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Our topics page describes some of the techniques we use to tackle brain function. In addition to using tools developed by other companies and groups, we also are actively developing our own tools. Here we describe some of our popular and recent solutions that may help other cognitive neuroscience teams. All tools are provided as open source (BSD license).

  • MRIcro is a simple image viewer with basic drawing tools. While we suggest people consider using the more advanced MRIcron, this older software remains popular.
  • MRIcron includes may sophisticated features and supports the modern NIfTI format. It includes the dcm2nii (DICOM to NIfTI converter) and npm (statistical analysis) tools.
  • MRIcroGL allows real-time interactive volume rendering, but requires a modern graphics card.
  • MRIcro for OSX is very fast, is simple to use and has a Mac-like interface (beta release).
  • Arterial Spin Labeling (ASL) notes and ASLtbx scripts.
  • Blindside allows double-blind transcranial direct current stimulation.
  • Center of Cancellation calculator measures severity of spatial neglect following brain injury.
  • Clinical toolbox for SPM for easy lesion masked normalization of CT and MRI scans.
  • ELEcro is a simple tool for electrophysiological analysis (ERP, EMG).
  • EMG recorder logs electrophysiological signals from a Mobi bluetooth EMG system simultaneously with event markers.
  • Fieldmap demo describes undistortion of EPI data.
  • fMRI simulator helps design efficient fMRI studies, and demonstrates the principles of fMRI signals.
  • Matlab scripts for adjusting the global contrast and brightness of an image.
  • Physiological Artifact Removal Tool (PART) can remove noise caused by respiration or cardiac pulsing from fMRI and ASL data.
  • Quality Assurance tools can help detect commons problems observed in neuroimaging studies.
  • My Slice Timing Correction scripts can adjust for the fact that our 3D images of the brain are based on a series of 2D slices that are acquired at slightly different times.
  • Perfusion-Weighted Imaging (PWI) tools allow us to determine how stroke disrupts blood-flow.
  • The JPEG image formats. JPEG specifies a number of image compression algorithms. Some of those popular for medical images are very different from the formats popular on web pages and digital cameras.
  • Spatial processing demo introduces matrices, affine transforms and interpolation kernels.
  • The SPM8 scripts page is a repository of simple Matlab scripts useful for brain imaging, they require SPM8 and Matlab to be installed.
  • Temporal processing demo introduces Fourier transforms, biquad filters (notch, low-pass, band-pass, gap).