prism

DICOM to NIfTI Conversion and fMRIPrep Pipeline (Pipeline for Reproducible Imaging Standardization and Management).

This repository contains a pipeline for converting DICOM files to NIfTI format using Heudiconv and subsequently processing the NIfTI files with fMRIPrep using Singularity.

Overview

This pipeline consists of two main stages:

1. DICOM to NIfTI Conversion (Heudiconv):
   • Uses Heudiconv (specifically, scripts script1 and script2) to convert DICOM files into NIfTI format.
   • Heudiconv helps organize and rename the converted NIfTI files based on the specified heuristic.
2. fMRIPrep Processing (Singularity):
   • Employs fMRIPrep (via script script6) within a Singularity container to perform preprocessing of the NIfTI files.
   • Singularity ensures a consistent and reproducible environment for fMRIPrep.

Repository Structure

.
├── script1        # Heudiconv script for initial conversion
├── script2        # Heudiconv script for further organization in BIDS
├── script6        # fMRIPrep execution script using Singularity
└── README.md      # This file

Prerequisites

Before running the pipeline, ensure you have the following installed:

• Heudiconv: Install Heudiconv following the instructions on the official documentation.
• Singularity: Install Singularity to run the fMRIPrep container.
• DICOM Files: Place your DICOM files in the appropriate directory.
• Heuristic File: Create a heuristic Python file that defines how to convert and name your DICOM files. This file will be utilized by script2.
• fMRIPrep Singularity Image: Download the fMRIPrep Singularity image.

Usage

1. DICOM to NIfTI Conversion (Heudiconv)

1. Modify Heuristic: Edit script1 and script2 scripts to point to your DICOM directory and your heuristic file.
2. Run scrip1: This script will perform the initial DICOM to NIfTI conversion.
3. Run script2: This script will further organize the converted NIfTI files.

2. fMRIPrep Processing (Singularity)

1. Modify script6: Edit script6 to point to the directory containing your converted NIfTI files, your desired output directory, and the location of your fMRIPrep Singularity image.

2. Run script6:

   This script will execute fMRIPrep within the Singularity container to preprocess your NIfTI files.

Customization

• Heuristic File: The behavior of Heudiconv can be customized by modifying the heuristic Python file. Refer to the Heudiconv documentation for details.
• fMRIPrep Options: The fMRIPrep processing can be customized by modifying the command-line options in script6. Refer to the fMRIPrep documentation for available options.
• Directory Paths: Ensure all directory paths in the scripts are correctly set to match your system.

Notes

• Ensure that you have sufficient disk space for the converted NIfTI files and fMRIPrep output.
• The processing time for fMRIPrep can vary depending on the size of your dataset and the available computing resources.
• For advanced customization of heudiconv, refer to the heudiconv documentation.
• For advanced customization of fmriprep, refer to the fmriprep documentation.