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.

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

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

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

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

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

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

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

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

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