Performs diagnostic checks to verify that system dependencies and environment variables required by ggseg.extra are properly configured.
Usage
setup_sitrep(detail = c("simple", "full"))Arguments
- detail
Character. Level of detail to display:
"simple"(default): Quick pass/fail overview"full": Detailed diagnostics includingfreesurfer::fs_sitrep()
Examples
setup_sitrep()
#> ✖ FreeSurfer not configured
#> ✖ ImageMagick not found
#> ✔ Chrome/Chromium
#> ✖ fsaverage5 not found
#>
#> ── Pipeline options
#> verbose: 1
#> cleanup: TRUE
#> skip_existing: TRUE
#> tolerance: 1
#> smoothness: 5
#> output_dir: /tmp/Rtmp6Us5V5
#>
#> ✖ Missing requirements for atlas creation
#> ℹ Run `setup_sitrep("full")` for details
setup_sitrep("full")
#>
#> ── FreeSurfer Setup Report ──
#>
#> ── FreeSurfer Directory
#> • Unable to detect
#>
#> ── Source script
#> • Unable to detect
#>
#> ── License File
#> • Unable to detect
#>
#> ── Subjects Directory
#> • Unable to detect
#>
#> ── Verbose mode
#> • TRUE
#> ! Determined from: `Default value`
#>
#> ── MNI functionality
#> • Unable to detect
#>
#> ── Output Format
#> • "nii.gz"
#> ! Determined from: `Default value`
#>
#> ── System Information
#> • Operating System: "x86_64-pc-linux-gnu"
#> • R Version: "4.5.3 (2026-03-11)"
#> • Shell: "/bin/bash"
#>
#> ── Testing R and FreeSurfer Communication
#> ✖ FreeSurfer installation not detected
#> • Use `options(freesurfer.home = '/path/to/freesurfer')` to set location
#> ✖ ImageMagick not found
#> ℹ Install from <https://imagemagick.org/script/download.php>
#> ✔ Chrome/Chromium: /usr/bin/google-chrome
#> ✖ fsaverage5 not found
#>
#> ── Pipeline options
#> verbose: 1
#> cleanup: TRUE
#> skip_existing: TRUE
#> tolerance: 1
#> smoothness: 5
#> output_dir: /tmp/Rtmp6Us5V5
#>
#> ℹ Set via `options(ggseg.extra.<name> = value)` or environment variables
#> `GGSEG_EXTRA_<NAME>`
#> ℹ See `vignette("pipeline-configuration")` for details
#>
#> ✖ Missing requirements for atlas creation