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freesurferformats Changes
=========================
Version 0.1.17
-------------------------
- Introduce 'default_label_name' parameter to read.fs.annot, better doc string for the same function.
- Add function fs.surface.to.tmesh3d to transform an fs.surface mesh datastructure into an RGL tmesh datastructure. This method does not require rgl.
- Replace all 'donttest' in examples with 'dontrun' so CRAN does not run them.
Version 0.1.16
-------------------
- Add experimental support for reading and writing Brainvoyager SMP files in format versions 4 and 5
- Add and export vertexdists.to.point function
- Allow MGH reading function to work with broken MGH files that contain no valid RAS header values but still claim so by setting the ras_valid flag in the header to 1
- Add some new example usage scripts in the GitHub repository
- Fix bug #25
- Add 2 extra params to read.fs.surface.asc to make it more flexible
Version 0.1.15
--------------
- disable all unit tests that require downloaded data on CRAN
- add Euclidean distance util functions for surface vertices, like vertexdists.to.point and closest.vert.to.point
- add doapply.transform.mtx function (it's just matrix multiplication with some input checks that are annoying to repeat)
Version 0.1.14
--------------
- support reading the MRtrix TCK format (in function read.dti.tck) and
- support reading the TRK format used by the Diffusion Toolkit and TrackVis in (function read.dti.trk).
- delete test data after unit tests have been run if (and only if) running on CRAN
Version 0.1.13
--------------
- support reading and writing Wavefront object files with non-standard vertex colors
- support reading NIFTI v1 files with FreeSurfer hack through our own, new NIFTI v1 reader. See read.nifti1.header() and read.nifti1.data() functions.
- support reading NIFTI v2 files through our own, new NIFTI v2 reader. See read.nifti2.header() and read.nifti2.data() functions.
- support writing NIFTI v1 files, see write.nifti1() ni1header.for.data() functions.
- support writing NIFTI v2 files, see write.nifti2() ni2header.for.data() functions.
- add function to check whether a file is in NIFTI v1 or NIFTI v2 format, see nifti.file.version() function.
- the read.fs.morph() function can now handle morphometry data files in NIFTI v1 format, including files with the FreeSurfer hack.
Version 0.1.12
--------------
- add support for reading meshes in GEO format
- add support for reading meshes in TRI format (also known as ICO mesh format)
- add support for reading meshes in OFF format, the Object File Format
- add support for reading meshes in OBJ format, the Wavefront object format
- add support for writing FreeSurfer patch files in the ASCII format version
- add support for reading and writing meshes in Brainvoyager SRF format
- add support for reading and writing morphometry data maps in Brainvoyager SMP format
- add many unit tests and test files, use covr
- deprecate (imo) useless parameter 'empty_label_name' to read.fs.annot. using it will show a deprecation notice. (Please open issue if you feel you need it.)
