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BIDS Input Data Preparation

This guide explains how to prepare your fetal brain MRI data in BIDS (Brain Imaging Data Structure) format for use with Fetpype.

Overview

Fetpype expects input data to follow the BIDS specification for neuroimaging datasets. This standardized format ensures reproducibility, facilitates data sharing, and enables automatic processing pipeline execution.

BIDS Structure

The BIDS structure is as follows:

dataset/
├── dataset_description.json           # Dataset metadata (required)
├── participants.tsv                   # Subject information (required for dHCP)
├── README                             # Dataset description (recommended)
├── CHANGES                            # Version history (recommended)
└── sub-<subject_id>/                  # Subject directories
    └── [ses-<session_id>/]            # Session directories (optional)
        └── anat/                      # Anatomical data directory
            ├── sub-<subject_id>[_ses-<session_id>][_acq-<acquisition>]_run-<run_number>_T2w.nii.gz
            ├── sub-<subject_id>[_ses-<session_id>][_acq-<acquisition>]_run-<run_number>_T2w.nii.gz
            ├── sub-<subject_id>[_ses-<session_id>][_acq-<acquisition>]_run-<run_number>_T2w.nii.gz
            └── ...

Note

More information on the structure of the participants.tsv file needed for the dHCP pipeline is provided on this page.

Naming Conventions

The naming convention for the files is as follows:

sub-<subject_id>[_ses-<session_id>][_acq-<acquisition>]_run-<run_number>_T2w.nii.gz

The following entities are supported:

  • sub-<subject_id>: Subject identifier
  • ses-<session_id>: Session identifier
  • acq-<acquisition>: Acquisition identifier
  • run-<run_number>: Run number

DICOM to BIDS Conversion

There are several tools that can be used to convert DICOM to BIDS. We recommend using dcm2bids. Other options are to use dcm2niix to create the nifti files and then convert the files to BIDS