Recover ECG from electrodes. Monodomain simulation

Question

I saw in a previous publication that you can obtain the values of electrodes using -phie_rec_ptf  from a monodomain simulation. I used as input 10 positions in a .pts file (LA, RA, LL, RL, V1-V6), however in my recovery file phie_recovery.igb, there seems to be 12 columns.

I assume the 12 columns are the 12 leads but I don't know in what order should the electrodes be in or,  if preferably, how to obtain the values of the 10 electrodes directly to later get the the 12 leads values. 

My .par is this:

simID    = /home/bio/jimena.rodriguez/OpenCARP/Simulations/MI_MRI_32/3N_3_ini_ecg

meshname = /home/bio/jimena.rodriguez/OpenCARP/IHD/MI_MRI_32/mesh_wo_scar_apex

num_imp_regions       = 1

imp_region[0].im      = tenTusscherPanfilov   # select ionic model

imp_region[0].name    = ENDO_FEC_Healthy_Base

imp_region[0].num_IDs = 2

imp_region[0].ID       = 311, 211

imp_region[0].im_param   = "flags=ENDO,GKs-40%"

imp_region[0].im_sv_init = "/home/bio/jimena.rodriguez/OpenCARP/Simulations/APs/ENDO/HEALTHY/BASE/ENDO_HEALTHY_BASE.sv"

num_gregions             = 1

gregion[0].name          = Healthy

gregion[0].num_IDs       = 2

gregion[0].ID            = 311,211

gregion[0].g_el          = 0.3

gregion[0].g_et          = 0.12

gregion[0].g_en          = 0.12

gregion[0].g_il          = 0.22

gregion[0].g_it          = 0.05

gregion[0].g_in          = 0.05

gregion[0].g_mult        = 1.0

num_stim                 = 2

stim[0].name             = "BasicLV"

stim[0].elec.vtx_file    = /home/bio/jimena.rodriguez/OpenCARP/IHD/MI_MRI_32/stim_Ext_LVstimulation_mesh_wo_scar.vtx

stim[0].ptcl.start       = 0.0

stim[0].pulse.strength   = 100.0

stim[0].ptcl.duration    = 5.0

stim[1].name             = "BasicRV"

stim[1].elec.vtx_file    = /home/bio/jimena.rodriguez/OpenCARP/IHD/MI_MRI_32/stim_Ext_RVstimulation_mesh_wo_scar.vtx

stim[1].ptcl.start       = 0.0

stim[1].pulse.strength   = 100.0

stim[1].ptcl.duration    = 5.0

dump_ecg_leads           = 1

phie_rec_meth            = 1

phie_rec_ptf = /home/bio/jimena.rodriguez/OpenCARP/IHD/MI_MRI_32/elec_file_src

bidomain    =   0

spacedt     =   1

timedt      =   1

parab_solve =   1 

dt          =   30

tend        =   15

Thanks!

Answer 1

Hi Jimena,

Thanks for bringing this up! At the moment the phie_recovery module does not implement the phie_rec_meth and dump_ecg_leads arguments. Although the parser accepts those parameters without raising an error, they are essentially placeholders and have no functionality. 

Can you share your phie_rec_ptf (in your case "elec_file_src") and the phie_recovery.igb? Alternatively a reproducible experiment could also help me pin down the issue.

Cheers, Julian

Comments

Hi Julian,

Sure. Here are all the files https://drive.google.com/drive/folders/1VRs9OMMAgirxpLRkQ9QqHzxzwrwdP3sR?usp=sharing .

This is not exactly the same example as before as I could not put the complete .par, but now everything is in there. The .par, the mesh, the elec_file_src, the .vtx files and the phie_recovery. The .sv files are not there but right now I just wanted to try is to recover the values at specific points without using the torso. The order of the points in elec_file_src are LA,RA,LL,RL,V1-V6.

If you need anything else, please let me know.

Thanks,

Jimena

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Hi Jimena,

I tried to replicate your results but when using the files that you gave me, my resulting phie_recovery.igb file has ten entries. So I was not able to reproduce the questionable result you were asking about.

To answer your question about the order of the points it should be the same order in the output as is in the input. 

Maybe it would be helpful for you to also have a look at the carputils code of the "Extracellular potentials and ECG" example on the openCARP website.

Cheers,

Julian