Useful Links

CUBIC blog



MRC/UCT Medical Imaging Research Unit

Cross-University Brain & Behaviour Initiative

MRC Unit for Anxiety and Stress Disorders


University of Stellenbosch Biomedical Engineering Research Group


Centre for High Performance Computing (CHPC)


iThemba Laboratory for Accelerator Based Sciences



University of Stellenbosch Research Ethics


University of Cape Town Research Ethics


MRI image/data processing software

FBIRN - Biomedical Informatics Research Network. Contains an extensive list of software tools.

Freesurfer - Powerful tools for grey matter volume analysis and visualisation on an unfolded brain surface. Running on the computer cluster at the CHPC.

FSL - Oxford University's comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data. Running on the computer cluster at the CHPC.

BrainVoyager - User-friendly fMRI and DTI analysis package.

Camino - Open source Java DTI analysis package

DTI Studio - DTI analysis tool developed at John's Hopkins University.

TORTOISEDTI - DTI analysis package developed by NIH Pediatric Neuroimaging. The usual tools plus resampling and re-orientation to a common space.

ImageJ - Image processing and analysis in Java

jMRUI - Magnetic Resonance User Interface. Spectroscopy processing.

LCModel - Automatic quantification of in vivo proton MR spectra.


MRIcro - Freeware 3D MRI image viewing and processing

MRIcron - Updated version of MRIcro with less basic image processing but including new features such as reslicing and rendering.

MRIconvert - Excellent tool for converting Dicom images to a variety of formats. Extracts DTI gradient tables.

SPM - University College London MATLAB package for implementing statistical parametric mapping for neuroimaging data.

Trackvis - Athinoula A. Martinos Center for Biomedical Imaging.  Rapid DTI processing and visualisation.

BrainLab - Commercial tool for stereotactic surgical planning. Seamlessly integrates fMRI, DTI and structural MRI.



American Journal of Neuroradiology

American Journal of Roentgenology - AJR

Applied Magnetic Resonance

Clinical Radiology

Concepts in Magnetic Resonance

IEEE Transactions on Medical Imaging 

Journal of Magnetic Resonance

Journal of Magnetic Resonance Imaging 

Medical Image Analysis

Medical Physics

Magnetic Resonance Imaging

Magnetic Resonance in Medicine

NMR in Biomedicine

Magnetic Resonance Materials in Physics, Biology and Medicine





FBIRN - Biomedical Informatics Research Network. MRI quality assurance procedures, best practices references for multi-site studies, and more...

MRI safety - Dr Frank Shellock's MRI safety page

DICOM - Digital Imaging and Communication in Medicine

NIFTI  - Neuroimaging Informatics Technology Initiative




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