Useful Links

CUBIC blog

The CUBE

Collaborators

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

Ethics
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.
MATLAB
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.

Journals
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
Radiology
Radiographics

Miscellaneous
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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