GLACIUS Temperature Reconstruction Software - MAC Version

GLACIUS Temperature Reconstruction Software - MAC Version

Author: 
Leeor Alon

GLACIUS is a software tool that enables rapid and optimal reconstruction of temperature maps directly from the scanner. It is compatible with the conventional Siemens MRI scanners, capable of reconstructing raw data provided from the scanner. The software is capable of robustly reconstructing phase information from 3D/2D gradient echo acquisitions and utilizing multiple receive coils for optimal phase reconstruction. The software works in Windows and OSX environments.

Optimal Phase Reconstruction for Thermometry

For ordinary MRI images, the phase of the image is typically discarded, however, PRF temperature mapping makes use of the phase maps. Typically, two phase maps are acquired, one before RF heating and one after RF heating and a subtraction of these two phase maps yields a map that is proportional to the temperature change. The angle between the phases can be calculated by assuming that Z1 is the complex image of the pre-heating acquisition and Z2 is the complex image of the post-heating acquisition. As result, the change in phase between the images is as follows:

Where Im(.) and Re(.) are the imaginary and real number operators. Furthermore, since the complex conjugate and inverse of the complex conjugate of Z2 have the same phase, the equation can be rewritten as:

Whenever using the tan-1 function it is better to use the four-quadrant function, known as atan2 in Matlab.

Many MRI coils have more than one element. GLACIUS uses the following algorithm for multi-coil phase reconstruction (1): Denoting the receiver channels by index j and defining s2 as the noise variance associated with the j-th channel, the phase difference map can be expressed as:

GLACIUS Tutorial

  1. Click on “Load Files for Temperature Recon” and select your pre- and post-heating sequences. Once the files are selected, in the bottom right it will say, “processing.” When the program it is done loading the files, it will show “Great success.”
  2. Then you can type in the mask threshold (typically a number between 0.01 to 0.2), then press the “calculate mask” button. If you need to refine the mask threshold, repeat number 2.
  3. Adjust the proton resonance frequency shift coefficient to the desired number. It is typically 0.01±0.002PPM/degree C.
  4. Click on the “calculate dPHI & dT Maps” button.
  5. Once the phase maps and dT maps are calculated you can adjust the threshold of the maps by choosing a minimum and maximum values and clicking on the “set axis” button on the right of the window.
  6. In temperature mapping experiments oil phantoms are added to the setup to account for B0 changes that are not temperature related. Click on the ”data cursor” icon on the top toolbox and click on the region where the oil phantoms are located in the phase map. Once you put the pointer on the oil phantom, you will see a phase value in radians.
  7. Enter the same but opposite value into the DC offset box in the top left. For example if a -0.05 radian is observed when putting the cursor on the phase map, then add 0.05 to the DC offset field. This will correct any DC B0 offsets that might occur in the MR system.
  8. Click the “calculate dPHI & dT Maps” button to compute the temperature difference.
  9. If the correction is sufficient you can now save the file by naming your filename on the bottom left corner and clicking the “save” button.
  10. If the correction is insufficient, click on the “extrapolation mask” button. This will bring you to a new window that will fit a polynomial to estimate a B0 map in 2D or 3D, based on the phase measured in the oil phantoms.
  11. In the new “extrapolationmask” window click the “load water sat file” button and chose a water suppression image to be loaded.
  12. Once the mask has been loaded, enter the threshold for the new oil mask and press the “calculate mask” button.
  13. Then choose the polynomial order. The program supports polynomial orders of 1 to 4. You can click the 3D checkbox if you want the polynomial fitting to occur in 3D. Otherwise, it will be conducted in 2D.
  14. Click the ”calculate extrapolated field” button and wait until the extrapolated B0 fields are calculated.
  15. Go back to the main window, and check the “interp” checkbox in the center top of the window.
  16. Set DC offset to 0 and click “calculate dPHI & dT Maps.
  17. You may have to play with the oil phantom mask, polynomial order and 2D/3D features until the fits are fine-tuned. After you are done save the filename as shown in step 9.
  18. A Matlab file will be saved. "handles.dT” corresponds to the temperature difference variable computed by the program.

References

  1. Bernstein MA, Grgic M, Brosnan TJ, Pelc NJ. Reconstructions of phase contrast, phased array multicoil data. Magnetic resonance in medicine : official journal of the Society of Magnetic Resonance in Medicine / Society of Magnetic Resonance in Medicine 1994;32(3):330-334.
 

PLEASE NOTE: The software available on this page is provided free of charge and comes without any warranty. CAI²R and the NYU School of Medicine do not take any liability for problems or damage of any kind resulting from the use of the files provided. Operation of the software is solely at the user's own risk. The software developments provided are not medical products and must not be used for making diagnostic decisions.

The software is provided for non-commercial, academic use only. Usage or distribution of the software for commercial purpose is prohibited. All rights belong to the author (Leeor Alon) and the NYU School of Medicine. If you use the software for academic work, please give credit to the author in publications and cite the related publications.

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Sponsors

Philanthropic Support

We gratefully acknowledge generous support for radiology research at NYU Langone Medical Center from:
 
• The Big George Foundation
• Raymond and Beverly Sackler
• Bernard and Irene Schwartz

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