Low Receiver Values: The Problems and Solutions - Eric Egolf

Summary:

As many of you know, we have been having some problems with the pixel and receiver values obtained from the 1.5 T GE scanner, Signa, in the Jefferson Building. The low pixel values stem from two parameters that Signa automatically sets, called the auto prescan receiver values. Signa gets the two auto prescan values during the 30 second prescan that each subject does before starting any of the experimental runs. The parameters for the auto prescan called R1 and R2. The auto prescan values should get set to R1 = 11 and R2 = 15. Generally this is what Signa sets them at, but sometimes (we aren’t sure as of yet why) these values get set to R1 = 11 and R2 =8 which results in poor data and low pixel values after reconstruction. Before every run, an RA should check the auto prescan values on Signa. If the RA notes bad auto prescan values, he can use a manual fix. It is possible to set the prescan values manually on Signa to obtain higher pixel values*. See appendix for more details.

* The pixel values in the reconstructed images obtained after manually setting the prescan values don’t seem to be quite as high as one would expect, but they are relatively close and more importantly they seem to give us good results after a statistical analysis.

Appendix A: Checking Receiver values in the recon.log

Every time you reconstruct images from the raw P file, i.e. using the epirecon command, a log file gets created called recon.log. This file contains all the parameters that were set on Signa for that particular subject along with the pixel values for each voxel. The first 43 lines of recon.log correspond to the parameters of the run, and the rest of the file corresponds to the pixel values. The receiver values should be somewhere between 6000 and 30000. The auto and manual prescan values are on lines 35 and 36 respectively.

Examples:

Correct Prescan Values
Auto Prescan Receiver Values (R1) = 11 & (R2) = 15
Manual Prescan Receiver Values (R1) = 11 & (R2) = 15

Incorrect Prescan Values
Auto Prescan Receiver Values (R1) = 11 & (R2) = 8
Manual Prescan Receiver Values (R1) = 11 & (R2) = 8

Prescan Values that were incorrect but noted and fixed by RA
Auto Prescan Receiver Values (R1) = 11 & (R2) = 8
Manual Prescan Receiver Values (R1) = 11 & (R2) = 15

Appendix B
Examples of Glass Brain and Brain Activation Map for subjects with low receiver values

Appendix C:
Glass Brain and Brain Activation Patterns for subject with manually fixed prescan values