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freesurfer 1.9.0

New features

• mri_vol2vol() wraps FreeSurfer’s mri_vol2vol to resample a volume onto another volume’s grid, using either a registration (reg) or the volumes’ headers (regheader = TRUE).
• fs_flag_cmd() is a new helper for flag-based FreeSurfer commands (--flag value), the counterpart to fs_cmd() for positional <input> <output> commands. It assembles the command from a named list of flags and is what mri_vol2vol() is built on.

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

freesurfer 1.8.0

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

freesurfer 1.8.0

• Added mri_synthstrip.

freesurfer 1.6.10

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

freesurfer 1.6.8

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

freesurfer 1.6.7

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

freesurfer 1.6.6

• Added read_annotation for reading annotation files.

freesurfer 1.6.5

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

freesurfer 1.6.3

• Added mri_deface to the NAMESPACE and capabilities.

freesurfer 1.6.0

• Released to CRAN after major changes to the package.

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

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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