What's the proper file format for a per-cell conductivity scale vector file (-gi_scale_vec parameter)?

Question

Hi all

I am able to read in a .txt file which is a list of scalars that acts as scaling factor for each cell's conductivity like so:
0.657
0.334
...
n-th element (n = n_cells)
This is read in when starting the simulation with the -gi_scale_vec option.
The simulation is not in line with this file sadly. The signal propagates in regions which should be non-conductive and otherwise does not correspond at all with the conductivity regions. I tried making it a vector by copying the element three times per line and separating with a whitespace (comma's didn't work). No avail.

This got me wondering: what kind of file format and content does carp expect? And does carp have a different way of numbering cells than, say, a .vtk file? How is this file supposed to look like?

Answer 1

Hi!

The format you were using is correct. Its simply one value per element (i.e. the default .dat format).

I suspect the issue being a wrong element mapping of your data. That is, the intracellular domain (= myocard) is not equal to the extracellular domain (= myocard plus bath) and you provide the gi_scale_vec for the myocard plus bath, thus the mapping is wrong for only the myocard. With the latest commit (6db200a68), I have added a basic data dimension check to catch this kinds of errors.

For providing a parameter vector for the intracelular domain, you have to first extract the intra domain into a seperate mesh and generate a parameter vector for that mesh.

If this is not the issue, I would need you to provide me an reproducing example to investigate further.

Comments

Hi Aurel!

Thanks for your answer.
Unfortunately, I'm not sure how to fix it based on your answer. My simulations are monodomain only, and all my nodes are defined as intra. Provided is a drive link with all the files needed for the simulation, including the carputils settings.yaml (in case you might need it). Let me know if you can acces the files and reproduce the same result.
https://mega.nz/folder/OzRAnJKa#3rgmPC5DBffAS4MmwxNlGA

Kind regards
Bjorge

---

I ran your simulation without problems. When re-reading your initial question, I better understood the issues you were having with the simulation results. You have reduced conductivity to 1e-6 in some regions and expected them to not activate at all.

As you may have observed, the activation front brakes down eventually in those regions, but not in the same smooth manner as you may have expected. This is because reducing conductivity does not electrically isolate.

What you really want to do is to turn off the sources directly by turning off the ionic channels required for activation. This can also be done by providing an adjustment file to the ionic models.

---

Shutting off the ionic channels fixed it. Thank you!