a plot view's overlay list no longer toggles overlay visibility on other (e.g. ortho) views.
  • Selecting an item in a plot view's overlay list no longer shows/hides its data plot - the eye_icon button needs to be clicked.

Removed

  • Removed all code and resources related to standalone versions of FSLeyes - this is now managed in a separate project.

0.22.6 (Wednesday April 18th 2018)

  • Fixed more libspatialindex issues with macOS standalone builds.

0.22.5 (Tuesday April 17th 2018)

Fixed

  • Fixed an issue with macOS standalone builds (problems with libspatialindex).

0.22.4 (Thursday March 29th 2018)

Fixed

  • Fixed a couple of bugs in FOD rendering.

0.22.3 (Tuesday March 19th 2018)

Added

Deprecated

0.22.2 (Sunday March 18th 2018)

Fixed

  • Fixed an error with the Override data range not being applied correctly.

0.22.1 (Thursday March 15th 2018)

Fixed

  • Fixed an error which was being raised on attempts to add ("hold") a data series to a plot.

0.22.0 (Tuesday March 13th 2018)

Added

  • New Freesurfer lookup table (freesurfercolorlut.lut, provided by Vincent Koppelmans) to replace the incomplete mgh-cma-freesurfer.lut lookup table.
  • FSLeyes can now load and save non-FLIRT affine transformation files.
  • Infrastructure for buildling FSLeyes conda packages.
  • Ortho view keyboard navigation shortcuts now work in edit mode.

Changed

  • The x-axis in a time series view now defaults to showing volumes, rather than being scaled by time. This can be toggled via the Use pixdims option in the time series control panel.
  • MGH images should no longer be displayed as unsaved. When an MGH image is copied/edited and saved, it will be saved as a NIfTI image.
  • Labels in FSLeyes .lut files no longer need to be in ascending order.
  • The FSLeyes settings directory should now be compatible across Python 2 and 3.
  • An error message is now displayed on attempts to load an invalid lookup table file.
  • Adjustments to standalone Linux builds, hopefully fixing libxcb related compatibility issues.

Fixed

  • FSLeyes should now run on macOS systems which have FreeGLUT installed.
  • Fixed a bug where viewing outlines of mask or label overlays would cause a GLXBadRenderRequest error.
  • Fixed a bug where mask overlays were not shown in a lightbox view over a SSH/X11 connection.
  • Fixed a problem with colour maps/luts not being listed in command line help.
  • Fixed a bug with the location panel History tab when running under Python 2.

Deprecated

0.21.1 (Monday February 5th 2018)

  • Adjustments to standalone linux builds, hopefully fixing the module 'wx' has no attribute '__version__' issue.

0.21.0 (Tuesday January 30th 2018)

  • FSLeyes is now able to load Freesurfer surface files, and mgh / mgz images.
  • The vertices of a 3D mesh (VTK, GIFTI, or Freesurfer file) can now be selected in both 3D and ortho views by holding down the shift key. If data is associated with the mesh vertices, it will be shown in the location panel, the time series panel, and the power spectrum panel. This feature is dependent on the presence of the Trimesh library, a new optional dependency.
  • Mesh vertex data is now shown on the histogram panel.
  • It is now possible to associate multiple vertex files with mesh overlays. For Freesurfer/GIFTI surfaces, if other vertex files are found (e.g. pial, white matter, inflated), they will be added as options.
  • Docked FSLeyes control panels can now be minimised by dragging the dock separator.
  • The 3D view now has a toolbar, and standard panels when it is opened.
  • The --version, --help and --fullhelp command line arguments can now be used on systems which do not have a display, and without Xvfb.
  • Initial display range for all volume overlays can now be set as a percentile, via the global --initialDisplayRange command line argument.
  • A small bugfix to 2D mesh outline drawing with weird reference image orientations.
  • Default 3D volume settings have been increased when running in an SSH/X11 environment.
  • Fixed some bugs with mask outline view.

