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.
