CV computation

Question

Dear all,

I was wondering if there is an equivalent to GLGradient from carpentry (https://carpentry.medunigraz.at/examples/tutorials/tutorials.05_pre_post_processing.05_igbutils.run.html?highlight=glgradient#exercise-3-glgradient) to compute conduction velocity on a given mesh. I wasn't able to find it on the openCARP website.

Thanks!!

Cheers,

T

Answer 1

Hi!

Use "meshtool extract gradient". This works for .dat files as well as .igb files.

Best, Aurel

Comments

Hi Aurel!

Thanks for your answer.

I tried now :

meshtool extract gradient -msh=path-to-my-mesh.pts  -idat=vm.igb -odat=gradient -ifmt=carp_txt

Where vm.igb is one beat of my simulation.

I get two files, one is the gradient.grad.igb and the other the gradient.gradmag.igb. The first one if I open with meshalyzer I can see that it shows the voltage gradient over time (mainly shown by the depolarization wave). The other one, which I thought might be the conduction velocity, is also a time-stack, which doesn't show any particular pattern but just noise. I would expect the CV file to be just 1 frame, and to show a particular pattern that can be expected from watching the voltage. On GLGradient one could define another option (--velocity) so one would get the velocity directly, but this extract gradient from meshtool doesn't seem to have it.

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Okay, I realize that I should do the gradient of the LAT :D

Thanks!

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This still doesn't seem to work :(

I have created my LATS file with igbapd:
igbapd -l -20 -O LAT_S1.dat  -s vm_S1.igb

since this also gives me the APD I extract the second column:
awk '{ print $2 }' LAT_S1.dat> LATS_S1_onecol.dat

The LATs on meshalyzer look good.

And now I run the extract gradient on the LATs:
meshtool extract gradient -msh=<path-to-my-mesh>.pts -idat=LATS_S1_onecol.dat-odat=CV

I get the CV.gradmag.dat and the CV.grad.vec. If I open the CV.gradmag.dat with meshalyzer on my mesh, it prints out a very weird 'zebra' pattern, that doesn't match with the expected result (from what one can observe in Vm). Is there something I am missing?

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I tried your approach myself and it works in general. You need a high temporal resolution in you vm.igb though (e.g. dt = 10 spacedt = 0.01).

Note that what you get when computing the gradient of LATs is the *inverse* conduction velocity, since it is the spatial derivative of a time field. It helps looking at the units: dt [ms] / dx [um], that is, change in activation time over change in space.

You can do something like the following to arrive at the final CV in [m/s]:

igbapd -l -20 -O LAT_S1.dat -s vm.igb
awk '{print $2}' LAT_S1.dat > LAT.dat
meshtool extract gradient -msh block_i -idat LAT.dat -odat iCV
awk '{v = $1; print (1.0/v)/1000.0}' iCV.gradmag.dat > CV.dat

Best, Aurel

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Cool! Thanks for your help Aurel! I guess the resolution is my problem here. I was running the simulations with dt=5 and spacedt=1. I will re-run with higher resolution!