High Dynamic Range

Attention

Using HDR can cause issues with some inline post-processing applications, such as AutoAlign or other processes. Using HDR also will ultimately change your imaging data. The study PI should be directly involved in any decisions regarding the usage of this option. Please consult with Aaron Jacobson or Conan Chen for discussing HDR, assisting with finalizing your protocol and for any general questions.

High Dynamic Range

High Dynamic Range (HDR) is an optional setting for protocols that must be manually turned on by the scan operator. Data acquired on the Prisma will typically be returned in either 12-bit or 16-bit format. For a 12-bit dataset, the values will range from 0 to 4095 (2^12 - 1). For a 16-bit dataset, the values will range from 0 to 65535 (2^16 - 1). The benefit of 16-bit format is the greater span of possible values for each pixel to take on. High Dynamic Range sets the sequence to use the 16-bit format on output.

For sequences that already use 16-bit format, there will be no difference. For sequences that use 12-bit format, HDR may be helpful for cases where the voxels of interest span only a small portion of the possible range and run into quantization effects that decrease precision.

The default format for a given scan is pre-decided by how it was programmed in the sequence. This default cannot be changed via the sequence parameter cards. By running the script bash CFMRI_HDR.bash, you can manipulate a flag will force 16-bit outputs from the scanner.

By default, this flag is set to off. That means a given scan will use the default format as specified by how it was programmed, which could be either 12-bit for 16-bit.

Manipulating the HDR Flag

The HDR flag can be controlled through the script bash CFMRI_HDR.bash. To access it, you need to be at the scanner console. On the keyboard, press Ctrl + Esc to open up the Windows start menu and then select Command Prompt. In the Command Prompt window, type bash CFMRI_HDR.bash to turn on HDR. With additional arguments, you can also turn the flag off, simply return the current status, or return help text on using the script. Examples are shown below.

# Turn on HDR. When called without any argument, it will turn HDR on by default.
>> bash CFMRI_HDR.bash
>> bash CFMRI_HDR.bash on

# Turn off HDR
>> bash CFMRI_HDR.bash off

# Check HDR status
>> bash CFMRI_HDR.bash status

# Return help text about usage
>> bash CFMRI_HDR.bash help

When do I need to run the script?

This flag is persistent across scans. For example, that means if the flag is turned on for your Localizer and left untouched, it will remain on for BOLD scan that follows afterwards. On the other hand, the flag will be reset to off whenever you go through a Patient Registration workflow to start a new Exam, or perform a system restart.

Example 1: You would like to use HDR for your entire session. You register a subject and start a session. You run bash CFMRI_HDR.bash, which turns the flag on, and leave it untouched for the rest of your session. At the end of your session, the flag is still on.

Example 2: You have been running your study in the default HDR off state (this is the case if you have not been manipulating the HDR flag) and are continuing to do so. The previous group used HDR and left the flag on. You go to register your subject and start the Exam. Upon clicking Exam, the flag is reset to the default off state. You do not need to run any script and can proceed with your session as you normally do.

Example 3: You would like to use HDR for one specific scan only in your protocol. You register your subject and start a session, which (re-)sets the HDR flag to off. You collect all of your scans up to the scan where you want to use HDR. Before starting the target scan, you run bash CFMRI_HDR.bash to turn the flag on. You run the scan to completion. For your subsequent scans, you want to use the sequence defaults, so you run bash CFMRI_HDR.bash off before completing the rest of your scan session.