Initializing a new dataset starting with non-BIDS data

This guide shows how to initialize a new Nipoppy dataset for a study with source imaging data that consists of DICOM files or non-BIDS NIfTI files.

The first step is to create an empty Nipoppy dataset using the nipoppy init command:

$ nipoppy init --dataset <PATH_TO_NEW_DATASET>

This will create the directory tree and copy an example manifest and an example global configuration file into it.

Attention

It is extremely unlikely that the example manifest accurately represents your dataset, so you will have to generate one yourself.

The default global configuration file also has dataset-specific fields that you will need to replace.

Then the raw imaging data should be added (symlinked/copied/moved) to <DATASET_ROOT>/sourcedata/imaging/pre_reorg and reorganized with nipoppy reorg to prepare it for BIDS conversion. See this guide for more information.