1.2.8

What's Changed

• FIX pass overlay_file arg when creating cutout. by @cchen23 in #496
• FIX update URL of retinotopy dataset by @mvdoc in #499
• ENH allow setting curvature values when starting webgl viewer by @mvdoc in #498
• FIX ensure correct datatype for mri_surf2surf by @mvdoc in #502
• FIX check if shapes exist before setting the labels in the WebGL viewer by @mvdoc in #501
• FIX do not use a default layout selection for multiple volumes by @mvdoc in #503
• FIX Improve masks returned by get_roi_masks and correctly split into left/right hemispheres by @mvdoc in #504
• Add codespell: workflow, config and fix typos it finds by @yarikoptic in #506
• FIX save surf2surf matrix with surface_type in filename by @mvdoc in #510
• FIX do not register colormap if already done by @Matlmr in #512
• MNT specify when to run actions by @mvdoc in #513
• ADD add multiple data at the same time if data is a list by @Matlmr in #514
• ENH,EXA add function to upsample from fsaverageX to fsaverage by @mvdoc in #519
• ENH Add more options for freesurfer's automatic alignment, move code for FSL's automatic alignment by @mvdoc in #528
• FIX,DOC make sure cmap filename ends with png by @mvdoc in #529
• ENH sort subject list and improve repr of transforms by @mvdoc in #530
• DOC Update README.md by @FrancisVila in #527
• FIX,MNT import surfaces generated from volumes with any voxel size by @mvdoc in #531
• FIX allow any character in mask name by @mvdoc in #533

New Contributors

• @Matlmr made their first contribution in #512
• @FrancisVila made their first contribution in #527

Full Changelog: 1.2.7...1.2.8

1.2.7

What's Changed

• MNT use latest ubuntu and more recent actions for publishing to pypi by @mvdoc in #481
• MNT: updated get_data to get_fdata to support latest nibabel (5.0). by @marklescroart in #482
• Removed dependency on 'six' library by @marklescroart in #483
• MNT require cython<3.0 to avoid breaking install by @mvdoc in #491
• EXA make path visible in fix_geodesic_path example by @marklescroart in #487

Full Changelog: 1.2.6...1.2.7

1.2.6

What's Changed

Fixes

• FIX update nibabel deprecated methods by @TomDLT in #457
• FIX Improve robustness of attribute query for JSProxy by @mvdoc in #456
• FIX Correctly handle NaNs in VertexRGB and VolumeRGB by @mvdoc in #458
• FIX add missing params to cortex.export.init by @mvdoc in #460
• FIX force vmin/vmax to 0/1 whenever an array is passed as alpha by @mvdoc in #461
• FIX when shared_range=True, use the alpha that is passed and do not create a Volume from alpha by @ctseng12 in #462
• FIX avoid registering the same colormap twice to matplotlib by @TomDLT in #464
• FIX get_roi_surfs is now py3 compatible and accepts overlay_file by @mvdoc in #467
• FIX git URL for pip install by @kroq-gar78 in #476
• FIX cortex.export.plot_panels correctly shows inflated surfaces for subjects without a flatmap by @mvdoc in #477
• FIX stop using expired deprecation for numpy 1.24 by @TomDLT in #479

Enhancements

• ENH enable loading of pycortex datasets that have old subject names by @marklescroart in #463
• ENH warn non-perceptually-uniform 2D colormap by @TomDLT in #466

Maintenance

• MNT fix typos by @kroq-gar78 in #459
• MNT warn about alpha only if dtype is not uint8 by @mvdoc in #465
• MNT deal with some nibabel deprecation errors by @mvdoc in #471
• MNT bump version to 1.2.6 by @mvdoc in #480

Full Changelog: 1.2.5...1.2.6

1.2.5

What's Changed

Fixes

• FIX: fixed bug in save_3d_views handling custom parameter dicts by @alexhuth in #439
• FIX Webgl racecondition by @alexhuth in #440
• FIX,REF Handle different header length for vox2ras tk by @mvdoc in #442
• FIX attempt to fix random crashes in save_3d_views by @mvdoc in #445
• FIX copy filestore in wheel by @TomDLT in #451
• FIX,DOC exception in get_roi_masks by @mvdoc in #452

New features

• NF new params for a multipanel figure with all views by @mvdoc in #446

Maintenance

• MNT change default fsl-prefix and 2D colormap by @mvdoc in #444
• MNT provide a more informative error if attribute not found in JSProxy by @mvdoc in #450
• MNT update CI badge to github actions by @TomDLT in #453
• MNT version 1.2.5 by @mvdoc in #454

Full Changelog: 1.2.4...1.2.5

1.2.4

What's Changed

• FIX do not show labels for invisible shapes by @mvdoc in #429
• MNT Deal with rgb vs rgba for different blender versions. by @cchen23 in #430
• FIX Check if overlays file exists before unlinking. by @cchen23 in #431
• FIX change location of filestore during the install by @TomDLT in #433
• REF Changed name of cortex.align.fs_manual to cortex.align.manual by @marklescroart in #434
• FIX ignore masked voxels when averaging with nanmean=True by @TomDLT in #436

Full Changelog: 1.2.3...1.2.4

1.2.3a

FIX: GitHub actions pushing to pypi

Full Changelog: 1.2.3...1.2.3a

1.2.3

What's Changed

• FIX BrainData division overrides for Python 3 by @kroq-gar78 in #405
• FIX division by 0 in quickflat.utils.make_flatmap_image when nanmean=True by @mvdoc in #404
• ENH Long-overdue update to Blender 2.8+ by @marklescroart in #406
• ENH added config file specfication of domain name; blank by default by @marklescroart in #407
• FIX Tiny blender bug fix by @marklescroart in #410
• MNT Setup github actions by @mvdoc in #411
• MNT enable actions on PRs by @mvdoc in #412
• FIX add downloaded subjects to the cortex database by @TomDLT in #413
• FIX create intermediate dirs for config file by @mvdoc in #415
• FIX update sources before apt-get installing by @mvdoc in #418
• ENH add option for intermediate image in bbregister by @TomDLT in #417
• FIX keep current sampler when dataview changes by @TomDLT in #420
• Revert "FIX keep current sampler when dataview changes (#420)" by @mvdoc in #421
• FIX keep current sampler when dataview changes - v2 by @TomDLT in #422
• FIX set interpolation and layers only for volumes by @mvdoc in #423
• FIX ensure c-ordering for flatmap image by @mvdoc in #424
• ENH add blend_curvature method to Vertex, Vertex2D, and VertexRGB by @TomDLT in #425
• ENH,FIX add dropout option to make_svg, fix transparency by @mvdoc in #426

New Contributors

• @kroq-gar78 made their first contribution in #405

Full Changelog: 1.2.2...1.2.3

1.2.2

What's Changed

• FIX add more informative error in get_texture if inkscape is not installed by @mvdoc in #391
• NF Add Blue/Purple/Red/Orange/Green colormap by @mvdoc in #395
• ENH Enhancements to cortex.export by @mvdoc in #394
• DEP Use encodebytes instead of encodestring. by @cchen23 in #397
• FIX set default imshow interpolation to nearest for composite.add_data by @mvdoc in #402
• FIX: allow vertex data to be passed to cortex.segment.cut_surface(). … by @marklescroart in #399
• MNT Release version 1.2.2 by @mvdoc in #403

New Contributors

• @cchen23 made their first contribution in #397

Full Changelog: 1.2.1...1.2.2

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)