3D simulation with susceptibility problem

[Xin Shen]

Hi,

My name is Xin Shen. I'm using your software to simulate my 3D sequence. However, when I tried to click on susceptibility button with multiple slices, it reported errors in MATLAB. I'm wondering if it is only graphic problem, or it actually influences the simulation results?

Best,

Hope to listen from you soon.

[tony.s...@gmail.com]

Hi Xin Shen,

Thanks for reporting, this is a bug in the matlab script: /usr/local/share/jemris/matlab/brainSample.m

Please change line 53 from

Z=[z(1):(z(Nz)-z(1))/(2*Nz-1):z(Nz)];

to

Z=[z(1):(z(Nz)-z(1))/(Nz-1):z(Nz)];

i.e. remove the factor "2" before Nz. That should solve the issue. I will include the fix in the next version on gitlab and on the jemris homepage, but this may take a while.

Hope your simulations will work now.

Best,

Tony

[Xin Shen]

Hi Tony,

That is very helpful. Thanks a lot!

Best,

Xin

[Xin Chen]

Hi Tony,

Another question about the brain phantom. The last few lines of branSample.m says

if add_susceptiblity
  BrainSample.DB = BrainSample.DB + 2*pi*1e6*DB*handles.sample.gamBo;
end

The first item on the right side is the water fat chemical shift which has positive number for fat protons (However, note that numerically fat protons have lower Larmor frequency than water protons). The 2nd item is off-resonance caused by susceptibility. My understanding is that for the 2nd item, negative numbers mean Larmor frequency below that of water protons. In this case, should it be

 

BrainSample.DB = BrainSample.DB - 2*pi*1e6*DB*handles.sample.gamBo ?

Please confirm or advise.

Thanks!