Quality Control (qc) - Neuroimage Pipeline

Quality Control¶

CLI flag: --mriqc [individual | group | all]

mriqc_preprocess¶

What it does: Runs MRIQC on a per-subject basis, computing image quality metrics (IQMs) for structural (T1w) and functional (BOLD) scans. Produces an HTML report per subject.

Tool: MRIQC (Singularity)
SLURM profile: heavy_long (64 GB, 24 h) — array job
Script: mriqc_individual.sh
Depends on: recon
Input: {output}/BIDS/
Output: {output}/quality_control/mriqc/sub-{subject}/

Config entry:

tasks:
  mriqc_preprocess:
    container: "mriqc_24.0.2.sif"

mriqc_post¶

What it does: Aggregates all individual MRIQC results into a group-level report with IQM distributions across subjects.

Tool: MRIQC (Singularity)
SLURM profile: light_short (16 GB, 4 h) — single job
Script: mriqc_group.sh
Depends on: mriqc_preprocess
Output: {output}/quality_control/mriqc/

Config entry:

  mriqc_post:
    container: "mriqc_24.0.2.sif"

Usage¶

# Run both individual and group QC
neuropipe run \
  --subjects 001,002,003 \
  --input /data/BIDS \
  --output /data/processed \
  --work /data/work \
  --project my_study \
  --session 01 \
  --mriqc all

# Individual QC only
neuropipe run ... --mriqc individual

# Group report only (individual already done)
neuropipe run ... --mriqc group