/BMsim_challenge

Repository for the Bloch-McConnell simulation (BMsim) challenge

Primary LanguageMATLAB

== BMsim challenge ==

Welcome to the repository of the Bloch-McConnell simulation (BMsim) challenge. The idea of the challenge can be summarized as follows:

  1. Every participant simulates 3 different well-defined cases / scenarios
  2. The simulation results from all participants are collected
  3. The median Z-spectrum wins

In this first challenge, we have chosen 3 different preparation schemes consisting of single block pulses / CW pulses only. Next challenges might cover more sophisticated cases using arbitrary shaped RF pulses as well.

Simulation results

To keep the burden for posting your simulation results as low as possible, we decided to collect the results in a simple Google Docs spreadsheet that can be found here:

https://docs.google.com/spreadsheets/d/1JN7VN-f1ktDrJgokb0FlUFwkH0MWYlPA_jSfnQoFOVc/

Please feel free to add your name / group in case it's not listed yet and post your results.

Simulation cases

General settings / assumptions:

  1. fully relaxed initial magnetization (Zi = 1) for every offset,this is equivalent to a very long recovery time 10*T1
  2. post-preparation delay = 6.5 ms, in the pulseq-file this corresponds to the gradient spoiler duration
  3. gyromagnetic ratio: 42.5764 MHz/T
  4. larmor frequency (3T): 127.7292 MHz/T
  5. Normalization scan at -300 ppm

Case 1: 2 pool model, APTw preparation - steady-state

  • pool model: 2 pool model of creatine as defined in case_1_2pool_model.yaml
  • prep. details:
    • pulse shape: block
    • pulse duration: 15 s
    • pulse power: 2 µT
    • offset list: -15:0.1:15 ppm

More details about the pool model and preparation scheme can be found in the corresponding README

Case 2: 2 pool model, APTw preparation

  • pool model: 2 pool model of creatine as defined in case_2_2pool_model.yaml
  • prep. details:
    • pulse shape: block
    • pulse duration: 2 s
    • pulse power: 2 µT
    • offset list: -15:0.1:15 ppm

More details about the pool model and preparation scheme can be found in the corresponding README

Case 3: 5 pool model, APTw preparation

  • pool model: 5 pool model of WM as defined in case_3_5pool_model.yaml
  • prep. details:
    • pulse shape: block
    • pulse duration: 2 s
    • pulse power: 2 µT
    • offset list: -15:0.1:15 ppm

More details about the pool model and preparation scheme can be found in the corresponding README

Case 4: 5 pool model, WASABI preparation

  • pool model: 5 pool model of WM as defined in case_4_5pool_model.yaml
  • prep. details:
    • pulse shape: block
    • pulse duration: 5 ms
    • pulse power: 3.7 µT
    • offset list: -2:0.05:2 ppm

More details about the pool model and preparation scheme can be found in the corresponding README

FAQ

How did you choose the value of the gyromagnetic ratio?

The NIST value of the shielded proton gyromagnetic ratio is 2.675153151 x 108 s-1 T-1. Dividing this value by 2 Pi yields 42.576384750950949004433240733872 MHz/T, which results in the used value of 42.5764 MHz/T when rounded to 4 digits.

Please make sure to use these values for gamma in your simulations:

  • 42.5764 MHz/T
  • 42.5764 x 2 x Pi s-1 T-1 (do NOT use the exact NIST value)

How do you define the pool size fraction f?

There could be different definitions of the fraction, some define water f=1, and all other relative to water. Others define M0i of each pool i and then normalize fi= M0i/sum_i(M0i)

This could lead to differences, but we decided NOT to dictate which definition to use.

How do you define the MT pool?

Some simulations use x, y, and z components to describe a Lorentzian MT pool. Others use only the z-component and assume a Lorentzian lineshape factor there. Again, we decided NOT to dictate how to simulate the MT.