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raw2bids.py

README.md

Format2BIDS

Format2BIDS reorganises raw files from any extension into the Brain Imaging Data Structure. The user specify how the files should be read into a directory. Then the tool scan all the files and move them into the right directories.

Input

A directory containing some files in any extension, with names containing at minimum the information of modality and patient number. A .JSON configuration file explaining how the filenames should be read.

Output

A directory as specified by the BIDS standard.

Example

A directory MyDataset with the following files :

MyDataset/
|
└── adhd_41278_FU12_T1_001.mnc
|
└── adhd_41278_FU24_T1_001.mnc
|
└── adhd_41578_BL00_RSFMRI_001.mnc
|
└── adhd_41578_BL00_RSFMRI_002.mnc

Will be transformed as :

MyDataset/
|
└── sub-41278/
|   |
|   └── anat/
|       |
|       └── adhd_41278_FU12_T1_001.nii
|       |
|       └── adhd_41278_FU24_T1_001.nii
└── sub-41578/
    |
    └── func/
        |
        └── adhd_41578_BL00_RSFMRI_001.nii
        |
        └── adhd_41578_BL00_RSFMRI_002.nii

Install

with pip
with singularity

Introduction

Usage

bids-validator

You can run the https://github.com/bids-standard/bids-validator to check your directory.