From NITRC Wiki

T1-Relaxometry with Double Angle Experiments

Prerequisites

• JIST Pre-Beta 1.3 or Newer: http://www.nitrc.org/frs/?group_id=228

References

• Smith SA, Edden RAE, Barker PB, van Zijl PCM. Measurement of T1 and T2 in the Cervical Spinal Cord at 3Tesla. MRM 60:213-219 (2008) : http://www3.interscience.wiley.com/journal/120173564/abstract
• Neema M, Goldberg-Zimring D, Guss ZD, et al., 3 T MRI relaxometry detects T2 prolongation in the cerebral normal-appearing white matter in multiple sclerosis, NEUROIMAGE Volume: 46 Issue: 3 Pages: 633-641 : http://www.ncbi.nlm.nih.gov/pubmed/19281850

Example

Method

• Download the layout file for double angle analysis : http://www.nitrc.org/frs/download.php/1097/T1-DoubleAngle-JIST.layout
• Sample data is not available at this time due to data-use restrictions.
• Load the layout file:

• Select "T2-DE" and specify a text file containing dual echo images for each subject.
• Select "MPRAGE" and specify a text file containing structural targets used for image registration.
• Select the "T2:DualEcho" module
  • Specify the "First Echo TE" in milliseconds
  • Specify the "Second Echo TE" in milliseconds
• Select Project->Layout preferences and specify an output directory.
• Select Project->Global preferences.
  • Ensure that you have selected the MIPAV JRE's for the java binary.
  • Otherwise, you must ensure that the MIPAV numerical libraries are on your default java classpath.
• Save the layout.
• Run the layout in the process manager.
• Enjoy your estimated T2 maps. The parameters are estimated in milliseconds.