0.20.1 (Friday January 11th 2018)

  • Fixed an issue with label overlays - the outline and width settings defaulted to being synchronised across images.
  • FSLeyes dependencies are now separated into core, optional and development dependencies.
  • Adjustments to standalone build environment.

0.20.0 (Wednesday January 10th 2018)

  • The location panel now has a history section, which contains a list of previously visited locations.
  • Volume display range can now be specified as a percentile on the command line
  • Colour maps and lookup table files can now be specified on the command line.
  • The --vertexData command line argument, for mesh overlays, can be specified multiple times. All vertex data files will be pre-loaded, and the first one will be selected.
  • New options on mask overlays to display the mask outline, and to apply interpolation on the display.
  • The threshold range for mask overlays is now exclusive - now, only values which are within the threshold limits are displayed. Previously, values which were within or equal to the limits were displayed.
  • :class:`.Profile` instances can now notify arbitrary listeners of mouse and keyboard events, instead of only notifying via sub-class methods.

0.19.1 (Wednesday January 3rd 2018)

  • Small fix related to per-view selected overlays.
  • Adjustments to per-view volume linking.

0.19.0 (Wednesday January 3rd 2018)

  • Volumetric DICOM data series can now be loaded into FSLeyes, via the File ⇒ Add from DICOM menu option. The DICOM to NIFTI conversion is performed using Chris Rorden's dcm2niix tool.
  • The selected overlay can now be different in different FSLeyes views.
  • Volume/timepoint properties can now be linked across views independently of other display properties. This is accessible via a new setting Link overlay volume settings in the view settings panel.
  • All new overlays are now linked by default. This is so that the volumes for 4D images will be synchronised by default.
  • Ortho edit mode has a new Invert selection option.
  • Bug fix in time series and histogram panels regarding non-Image overlays (e.g. surfaces).
  • Work around in screenshot logic for a bug in matplotlib (see matplotlib/matplotlib#10084).

0.18.2 (Thursday December 7th 2017)

  • Fixed another bug drawing label overlays - were not being drawn correctly when both image and LUT had low number of labels.

0.18.1 (Wednesday December 6th 2017)

  • Fixed bug in render (introduced by new --selectedOverlay command line option)

0.18.0 (Wednesday December 6th 2017)

0.17.2 (Wednesday November 15th 2017)

  • Fixed API documentation generation

0.17.1 (Monday Novermber 13th 2017)

0.17.0 (Sunday November 12th 2017)

  • Adjustments to the use of GL_LUMINANCE textures - they are now only used as a fallback if there are are absolutely no other options, as they do not display correctly on some more recent GL drivers.
  • Improved the version update notification dialog.
  • Fixed use of the help function in the python shell.
  • The :attr:`.Volume3DOpts.dithering` property, and the --dithering command line option are now deprecated - a suitable dithering level is now automatically determined.
  • Removed some XNAT account credentials which were accidentally hard-coded.

0.16.0 (Tuesday October 31st 2017)

  • Removed the --skipupdatecheck command line option - the default behaviour is now not to check for updates on startup. This can be enabled via the new --updatecheck option.
  • Added the ability to load images from an XNAT server.
  • Application font size can now be set via the --fontSize command line option.
  • 3D volume clipping planes can now be applied as the intersection (default), union or complement of all active clipping planes.
  • Bugfix in CLI generation - --overrideDataRange option does not get generated if data range override is disabled.
  • Display space warning popups/changes are no longer used - instead, a little warning message is shown alongside a button that allows the user to change the display space manually.

0.15.2 (Friday November 24th 2017)

  • A couple of wxPython 3.0.2.0 compatibility bug-fixes (backported from 0.18.0).

0.15.1 (Saturday October 7th 2017)

  • Crop image dialog now has ability to load/save crop parameters
  • New 'resample' tool, allowing an image to be resampled to another resolution.

