MRIcron video tutorials code


These Flash videos are designed to help users learn how to use some of MRIcron's features. The videos were created with a free program called Wink. Optionally, you can download the sample datasets and Matlab scripts, so that you can try out these analyses yourself. Download this file for SPM5, or this file for SPM8.

  1. Watch the video: Use MRIcron to draw a lesion map. (If you do not see a 'Draw' menu or drawing tools with your version of MRIcron, select Help/Preferences and choose the 'Show drawing menu and tools' checkbox).
  2. Watch the video: Coregister a patient lesion to standard stereotaxic space. While T1 scans have great anatomical contrast, they often do not show the full extent of a brain injury. In contrast, T2, DWI and FLAIR images often show injury, but typically do not have the anatomical contrast to normalize well. This video shows a solution to this: lesions are mapped on the T2 scan, the T2 scan is than coregistered to the T1 scan and finally the T1 scan is normalized to standard space. This script uses SPM5's unified segmentation and normalzation, which is exceptionally robust for the presence of lesions (see Crinion et al., 2008.
  3. Watch the video: Use NPM to analyze the data of 24 simulated stroke patients.
  4. Watch the video: Use SPM5's unified segmentation and normalization to remove the scalp from a T1-weighted image. The video shows how these images can be used for rendering. This technique is often more robust then the popular 'Brain Extraction Tool'.