BrainVISA Changelog =================== Changes history in BrainVISA ++++++++++++++++++++++++++++ .. image:: _static/images/cort_news.png :align: left +---------------------------------------------------+------------------------------------------------------------+------------------------------------------------------+ | :axon:`Axon changelog ` | :anatomist:`Anatomist changelog ` | :aimsdata:`Aims changelog ` | +---------------------------------------------------+------------------------------------------------------------+------------------------------------------------------+ December 2025, new BrainVISA release: 6.0.0 ------------------------------------------- BrainVisa 6 is now distributed as Conda / Pixi packages, which enable again modularity (you can install a subset of the BrainVisa tools) and inter-operability with other tools (you can install any conda package along with BrainVisa tools). Containerization is still supported however, since this is obviously still useful in some cases. On the functionalities side, changes are not fundamental, but we can cite notably: * ``morphologist-cli`` commandline, allows to run Morphologist easily and scalably. * Morphologist outputs a summary report (PDF, JSON) and QC status at the end of the pipeline execution * morphologist: important bug fixed in sulcal measurements (cortical thickness and opening) after a fold split by the automatic sulci identification * A new snapshot utility process is available in Axon (``brainvisa``), which is a simpler version of the former "SnapBase" tool, which had been removed in 5.1 versions because its maintenance was discontinued. The new process is named "snapbase", as a replacement. * The BIDS files organization for Morphologist has been widely changed, in order to fit more standard BIDS schemas, and fix problems in the earlier version. For this reason, data processed with the 5.x BIDS schema will not be reusable with 6.x. * the DISCO toolbox has finally been made available in the pubic release, thanks to the matlab-compiled code. We do not expect many many users for it, but it is useful for our needs, and at last it is available. * anatomist: Important improvements in windows blocks: block grid elements can be resized, moved and reordered, and windows can be dropped at the desired place. A new empty block can be opened (ctrl+N) and will become a "default block": all new windows will open, by default, in this block. * anatomist: 3 new windows types: Values plots, Stats plots, Info window. * anatomist: The new windows types, plus the profile window, can now display data (timecourses) from both volumes and textured meshes. * anatomist: Change in behavior of palettes with "zero at the center", allowing to have a modifiable low threshold. See the doc... * aims / anatomist: Support for reading various Freesurfer native formats: surfaces (meshes), curvature, annotations, .xfm affine transformation files, .lta affine transformations. * aims / anatomist: Support for MIF (MRTrix volumes) format reading * anatomist: New palette window, smaller, shows only what is useful and pops-up things when needed * anatomist: New control for measurements: allow to draw lines by clicking on 3D objects. The length of the line is displayed. Interestingly, this control may also be used to draw filar polygons meshes. * aims: Referential and axes manipulation in Volume: axes orientation is no longer fixed to LPI orientation but may be queried, and changed. Transformations are updated when axes orientation is changed. * aims: Performance improvements in conversion, copy and assignation of pyaims vector classes. They used to be versy slow, they are now fast. * aims / anatomist: Improvements and optimizations in GLTF IO (gloablly more than 10 times faster). * aims: Complete rework of Transformation classes: N-dimensional transforms are supported, non-linear ones (warp fields as FFD) etc. * aims: The old command ``AimsResample``, obsolete since 5.0 and replaced with ``AimsApplyTransform``, has been removed. * aims, anatomist: Transformation graphs implementation and IO * aims: ``AimsApplyTransform`` has been reworked and based on transformation graphs. It simplifies the way referentials and transformations are addressed, and in many cases also avoid the needs to supply a transformation file when all info is in the objects headers. Transformations from/to disk space is also supported. Output space can be completely specified also. * aims: FFD transformations (vector fields) composition. Transformation chains may also compose FFD fields (they did not, before). AimsComposeTransformation thus now also supports non-linear FFD fields. * many many bug fixes and other more minor things June 2024, new BrainVISA release: 5.1.2 --------------------------------------- Bug-fix and minor imprivements release: * Axon command-line runner (``axon-runprocess``) allows to enable/disable pipeline nodes * More complete support for GLTF 3D scenes format in Anatomist and AIMS libraries * Fixes in ROI/label volume edition, which could involve data loss. * Bugs, crashes, memory leaks fixes March 2023, new BrainVISA release: 5.1.1 ---------------------------------------- Bug-fix and minor imprivements release: * Fixes and improvements under the hood in AIMS / PyAIMS libraries. * Possible crash in sulci deep CNN recognition fixed. * Fixes in Anatomist colormaps tables handling. * Brainvisa switches back to using an older API to display HTML docs because it could cause crashes on old linux systems (even inside a container) January 2023, new BrainVISA release: 5.1.0 ------------------------------------------ * This containerized release is based on an Ubuntu 22.04 system, and compiled for Python 3.10 and Qt 5. This is thus the first official binary release based on Python3 (yes, finally...) * It also ships a copy of SPM12-standalone, preconfigured in Axon (brainvisa) in order to work out-of-the-box without user configuration. * Towards BIDS compatibility: Morphologist (in Axon and Capsul) can now support a new BIDS-compatible ontology. The Freesurfer toolbox also supports a new BIDS-like ontology. * Several significant news in Anatomist, see :anatomist:`Anatomist changelog ` * The image processing libraries (AIMS/PyAIMS) have been cleaned from some