struc_preproc_part_3.sh — FastSurfer + Output Organisation

Location: BRC_structural_pipeline/scripts/struc_preproc_part_3.sh

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Purpose

Final processing stage that:

1. Optionally runs FastSurfer cortical reconstruction
2. Calls output_organization.sh to move all intermediate outputs into the canonical BRC folder hierarchy
3. Calls Show_version.sh --showdiff=yes to record total pipeline runtime in the log

T2 + FastSurfer

If both --t2=yes and --dofastsurfer=yes are set, the script logs a WARNING stating that T2 data will be ignored by FastSurfer (which currently accepts only T1 input).

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Parameters

Parameter	Type	Description
--dofastsurfer	yes/no	Whether to run FastSurfer
--fastsurferfoldername	String	Subject name for FastSurfer output directory
--starttime	Unix timestamp	Pipeline start time (seconds since epoch); used to compute total runtime
--subid	String	Subject identifier written to the timing log
--processedt1folder	Path	FastSurfer SUBJECTS_DIR
--t2	yes/no	Whether T2 data is present (passed to output_organization.sh)
--rawt1folder	Path	Raw T1 folder (passed to output_organization.sh)
(all other paths)	Path	Complete set of folder paths forwarded to output_organization.sh
--logt1folder	Path	Log file path

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Calls

struc_preproc_part_3.sh
  ├── run_fastsurfer.sh          (only if --dofastsurfer=yes)
  ├── output_organization.sh     (always)
  └── Show_version.sh --showdiff=yes

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FastSurfer Command

run_fastsurfer.sh \
  --t1 <rawT1Folder>/T1_orig.nii.gz \
  --sid <FastSurferFolderName> \
  --sd <processedT1Folder>

The Python module brcpython-img (cluster mode) or brcpython (local mode) is loaded before invoking FastSurfer.