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struc_preproc_part_1.sh — Stage 1 Dispatcher

Location: BRC_structural_pipeline/scripts/struc_preproc_part_1.sh

Purpose

Thin dispatcher script for processing Stage 1. Receives the full set of folder paths and processing flags from struc_preproc.sh and invokes:

  1. run_T1_preprocessing.sh — core T1 processing
  2. run_T2_preprocessing.sh — core T2 processing (only if --t2=yes)

T2 preprocessing runs after T1 preprocessing completes because it depends on T1 outputs (brain mask, bias field, registration transforms).

Parameters

Parameter Type Description
--tempt1folder Path T1 temporary working directory
--rawt1folder Path Directory containing T1_orig.nii.gz
--dosubseg yes/no Whether to run FSL FIRST subcortical segmentation
--dotissueseg yes/no Whether to run FSL FAST tissue segmentation
--docrop yes/no Whether to crop the field of view
--dodefacing yes/no Whether to apply de-facing
--fastt1folder Path FAST output temporary directory
--firstt1folder Path FIRST output directory
--sienaxt1folder Path SIENAX permanent output folder
--biancatempfolder Path BIANCA temporary working directory
--regtempt1folder Path T1 registration temporary folder
--t2 yes/no Whether a T2 image is present
--tempt2folder Path T2 temporary working directory
--rawt2folder Path Directory containing T2_orig.nii.gz
--regtempt2folder Path T2 registration temporary folder
--sienaxtempfolder Path SIENAX temporary working directory
--t2lesionpath Path Path to the T2 lesion mask (may be empty)
--fbet Float BET fractional intensity threshold
--regtype 1/2/3 Registration strategy
--logt1folder Path Log file path

Calls

struc_preproc_part_1.sh
  ├── run_T1_preprocessing.sh   (always)
  └── run_T2_preprocessing.sh   (only if --t2=yes)