0.15.0 (Thursday September 21st 2017)

  • Removed NiftiOpts.customXform property. Volume overlays can now be aligned to a reference image by setting the transform property to 'reference'. Volume to reference transformation is now handled by individual NiftiOpts instances, rather than centrally by the DisplayContext.
  • Fix to canvas screenshot save - was always saving to current working directory.
  • Nudge panel now displays a warning if the display space is set such that transform changes would not be seen.
  • Various bug fixes to command line generation - --orientFlip, --fgColour, --displaySpace, and overlay order.
  • Fix to pyinstaller/CentOS7 build.
  • Fix to image display on some VM environments - images were displayed at low contrast due to use of luminance texture.

0.14.2 (Wednesday September 13th 2017)

  • Bugfix to vector image handling, caused by 4D addition in 0.14.1
  • Improvements to performance of histogram panel

0.14.1 (Monday September 11th 2017)

  • Support for images with more than 4 dimensions.
  • Overlay display panel has a 'dimension' spin control for images, allowing the volume value to control different dimensions.

0.14.0 (Thursday August 24th 2017)

  • Display space is no longer a global setting, but can be changed independently on different views.
  • 3D view always displays in world coordinate system
  • Added command line interface for 3D view and overlay settings
  • Changes to command line for setting ortho centr
  • VEST lookup table files are no longer normalised when loaded
  • Canvases now have a foreground colour option, which controls text, cursor, etc.

0.13.1 (Monday August 14th 2017)

  • Movie mode working in 3D
  • Histogram view has ability to calculate histogram from an ROI
  • Fixes to handling of GL canvas/colour bar background colour
  • Screenshots can now be generated from a script/shell
  • Line vector width is now floating point rather than integer

0.13.0 (Thursday August 10th 2017

  • New 3D view, with volume ray-casting and mesh visualisation
  • OpenGL 1.4 ARB shader program parser now allows sub-routines with arbitrarily named parameters
  • Overlay display panel code refactored to make it easier to customise

0.12.4 (Friday July 14th 2017)

  • New 'Tools' menu, intended for things which don't fit anywhere else.
  • Apply/save FLIRT transform, and seed correlation menu options moved to new Tools menu.
  • Time series view has a feature to generate mean time series from a mask
  • New HSV colour map
  • Order of paths in 'recent paths' menu inverted.
  • Fix an issue with py2app command line handling under python 3

0.12.3 (Monday June 12th 2017)

  • Fixes to macOS build

0.12.2 (Monday June 12th 2017)

  • Voxels with a value of NaN are now clipped for volume overlays
  • Bug fixes to melodic classification panel

0.12.1 (Sunday June 11th 2017)

  • Bug fix to histogram auto-bin option for images with no data range
  • Allow Unicode characters in GLSL shader files
  • Changes to FSLeyes build process

0.12.0 (Sunday June 4th 2017)

  • Fixed screenshot under Python 3
  • Changes to FSLeyes assets directory (icons, data files, etc)
  • Changes to FSLeyes build process

0.11.0 (Saturday May 27th 2017)

  • Re-added 'Reset display range' button to toolbar for volume overlays
  • Lightbox panel now defaults to Z axis
  • Fixed icon button centering under OSX
  • Fixes to execution and screenshot generation to work around issues in remote (vnc/x2go) execution environments.
  • FSLeyes settings are now stored in user's home directory on all platforms.
  • Fixes to off-screen orthographic and lightbox rendering
  • Fixes to ortho edit mode 'target image' option
  • Many python 2/3, and wxPython 3/4 compatibility fixes

0.10.1 (Thursday April 20th 2017)

  • First public release as part of FSL 5.0.10
  • Melodic classificaiton panel can now be used with any 4D image, not just melodic_IC images.
  • Bug fix to edit mode - was broken for 4D images
  • Volume clipping range can now be specified as a percentile on the command line