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 '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

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

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

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

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.

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')

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

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

CRAN release v0.1.0

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