Script Reference¶

This section provides detailed technical documentation for each script in the BRC Structural Pipeline.

Script Inventory¶

Script	Location	Role
`struc_preproc.sh`	Root	Entry point — argument parsing, directory setup, dispatching
`struc_preproc_part_1.sh`	`scripts/`	Stage 1 dispatcher — T1 and T2 preprocessing
`struc_preproc_part_2.sh`	`scripts/`	Stage 2 — FreeSurfer `recon-all`
`struc_preproc_part_3.sh`	`scripts/`	Stage 3 — FastSurfer + output organisation
`run_T1_preprocessing.sh`	`scripts/`	Core T1 processing (BET, registration, bias, FAST, FIRST)
`run_T2_preprocessing.sh`	`scripts/`	Core T2 processing (co-registration, bias, BIANCA)
`run_T1_sienax.sh`	`scripts/`	Brain volume estimation (SIENAX approach)
`run_T2_bianca.sh`	`scripts/`	White matter lesion detection (BIANCA)
`output_organization.sh`	`scripts/`	Moves outputs to canonical BRC folder hierarchy
`FSL_anat.sh`	`scripts/`	Full FSL anatomical preprocessing (fsl_anat-style)
`run_preprocessing.sh`	`scripts/`	FreeSurfer-based intensity normalisation
`move_rename.sh`	`scripts/`	Legacy output organisation for fsl_anat-based path

Argument Parsing Convention¶

All sub-scripts use a shared getopt1 function for parsing --key=value style arguments:

getopt1()
{
    sopt="$1"
    shift 1
    for fn in $@ ; do
        if [ `echo $fn | grep -- "^${sopt}=" | wc -w` -gt 0 ] ; then
            echo $fn | sed "s/^${sopt}=//"
            return 0
        fi
    done
}

Arguments are passed positionally as --key=value pairs and extracted by name. An unmatched key returns an empty string.