Changes in version 1.8.1.900                      

Deprecations

  - readmgz() is deprecated, use read_mgz() instead
  - readmgh() is deprecated, use read_mgh() instead
  - set_fs_subj_dir() is deprecated, use Sys.setenv(SUBJECTS_DIR = path)
    or options(freesurfer.subj_dir = path) instead

Bug Fixes

  - Fix get_fs() returning a vector instead of a string when add_home =
    FALSE, which caused malformed commands
  - Fix mri_mask() argument order: now correctly passes <input> <mask>
    <output> to FreeSurfer

Major Changes

  - Consolidate MNC conversion functions: nii2mnc() and mnc2nii() now in
    single file with shared validation
  - Consolidate trac functions: trac_all() and trac_manual() merged into
    tracker.R
  - Refactor fs_cmd() with improved same-file handling and error
    checking
  - New check_fs_result() for consistent FreeSurfer command result
    validation

CLI Messaging

  - New internal functions fs_abort(), fs_warn(), fs_inform() wrapping
    cli package
  - Substitute warning, stop, message and cat with corresponding cli
    functions for more modern stdout and stderr output

FreeSurfer Environment

  - Add function fs_sitrep() to check, verify and output information on
    FreeSurfer-R communication
  - Refactor get_fs() with new get_fs_* functions for fine-grained
    control of each setting
  - New roxygen2 template for consistent fs_home parameter documentation

Wrapper Function Improvements

  - Improve mri_convert() with better format validation and error
    handling
  - Improve mri_info(), mri_mask(), mri_segment(), mri_watershed() with
    consistent patterns
  - Improve mri_synthstrip() with better parameter handling
  - Improve mris_convert() family and mris_euler_number() with better
    output handling
  - Improve nu_correct() with better MNC file handling
  - Improve stats2table() with better error messages
  - Improve surf_convert() with better output parsing

Read Functions

  - Improve read_annotation(), read_aseg_stats(), read_fs_table() with
    better error handling
  - Improve read_fs_table() with separator auto-detection
  - Improve freesurfer_read3() with better error messages

Other Improvements

  - Simplify management of common parameter information
  - Creates containing folder of tempfiles if necessary
  - Improved handling of running examples with @examplesIf
  - Split single vignette into several smaller vignettes with more
    tutorial-like structure and language
      - Original vignette is saved as "paper.Rmd" and is ignored by R
        build
  - Major test suite expansion: 801 tests with ~96% code coverage
  - Remove duplicate code in utils.R

                        Changes in version 1.8.0                        

  - Adds ... to all functions that call fs_cmd, to allow user control of
    system().

  - Added mri_synthstrip.

                 Changes in version 1.6.10 (2024-05-14)                 

  - Fixes for new neurobase - need new push to CRAN.

                 Changes in version 1.6.8 (2020-12-08)                  

  - Fixing vignette for fslr checking.
  - Fixing examples for Suggests.
  - Added argument for requirement for license for have_fs,

                 Changes in version 1.6.7 (2020-03-30)                  

  - Trying to fix source vs . when using Linux machines.
  - Added checks for FSL in vignette.

                        Changes in version 1.6.6                        

  - Added read_annotation for reading annotation files.

                 Changes in version 1.6.5 (2019-07-18)                  

  - Added some workarounds from the examples for different freesurfer
    versions.
  - Fixed import with download.file

                        Changes in version 1.6.3                        

  - Added mri_deface to the NAMESPACE and capabilities.

                        Changes in version 1.6.0                        

  - Released to CRAN after major changes to the package.

  - Added a NEWS.md file to track changes to the package.