MRI Physics, BIDS, DICOM, and data formats

This note outlines some of the basic physics, principles and data aspects of dealing with MRI

General resources for learning about MRI

• Some web-based tutorials
  • http://www.simplyphysics.com/page2_1.html
  • http://mriquestions.com/index.html
  • http://www.mri-physics.net
  • https://www.cis.rit.edu/htbooks/nmr/inside.htm
• A textbook: http://www.mri-physics.net/bin/mri-physics-en-rev1.3.pdf
• MR physics and k-space: Kiruluta & González, Handbook of Clinical Neurology, 2016, MR Imaging: deconstructing timing diagrams and demystifying k-space

Image formats

• Complexities in DICOM to NIFTI conversion: Li et al., Journal of Neuroscience Methods, 2016, The First Step for Neuroimaging Data Analysis: DICOM to NIfTI Conversion
• A conversion tool useful for multiframe fMRI data: https://www.nitrc.org/projects/mricrogl/
  • NB: DCM2niix and Mrtix have different co-ordinates systems, according to some users at MBI. If you are using dcm2niix for the functional data, you should use dcm2niix to converting structural image as well.
• Coordinate transforms in nifty headers: http://gru.stanford.edu/doku.php/mrTools/coordinateTransforms
• Tutorial on dicom to BIDS conversion: https://www.youtube.com/watch?v=pAv9WuyyF3g
• R tool for dicom to BIDS-ready nifti: https://github.com/wulms/bidsconvertr
• A tool for curating BIDS data: Covitz et al., NeuroImage, 2022, Curation of BIDS (CuBIDS): A Workflow and Software Package for Streamlining Reproducible Curation of Large BIDS Datasets
• An overview of BIDS: Poldrack et al., Imaging Neuroscience, 2024, The Past, Present, and Future of the Brain Imaging Data Structure (BIDS)

Misc tools

• Some tools for MRI QC: https://poldracklab.github.io/mriqc/
• Tool for freesurfer QC: https://github.com/raamana/visualqc