Table of contents:

Converting MRI DICOM data to BIDS format

The raw data from the scanner are in DICOM format. To start working with the MIR data you first need to convert them to NIfTI format and organise them according to the BIDS standard.

Where is your raw data

The raw data that come from the MRI scanner are stored at /mridata/cbu/[your project code]. You can see all your participant scan directories, for example, with a command like this (replace 'MR21002' with your project code):

ls -d /mridata/cbu/*_MR21002/*

/mridata/cbu/CBU210700_MR21002/20211208_143530/
/mridata/cbu/CBU210711_MR21002/20211213_103712/
/mridata/cbu/CBU220006_MR21002/20220106_115411/
/mridata/cbu/CBU220011_MR21002/20220107_125238/
...

The first part of the folder name which follows the project code, is the acquisition date. E.g., the data of the first subject in the example above was acquired on 08/12/2021 ('20211208'). Each subject's folder contains data like this:

ls /mridata/cbu/CBU210700_MR21002/20211208_143530

Series001_64_Channel_Localizer/
Series002_CBU_MPRAGE_64chn/
Series003_bold_mbep2d_3mm_MB2_AP_2_SBRef/
Series004_bold_mbep2d_3mm_MB2_AP_2/
Series005_bold_mbep2d_3mm_MB2_AP_2_SBRef/
Series006_bold_mbep2d_3mm_MB2_AP_2/
Series007_bold_mbep2d_3mm_MB2_AP_2_SBRef/
Series008_bold_mbep2d_3mm_MB2_AP_2/
Series009_bold_mbep2d_3mm_MB2_AP_2_SBRef/
Series010_bold_mbep2d_3mm_MB2_AP_2/
Series011_bold_mbep2d_3mm_MB2_PA_2_SBRef/
Series012_bold_mbep2d_3mm_MB2_PA_2/
Series013_fieldmap_gre_3mm_mb/
Series014_fieldmap_gre_3mm_mb/

Each Series### folder contains DICOM files of the particular scan. The name of the folder is the same as what a radiographer named the scan in the MRI console. Usually, the name is very indicative of what type of scan it is. Ideally, you'd also know yourself what type of scans were acquired for your project. In the example above, we acquired a T1w anatomical/structural scan (MPRAGE), five multi-band functional scans with single-band reference scans for each of them, and two field maps.

.. need to convert .. Several conversion tools exist (see a full list here). We recommend using HeuDiConv.

DICOM to BIDS using HeuDiConv

HeuDiConv is available on our computing system as an Apptainer image /imaging/local/software/singularity_images/heudiconv/heudiconv_latest.sif

Converting DICOM data to BIDS using HeuDiConv involves 3 main steps:

1. Discovering what type of scans there are in your data
2. Creating a heuristics file specifying how to translate the scans into BIDS format
3. Converting the data

Type of scans in your data

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Heuristics

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Example 1

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Example 2

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Converting

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Code examples

code_examples on GitHub