obsolete data structure, and improved in several ways. Some old commands (Vip) have also been removed when existing in a newer shape. * Very important performance improvements in Soma-Workflow, the parallel execution tool. * The SnapBase tool, which had not been maintained for years, has been removed. * Morphologist: the CNN sulci recognition could produce (in rare bad cases) both sulcus vertices with disconnected voxels, and adjacent cut vertices with the same label (which was not severe but useless). This has been reworked and fixed. As a consequence, the outputs of CNN sulci recognition are different in 5.1 and 5.0. * Minor improvements, and many fixes in both infrastructure and toolboxes. December 2021, new BrainVISA release: 5.0.4 ------------------------------------------- Bug-fix release: * various fixes in aims, anatomist, axon, capsul... * fixed brainvisa (axon) docs not present in 5.0.3 packages * Fixed use of libjxr in Openslide format support October 2021, new BrainVISA release: 5.0.3 ------------------------------------------ Bug-fix release: * Fixes in Aims libraries (Mesher, AimsRegisterFFDEstimate, AimsTex2Vol) * Minor improvements in aims docs * Fixes in Anatomist: crash in Fusion3D using more than 2 volumes, folds split, CutMesh referentials issue, ... * Detailed doc about palettes and texturing in Anatomist * Fixed processes doc given in axon-runprocess June 2021, new BrainVISA release: 5.0.2 --------------------------------------- Fixes for the following issues: * unable to read Nifti files whose name is shorter than 7 characters. * all commands fail to start with nvidia-container-cli: initialization error: nvml error: driver not loaded. * Spurious 's in BrainVISA process documentations * aimsalgo.resampleBucket() has a bug * Uncatched exceptions that occurs in BrainVISA lead to a crash of the application * Missing includes dependency in Makefiles * Opening Graph file by clicking the "eye" button crashes BrainVISA * cartoFSLmatToTrm.py returns all-NaN transformation matrices March 2021, new BrainVISA release: 5.0.1 ---------------------------------------- * Small improvements and fixes January 2021, new BrainVISA release: 5.0.0 ------------------------------------------ * Brings a new installation method as virtual containers or virtual machines. * Morphologist sulci identification is using a new method (based on deep learning CNNs) * Many smaller improvements and fixes September 2018, BrainVISA bugfix update: version 4.6.1 ------------------------------------------------------ Fixes a number of issues, including the broken Mac package. Most other are relatively small fixes and improvements. * Anatomist: * Allow to put independently several volumes in the same window: a fusion will be created on-the-fly * New little image "math" module The Constellation toolbox has still not been finished for this release. Febuary 2018, new BrainVISA release: version 4.6.0 -------------------------------------------------- * General: * Windows version has been fixed * Windows 64 bits version * Stopped the Fedora-4 32 bits version. All linux builds are in 64 bits. * Anatomist: * Supports object of any dimensionality (not limited to 4D any longer) * Partial support for CIFTI connectivity matrices * New referentials window, rewritten in 3D * Windows snapshots of any dimension, rendered off-screen * Save/reload fusion objects and multiple objects (.aobj format) * Display normals of a mesh * Display vector fields * Many other fixes and smaller improvements * New project: :axon:`Primatologist ` Which is part of the BrainRat project from Mircen BioPicsel lab. * Coming soon * :axon:`Constellation `, the connectivity-based parcellation toolbox for BrainVisa, is still a bit delayed because of recent changes, and to allow us to ship an atlas with it. We hope it will be released soon, before a full new brainvisa release. * Highres-Cortex, :hr_cortex:`See the doc `. As for Constellation the release will be delayed a little bit. * Removed obsolete toolbox Connectomist-1 This toolbox was almost unmaintained for about 10 years. Parts still useful have been integrated in the :aimsusr:`AIMS ` library, and in :axon:`Constellation ` * Notably nothing important in :axon:`Morphologist `... a few minor improvements in :morphouiusr:`morphologist UI ` * For developers: * Ported all libraries to Qt5 or Qt4 * Support for python3 in a subset of projects (noticeably excluding Axon) * Support for C++11 in all C++ libraries, also compiles using LLVM compiler * :capsul:`Capsul ` has notably improved and matured, integration in Axon has also improved (although it is not entirely integrated yet) * New development and build system in Docker containers: :casadistro:`casa-distro project ` Febuary 2016, new BrainVISA release: version 4.5.0 -------------------------------------------------- * Morphologist: * Imporoved meshes. * Additional optional step to skull-strip the brain and use it in a second normalization step, to improve alignment robustness. * A variant of the pipeline is the premise to the future redesigned pipelining system (Capsul): "Morphologist CAPSUL iteration". It should behave the same way, but preparing a large iteration on many subjects should be more efficient and faster. The process produces a workflow, to be run in :soma_workflow:`soma_workflow_gui ` * **Morphologist UI**: a new simplified interface to the Morphologist pipeline. See :morphouiusr:`the documentation ` * Cortical_surface: * New sulcus parameterization, faster, more robust, better properties. * Improved version of the Hip-Hop cortical parameterization process * The MarsAtlas cortical parcellation model has arrived ! * Sulcal pits computation for individual subjects.See in Anatomy section. * The Depth Potential Function (DPF) computation is now included in the Anatomy / tools section * Anatomist: * Supports Wavefront .obj format * Supports NIFTI-2 format * Supports Trackvis .trk format * Can save and reload textured meshes with colormap (as .obj), especially convenient to import/export with other software like Blender. * Shader-based rendering of fibers, with coloring * Major improvements in SurfPaint module * Improvements in transparent objects rendering (possibility to sort polygons) .. raw:: html :file: _static/changelog.html