External Dependencies¶
Target Audience
System administrators and TRE operators installing the pipeline.
The pipeline requires several external tools to be installed and accessible on the system PATH. This page lists each dependency, what it is used for, and which pipeline flags require it.
Required for All Runs¶
| Tool | Environment Variable | Used For |
|---|---|---|
| FSL | FSLDIR |
BET, FAST, FLIRT, FNIRT, FIRST, BIANCA, SIENAX, image maths |
| BRC Global Scripts | BRC_GLOBAL_SCR |
Logging (log.shlib), version tracking (Show_version.sh) |
| BRC Pipeline Scripts | BRC_SCTRUC_SCR |
All structural sub-scripts |
| BRC Global Data | BRC_GLOBAL_DIR |
Templates (MNI masks, facemask, FNIRT config), BIANCA classifier |
Conditionally Required¶
| Tool | Required When | Environment Variable |
|---|---|---|
FreeSurfer (recon-all, mri_convert) |
--freesurfer flag is set |
Must be on PATH |
FastSurfer (run_fastsurfer.sh) |
--fastsurfer flag is set |
Must be on PATH |
ANTs (antsRegistrationSyN.sh, antsApplyTransforms) |
--regtype 3 |
ANTSPATH |
c3d (c3d_affine_tool) |
--regtype 3 (ITK→FSL transform conversion) |
C3DPATH |
| jobsub | CLUSTER_MODE=YES |
JOBSUBpath |
Environment Variables Reference¶
| Variable | Required | Description |
|---|---|---|
FSLDIR |
Always | FSL installation directory (e.g. /usr/local/fsl) |
BRC_GLOBAL_SCR |
Always | Path to BRC global utility scripts |
BRC_SCTRUC_SCR |
Always | Path to structural pipeline scripts/ directory |
BRC_GLOBAL_DIR |
Always | Path to BRC global data (templates, configs, BIANCA classifier) |
BRCDIR |
Always | Root BRC directory (contains Show_version.sh) |
CLUSTER_MODE |
Optional | Set to YES to submit jobs to a cluster scheduler |
JOBSUBpath |
When CLUSTER_MODE=YES |
Path to jobsub binary |
FAST_t |
Optional | FSL FAST image type flag — 1 (T1w), 2 (T2w), 3 (PD). Default: 1 |
ANTSPATH |
When --regtype 3 |
Path to ANTs binaries directory |
C3DPATH |
When --regtype 3 |
Path to c3d binaries directory |
RUN |
Optional | Command prefix for execution (leave blank for local runs) |
Subject |
Cluster mode | Subject identifier used to name cluster job IDs |
BRC Templates¶
The BRC_GLOBAL_DIR must contain the following files used during processing:
| Template File | Used In | Purpose |
|---|---|---|
templates/MNI152_T1_1mm_brain_mask_dil_GD7 |
FNIRT | Dilated MNI brain mask for FNIRT reference masking |
templates/MNI152_T1_1mm_BigFoV_facemask |
Defacing | Face region mask in MNI space |
templates/MNI_to_MNI_BigFoV_facemask.mat |
Defacing | Affine from MNI to BigFOV facemask space |
templates/bianca_class_data |
BIANCA | Pre-trained k-NN classifier for lesion detection |
config/bb_fnirt.cnf |
FNIRT | FNIRT configuration file |