freesurferformats - v0.1.18 -- Minor updates for CRAN

v0.1.18

• Change some minor docstring issues in internal functions (requested by CRAN team)

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Published by dfsp-spirit over 2 years ago

freesurferformats - Mostly CRAN fixes

Version 0.1.17

• Introduce 'defaultlabelname' 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.

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Published by dfsp-spirit over 4 years ago

freesurferformats - Small fixes and improvements, support Palm output files

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. Allows to work with files written by palm.
• 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

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Published by dfsp-spirit over 4 years ago

freesurferformats - CRAN maintenance and some new helper functions

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)

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Published by dfsp-spirit about 5 years ago

freesurferformats - DTI track format support: TCK and TRK

This release adds support for 2 different Diffusion Tensor Imaging file formats: * the MRtrix TCK format (in function read.dti.tck) and * the trk format used by the Diffusion Toolkit and TrackVis in (function read.dti.trk).

I would have waited longer, but a release was needed for technical reasons related to CRAN.

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Published by dfsp-spirit over 5 years ago

freesurferformats - The Nifti Release

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() and ni1header.for.data() functions.
• support writing NIFTI v2 files, see write.nifti2() and 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.
• the read.fs.morph() function can now handle morphometry data files in NIFTI v2 format.

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Published by dfsp-spirit almost 6 years ago

freesurferformats - More mesh formats, Brainvoyager support, transforms

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 'emptylabelname' 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

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Published by dfsp-spirit almost 6 years ago

freesurferformats - Transforms, more mesh formats and better GIFTI support

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 optionaldata with optdata in function names to prevent clash with fsbrain names

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Published by dfsp-spirit about 6 years ago

freesurferformats - NIFTI, GIFTI, mesh exports!

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

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Published by dfsp-spirit about 6 years ago

freesurferformats - More surface formats

• Add support for reading and writing VTK meshes
• support a simple txt morphometry data format

see CHANGES file for more details

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Published by dfsp-spirit about 6 years ago

freesurferformats - More file formats and improved MGH header support

• Add support for reading surfaces in FreeSurfer ASCII surface format (integrated into read.fs.surface)
• Add high-level functions 'readnisurface' and 'readnisurfacefile' 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

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Published by dfsp-spirit over 6 years ago

freesurferformats - The S3 release

• 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

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Published by dfsp-spirit over 6 years ago

freesurferformats - Write annotations, colorLUT support

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

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Published by dfsp-spirit over 6 years ago

freesurferformats - Write labels

Changes for this release:

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

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Published by dfsp-spirit over 6 years ago

freesurferformats - Bugfixes for surface loading

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)

This release fixes a bug in the read.fs.surface function that lead to incorrect loading of the faces. The vertex indices where loaded column-major order, which resulted in broken neighborhood definitions. This has been fixed in this release and unit tests were added to prevent regression.

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Published by dfsp-spirit over 6 years ago

freesurferformats - Old annotations and new labels

changes for 0.1.3:

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')

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Published by dfsp-spirit over 6 years ago

freesurferformats - Version 0.1.2: Read surface files

Version 0.1.2

• Add support for reading and writing surface files
• Hide internal header data in return value of read.fs.mgh
• Export functions to determine morph file format from file name and vice versa

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Published by dfsp-spirit almost 7 years ago

freesurferformats - CRAN release v0.1.1

Changes for 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

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Published by dfsp-spirit almost 7 years ago

freesurferformats - CRAN release v0.1.0

First release on CRAN. Includes functions to read MGH,MGZ and curv format files.

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Published by dfsp-spirit almost 7 years ago