Data Analysis

How to open your MRI data

The data for each MRI scan generated by our MRI system is stored in binary raw file. After the your imaging sesson, A CD-ROM contain all the image data will be available for pick up.

Amira

Amira software is developed my Mecury Computer System ( formerly TGS ). It offers superb capability and performance in image segmentation, surface reconstruction and direct volume rendering. Our working experience has proved that it is a very powerful tool for MRI data analysis. The following is just a few examples:

Brain segmentation and volume measurement
Cardiac measurement: ventricular volume, muscle volume
Body fat measurement: total and distribution
Intestine contractility evaluation
3D reconstruction and customized animation ( with movie file output for demonstration and presentation )

Amira software is also the standard image processing tool for our CT/SPECT imaging data.

We installed Amira software on two workstations optimized for high-performance image processing. To sign up to use the software, please contact Belinda Rivera. For technical capability of the software or assistance on use the software on our workstations (An appointment is required if you need on-site help), please contact Lingyun Hu.

The workstations are located in Taub Animal Facility.

Just as most cutting-edge visualization software, Amira software requires Linux operating system being installed in our workstations. However, knowledge of Linux is not required for the use of Amira software.

Amira 3D Rendering of mouse skeleton

ImageJ

ImageJ is the software developed by NIH for image processing. It is based on Java technology and is available for Unix, Linux, Windows, Mac OS X and Mac OS 9. It offers much less functionality than Amira, but is always an efficient tool for you to open the MRI dataset on your own computer for image viewing, exporting, and simple measurement.

More detail of ImageJ and download link is available at http://rsb.info.nih.gov/ij/