pennsieve-ieeg-recon

This application performs iEEG reconstruction using pre-implant MRI, post-implant CT, and electrode coordinates.

Environment Variables

The application uses two key environment variables:

• INPUT_DIR: Directory containing input files (default: /data/input)
• OUTPUT_DIR: Directory for output files (default: /data/output)

Usage Examples

Pull the Container

First, pull the container from Docker Hub:

docker pull nishantsinha89/ieeg_recon:latest

Basic Usage (Using Environment Variables)

Mount your data directories and run with default file names:

docker run -v "/path/to/your/data:/data/input" \
  -v "/path/to/your/output:/data/output" \
  nishantsinha89/ieeg_recon:latest \
  --t1 "/data/input/T1.nii.gz" \
  --ct "/data/input/CT.nii.gz" \
  --elec "/data/input/electrodes.txt" \
  --output-dir "/data/output" \
  --modules "1,2,3,4" \
  --qa-viewer niplot \
  --reg-type gc_noCTthereshold

Expected file structure in INPUT_DIR (/data/input):

/data/input/
├── T1.nii.gz                    # Pre-implant MRI
├── CT.nii.gz                    # Post-implant CT  
└── electrodes.txt               # Electrode coordinates

Advanced Usage (Using Demo Data)

Run with the included demo data for testing and learning:

docker run -v "$(pwd)/demodata/input:/data/input" \
  -v "$(pwd)/demodata/output:/data/output" \
  nishantsinha89/ieeg_recon:latest \
  --t1 "/data/input/T1.nii.gz" \
  --ct "/data/input/CT.nii.gz" \
  --elec "/data/input/electrodes.txt" \
  --freesurfer-dir "/data/input/freesurfer" \
  --output-dir "/data/output" \
  --skip-existing \
  --modules "1,2,3,4" \
  --qa-viewer niplot \
  --reg-type gc_noCTthereshold

Demo data structure:

demodata/input/
├── T1.nii.gz                    # Demo pre-implant MRI
├── CT.nii.gz                    # Demo post-implant CT  
├── electrodes.txt               # Demo electrode coordinates
└── freesurfer/                  # Demo FreeSurfer directory

Minimal Usage (Required Arguments Only)

Run with only the required arguments:

docker run -v "/your/data:/data/input" \
  -v "/your/output:/data/output" \
  nishantsinha89/ieeg_recon:latest \
  --t1 "/data/input/T1.nii.gz" \
  --ct "/data/input/CT.nii.gz" \
  --elec "/data/input/electrodes.txt" \
  --output-dir "/data/output" \
  --modules "1,2,3,4"

Interactive Mode

Run the container interactively to explore and debug:

docker run -it --entrypoint bash \
  -v "/your/data:/data/input" \
  -v "/your/output:/data/output" \
  nishantsinha89/ieeg_recon:latest

File Naming Conventions

When using environment variables, the application expects these default file names in INPUT_DIR:

File Type	Default Name	Description
T1 MRI	T1.nii.gz	Pre-implant structural MRI
CT	CT.nii.gz	Post-implant CT scan
Electrodes	electrodes.txt	Electrode coordinates (space-separated)

Output Structure

All outputs are written to OUTPUT_DIR with this structure:

OUTPUT_DIR/
└── ieeg_recon/
    ├── module1/          # Electrode coordinates in CT space
    ├── module2/          # Registration and electrode spheres
    ├── module3/          # Brain region mapping
    └── module4/          # MNI space transformation

Command Line Options

Option	Description	Required	Default
--t1	T1 MRI file path	Yes	None
--ct	CT file path	Yes	None
--elec	Electrode file path	Yes	None
--output-dir	Output directory	Yes	None
--freesurfer-dir	FreeSurfer directory path	No	None
--env-path	Environment file path	No	.env
--modules	Modules to run	No	"1,2,3,4"
--qa-viewer	Quality assurance viewer	No	"niplot"
--reg-type	Registration type	No	"gc_noCTthereshold"
--skip-existing	Skip if output exists	No	False
--save-channels	Save individual channels	No	False

Note: The --t1, --ct, --elec, and --output-dir arguments are required and must be specified for the application to run.