The provided Bash scripts are used to convert raw magnetic resonance imaging (Magnetic Resonance Imaging, MRI) data from the Digital Imaging and Communications in Medicine (DICOM) standard format into a Brain Imaging Data Structure (BIDS)-compliant dataset. The scripts convert DICOM files into the Neuroimaging Informatics Technology Initiative (NIfTI) format, which can be used for preprocessing MRI data. In addition to the NIfTI files, the conversion also generates the metadata required by the BIDS standard. Dataset quality and compliance can be checked using a BIDS validator (e.g.,  https://bids-standard.github.io/bids-validator/). The two scripts are adapted for different experimental sessions: script_dcm2nii_S1.sh is used for data from the first session (S1), while script_dcm2nii_S2.sh is used for the second session (S2). The scripts differ in that S2 additionally processes diffusion-weighted imaging (DWI) data. Both scripts were developed as part of my own work with my individual MRI data. If you want to use them on your own data, you may need to adjust the scripts to match your raw data’s naming conventions. For more information, see the ReadMe file.

Description

Title

• DICOM to BIDS NIfTI conversion

Creator or Contributor

• Name

  Cara Oster

  Role

  creator

  ORCID

  https://orcid.org/0009-0009-7133-0705

  Affiliation

  Ruhr University Bochum

  Role

  creator

Resource type

• Software

Keyword

• NIfTI (Neuroimaging Informatics Technology Initiative)
• conversion
• Bash script
• DICOM (Digital Imaging and Communications in Medicine)
• BIDS (Brain Imaging Data Structure)

License

• http://opensource.org/licenses/MIT

Description

• The provided Bash scripts are used to convert raw magnetic resonance imaging (Magnetic Resonance Imaging, MRI) data from the Digital Imaging and Communications in Medicine (DICOM) standard format into a Brain Imaging Data Structure (BIDS)-compliant dataset. The scripts convert DICOM files into the Neuroimaging Informatics Technology Initiative (NIfTI) format, which can be used for preprocessing MRI data. In addition to the NIfTI files, the conversion also generates the metadata required by the BIDS standard. Dataset quality and compliance can be checked using a BIDS validator (e.g., https://bids-standard.github.io/bids-validator/). The two scripts are adapted for different experimental sessions: script_dcm2nii_S1.sh is used for data from the first session (S1), while script_dcm2nii_S2.sh is used for the second session (S2). The scripts differ in that S2 additionally processes diffusion-weighted imaging (DWI) data. Both scripts were developed as part of my own work with my individual MRI data. If you want to use them on your own data, you may need to adjust the scripts to match your raw data’s naming conventions. For more information, see the ReadMe file.

Date

• Published

  2026-01-19

Language

• English

Identifier

• DOI

  10.60517/m326m614j

Funding reference

• Funder name

  European Research Council

  Award number

  101096046

  Award title

  InnerMap

Publisher

Date created

• 19/01/2026

Last modified

• 2026-01-19