Environment Variables Reference¶
This page provides a complete reference for all environment variables used by the BRC Structural Pipeline.
Required Variables¶
These must be set before running any part of the pipeline:
| Variable | Description | Example |
|---|---|---|
FSLDIR |
FSL installation directory | /usr/local/fsl |
BRC_GLOBAL_SCR |
Path to BRC global utility scripts (log.shlib, etc.) |
/opt/brc/global/scripts |
BRC_SCTRUC_SCR |
Path to structural pipeline scripts/ directory |
/opt/brc/BRC_structural_pipeline/scripts |
BRC_GLOBAL_DIR |
Path to BRC global data directory (templates, configs) | /opt/brc/global |
BRCDIR |
Root BRC directory (Show_version.sh lives here) |
/opt/brc |
Optional Variables¶
| Variable | Default | Description |
|---|---|---|
CLUSTER_MODE |
NO |
Set to YES to submit pipeline stages as cluster jobs |
JOBSUBpath |
— | Path to jobsub binary. Required when CLUSTER_MODE=YES |
FAST_t |
1 |
FSL FAST image type: 1 = T1w, 2 = T2w, 3 = PD |
RUN |
(blank) | Command prefix for execution (blank for local) |
Subject |
— | Subject identifier used to name cluster job IDs |
Conditionally Required Variables¶
These are required only when specific pipeline options are used:
| Variable | Required When | Description |
|---|---|---|
ANTSPATH |
--regtype 3 |
Path to ANTs binaries directory (e.g. /opt/ANTs/bin) |
C3DPATH |
--regtype 3 |
Path to c3d binaries directory (e.g. /opt/c3d/bin) |
Setting Up the Environment¶
A typical setup script might look like:
# FSL
export FSLDIR=/usr/local/fsl
source ${FSLDIR}/etc/fslconf/fsl.sh
# BRC Pipeline
export BRCDIR=/opt/brc
export BRC_GLOBAL_SCR=${BRCDIR}/global/scripts
export BRC_GLOBAL_DIR=${BRCDIR}/global
export BRC_SCTRUC_SCR=${BRCDIR}/BRC_structural_pipeline/scripts
# Optional: ANTs (for --regtype 3)
export ANTSPATH=/opt/ANTs/bin
export C3DPATH=/opt/c3d/bin
# Optional: cluster mode
export CLUSTER_MODE=NO
export FAST_t=1