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Changelog

1.2.2

Added

  • Enhancements to cortex.export (#394)
  • Add Blue/Purple/Red/Orange/Green colormap (#395)

Fixed

  • Add more informative error in get_texture if inkscape is not installed (#391)
  • Handle byte encoding with newer Python versions (#397)
  • Allow vertex data to be passed to cortex.segment.cut_surface (#399)
  • Set default imshow interpolation to nearest for composite.add_data (#402)

1.2.1

Added

  • Allow option to perform automatic alignment with Freesurfer's BBR for volumes without distortion correction (5d7d6ca)
  • Add line_lanczos to available mappers (7721253)
  • Use Freesurfer's BBR by default for automatic alignment (#384)

Fixed

  • Parameter names for freesurfer.import_flat (4371b26)
  • Fix left/right location of hemispheres for medial-pivot view (c3b029e)
  • Animation functions in webgl.view (#372)
  • Various fixes to 2D volumes
  • Installation with numpy < 1.2 (#385)
  • String encoding in openctm.pyx (6dc80db)

1.2.0

Added

  • More functionality to import fMRIprep-processed data (#315)
  • Function to rotate flatmaps (f88a)
  • Option to ignore NaNs when averaging across the thickness of cortex (#355)
  • New views for cortex.export.plot_panels and passing of additional kwargs (#361, #362)
  • Specify colorbar location with default positionings for quickflat (#364)
  • Pass custom colors for VolumeRGB (#366)

Fixed

  • Bug with automatic creation of SVGs with ROIs (#340)
  • Python 2/3 compatibilities for svgoverlay (#352)
  • from_freesurfer/to_freesurfer handling of NIFTI images (#354)
  • ROI label display parameters (#356)
  • Improve documentation for install and demo (#359)
  • Inkscape compatibility with newer versions (#365)
  • Use correct contrast for automatic alignment with FreeSurfer's bbregister (39d8)

1.1.1

Fixed

  • Installation fix for PyPi

1.1.0

Added

  • Added function cortex.utils.download_subject to download new subjects for pycortex from web URLs. This function allows users to download FreeSurfer's fsaverage surface, with a flatmap and ROI labels made by Mark Lescroart (#344)
  • Vertex objects have a new method .map() that allows mapping from one surface to another (#334)
  • Add cortex.freesurfer.get_mri_surf2surf_matrix to create a sparse matrix implementing the mri_surf2surf command (#334)
  • Add function to plot and save 3D views and plot panels (#337)
  • Axis object can be passed to quickshow (#325)
  • Help menu for the 3D WebGL viewer can be accessed with a shortcut (#319, #321)
  • New keyboard shortcuts (list)
  • Convenience function to import data preprocessed with fmriprep (#301)
  • Added option to use FreeSurfer's BBR for automatic alignment and function to use Freeview for manual alignment

Fixed

  • Fix DataView2D to allow plotting of 2D datasets with quickflat
  • Fix VertexRGB and VolumeRGB when alpha is not set
  • Allow arbitrary positioning of the colorbar with quickflat
  • Make quickflat more robust to extraneous polygons (#333)
  • Fix mouse behavior when unfold > 0.5 in WebGL viewer (#330)
  • Sub surfaces fixes (#307)
  • Firefox compatibility fixes (#306)
  • Miscellaneous python 3 fixes