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Pulse Sequence Diagrams Using Metapost

Thomas Wilkinson

In which I use MetaPost to generate publication quality pulse sequence diagrams...

Pulse sequences are the series of radio-frequency pulses required to generate an MR image. If you are an MR Physicist you will see these a lot and probably wondered how can I generate nice pulse sequences for my thesis, papers etc. Well handily using MetaPost and these files you can! First install Tex Live*:

sudo USE="doc dvi2tty dvipdfm extra games graphics music png pstricks science truetype X" emerge -av texlive

Then install MetaPost:

sudo emerge -av metapost

Then ensure you have all the necessary files from CTAN which aren't installed alongside metapost†:

mkdir ~/texmf
mkdir ~/texmf/metapost 
cd ~/texmf/metapost
wget http://mirrors.ctan.org/graphics/metapost/base/texmf/metapost/base/README
wget http://mirrors.ctan.org/graphics/metapost/base/texmf/metapost/base/TEX.mp 
wget http://mirrors.ctan.org/graphics/metapost/base/texmf/metapost/base/boxes.mp 
wget http://mirrors.ctan.org/graphics/metapost/base/texmf/metapost/base/format.mp 
wget http://mirrors.ctan.org/graphics/metapost/base/texmf/metapost/base/graph.mp 
wget http://mirrors.ctan.org/graphics/metapost/base/texmf/metapost/base/marith.mp 
wget http://mirrors.ctan.org/graphics/metapost/base/texmf/metapost/base/mfplain.mp 
wget http://mirrors.ctan.org/graphics/metapost/base/texmf/metapost/base/mpost.mp 
wget http://mirrors.ctan.org/graphics/metapost/base/texmf/metapost/base/plain.mp 
wget http://mirrors.ctan.org/graphics/metapost/base/texmf/metapost/base/rboxes.mp 
wget http://mirrors.ctan.org/graphics/metapost/base/texmf/metapost/base/sarith.mp 
wget http://mirrors.ctan.org/graphics/metapost/base/texmf/metapost/base/string.mp 
wget http://mirrors.ctan.org/graphics/metapost/base/texmf/metapost/base/texnum.mp 
wget http://mirrors.ctan.org/graphics/metapost/base/texmf/metapost/base/troffnum.mp

Do this in /usr/share/texmf to allow all users to access the files. Finally, download the pulse sequence files from http://www.celos.net/comp/pulses/ to the directory you intend to run MetaPost from.

Now write your pulse sequence into a metapost file. Below is an example of a generic FLASH sequence - basically treat each part of your sequence as a line and follow the documentation in the pulse.mp file:

%FLASH sequence 
beginfig(1); 
input pulses.mp; 
initf; 
startline(rf,"RF"); 
xline(2); 
xpulse(1,1,""); 
xline(6); 
startline(g0,"Gx"); 
xline(1); 
xsquare(2,0.5); 
xsquare(1,-0.5); 
xline(5); 
startline(g1,"Gy"); 
xline(3); 
xtable(1,0.8,5, -1); 
xline(5); 
startline(g2,"Gz"); 
xline(3); 
xsquare(2,-0.5); 
xsquare(3,0.5); 
xline(1); 
endfig; 
end;

The section below if added after the image but before endfig; will add a white background instead of a transparent one.

% save image to temp variable 
picture pic; 
pic := currentpicture; 
% clear image currentpicture := nullpicture; 
% fill a bounding pox of pic with color 
fill bbox pic withcolor white; 
% re-draw pic ontop 
draw pic;

If you have ImageMagick installed you can easily convert the image to a png or similar for use in Windows or uploading to your blog:

convert -density 300 flash.1 flash.png

You should end up with a nice pulse sequence diagram:

See this content in the original post

*Gentoo installation shown

†Gentoo doesn't pull in these files and I found the solution here: http://tiaozhanshu.com/doc/funtoo/metapost

Tom Out!

P.S. Now a Major Github repository! https://github.com/tawilkinson/pulses

References

[1] Haase, A., et al. (1986) FLASH Imaging. Rapid NMR Imaging Using Low Flip-Angle Pulses. Journal of Magnetic Resonance, 67, pp 258-66.