- add experimental support for CIFTI v2 morphometry data files (.dscalar.nii), based on the 'cifti' package by J. Muschelli
- add support for reading transformation matrices from files in LTA and register.dat formats
Version 0.1.11
--------------
- export readable.files function
- support reading and writing meshes in mz3 format
- support writing PLY2 ASCII mesh format
- support reading mesh in BYU format
- support automatic conversion of quadrangular BYU meshes to triangular upon import
- add support for reading GIFTI format labels
- add support for reading GIFTI format annotations
- add support for writing GIFTI format labels
- add support for writing GIFTI format annotations
- export rotate2D and flip2D to namespace
- add support for reading transformation matrices from xfm files: read.fs.transform
- rename all optional data functions: replace optional_data with opt_data in function names to prevent clash with fsbrain names
Version 0.1.10
--------------
- read.fs.label improvement: do not increment indices for volume labels, better print support for them
- support exporting surface meshes in Stanford triangle format (.ply)
- support reading surface meshes in Stanford triangle format (.ply)
- support exporting surface meshes in Wavefront object format (.obj)
- support exporting surface meshes in Object File Format (.off)
- support reading surface meshes in PLY format, including Blender exports with vertex colors and normals
- add general GIFTI writer (requires xml2)
- add support for writing surfaces in GIFTI format
- add read.fs.volume() function that support MGH, MGZ and NIFTI formats
- add experimental support for reading NIFTI volumes as fs.volume instances (via oro.nifti package), including header computation
Version 0.1.9
-------------
- Add support for reading brain surface meshes in VTK ASCII file format
- Add support for writing brain surface meshes in VTK ASCII file format
- Add 'format' parameter to write.fs.surface, the function can now derive the format from the filename like similar functions
- Add support for reading morph data from text files with one numeric value per line (.txt format)
- Minor improvements to the vignette
Version 0.1.8
-------------
- Add support for reading surfaces in FreeSurfer ASCII surface format (integrated into read.fs.surface)
- Add high-level functions 'read_nisurface' and 'read_nisurfacefile' to read surface files in different formats
- Add support for writing surfaces in FreeSurfer ASCII surface format: 'write.fs.surface.asc'
- Turn return value data structure of read.fs.mgh into 'fs.volume' class and implement 'print' and 'is' S3 methods
- Support reading the ASCII version of FreeSurfer curv format files (integrated into read.fs.curv)
- Support reading the FreeSurfer weight or 'w' format files (read.fs.weight), both ASCII and binary subtypes are supported
- Add support for reading binary patch files
- Add support for reading ASCII patch files
- Fix skipping header bytes while reading mgz files (issue #10)
- Read fov MR acquisition parameter from MGH header, make mr_params parameter of write.fs.mgh length 5 from 4
- Compute dof and various other header fields from MGH header data, add new functions to derive matrices
- Add a third vignette that explains how to compute the MGH header data
Version 0.1.7
-------------
- Fix input data check in write.fs.mgh
- Turn return value data structure of read.fs.annot into 'fs.annot' class and implement 'print' and 'is' S3 methods
- Turn return value data structure of read.fs.label into 'fs.label' class and implement 'print' and 'is' S3 methods
- Support 'fs.label' instances as parameter for 'write.fs.label'
- Turn return value data structure of read.fs.surface into 'fs.surface' class and implement 'print' and 'is' S3 methods
Version 0.1.6
-------------
- Add support for reading color lookup table (LUT) files, like FREESURFER_HOME/FreeSurferColorLUT.txt: read.fs.colortable
- Add support for writing LUTs: write.fs.colortable
- Add support for extracting a LUT from an annotation: colortable.from.annot
- Add support for writing annotations: write.fs.annot
Version 0.1.5
-------------
- Add function write.fs.label() to write label files
- Docs: Remove commas from parameter names in doc strings
- Infrastructure: Add DOI generation for github releases via zenodo.org
Version 0.1.4
--------------
- Docs: link related via families, so they show up in the 'see also' section
- Fix errors in indexing example of the vignette (PR #7, thanks @AndrewLawrence)
- Fix bug in reading faces of surfaces (bug #8, thanks @AndrewLawrence)
Version 0.1.3
--------------
- Add support for reading label files (like subject/label/lh.cortex.label)
- Add example label file
- Add support for reading annotation files in old format (like fsaverage annot file 'aparc.a2005s.annot')
Version 0.1.2
---------------
- Add support for reading and writing surface files
- Hide internal header data in return value of read.fs.mgh
- Add example surface file
- Export functions to determine morph file format from file name and vice versa
Version 0.1.1
------------------
- Extended read.fs.mgh to support reading MGH header and allow squashing of empty dimensions
- Added function to read annotation files: read.fs.annot
- Added convenience function to read morphometry data (curv, MGH or MGZ): read.fs.morph
- Added function to write mgh and mgz files: write.fs.mgh
- Added function to write curv files: write.fs.curv
- Added convenience function to write morphometry data (curv, MGH or MGZ): write.fs.morph
- Extend vignette
Version 0.1
-------------
- Added functions to read files in MGH, MGZ and curv formats: read.fs.mgh and read.fs.curv
- Added vignette
- Added unit tests