Process Data¶

This guide walks through a complete DCEPrep run from start to finish using Docker.

Prerequisites¶

Docker installed and running (see Installation)
MATLAB and FreeSurfer license files available
BIDS-organized data (see BIDS Data Setup)

Step 1 — Point to your data¶

Edit run_docker.sh line 24 to point to your BIDS rawdata directory:

DATA_DIR="/path/to/your/bids/rawdata"

Step 2 — Launch the container¶

./run_docker.sh

The container starts with DCEPrep's working directory as the current directory and your data directory mounted inside.

Step 3 — Run preprocessing¶

./preprocess_all.sh -d /data/rawdata -b -Z -m

Flag	What it does
`-d /data/rawdata`	Path to your BIDS rawdata folder (required)
`-b`	Bias field correction
`-Z`	Z-axis slice normalization
`-m`	Head motion correction

For a first run on new data, add -c to start with a clean derivatives folder:

./preprocess_all.sh -d /data/rawdata -b -Z -m -c

Step 4 — Run analysis¶

./DCE_all.sh -d /data/rawdata -s

Flag	What it does
`-d /data/rawdata`	Path to your BIDS rawdata folder (required)
`-s`	Skip cases whose Ktrans maps already exist

Add -f to enable FreeSurfer white matter parcellation for subregion analysis:

./DCE_all.sh -d /data/rawdata -s -f

Step 5 — Review outputs¶

After the analysis completes, find your reports in each subject/session's derivatives folder:

derivatives/
└── sub-01/
    └── ses-01/
        ├── case_report.html       # Per-case QC report
        ├── dce/
        │   ├── sub-01_ses-01_Ktrans.nii
        │   └── sub-01_ses-01_vp.nii
        └── anat/
            └── sub-01_ses-01_space-DCEref_T1map.nii

A population_report.html is generated at the top of the derivatives tree once all cases finish.

Common first-run example¶

This is a typical first run with all major corrections enabled and comparison mode to keep outputs labeled:

# Preprocess with bias correction, z-normalization, and auto AIF
./preprocess_all.sh -d /data/rawdata -b -c -Z -A -C fullPrep

# Analyze with FreeSurfer parcellation, skipping already-processed cases
./DCE_all.sh -d /data/rawdata -s -f -C fullPrep