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0 votes
by (130 points)


I am trying to add a fibrotic region to the center of my tissue using a similar method as used in tutorial 21_reentry_induction. However i get the following warnings 

L3 : Region tag 2 in gregion_i[0] not found in element list for Intracellular domain grid.

L3 : Region tag 3 in gregion_i[1] not found in element list for Intracellular domain grid.

and the resulting mesh completely removes a subset of elements, rather than altering their conductance/ionic state.
My mesh is a 10x10x0.1mm block of 0.1mm resolution
I implement my ionic model as such:
imp_reg = ['-num_imp_regions', 1,
           '-imp_region[0].im', 'Courtemanche',
           '-imp_region[0].num_IDs', 1,
           '-imp_region[0].ID[0]', "1",
           '-imp_region[0].im_param', gNa]
And try to implement the change in conductance in fibrosis elements as below:
# Retag fibrotic elements

dyn_reg = ['-numtagreg', 2]
dyn_reg.extend(tagregopt(1, 'type', 4))
dyn_reg.extend(tagregopt(1, 'elemfile', f_fib))
dyn_reg.extend(tagregopt(1, 'tag', 2))
dyn_reg.extend(tagregopt(1, 'type', 4))
dyn_reg.extend(tagregopt(1, 'elemfile', f_slow_conductive))
dyn_reg.extend(tagregopt(1, 'tag', 3))

g_reg = ['-num_gregions', 2,
         '-gregion[0].num_IDs', 2,
         '-gregion[0].ID[0]', 1,
         '-gregion[0].ID[1]', 3, #3='normal' conducting element
         '-gregion[0].g_il', gi,
         '-gregion[0].g_it', gi,
         '-gregion[0].g_in', gi,
         '-gregion[0].g_el', ge,
         '-gregion[0].g_et', ge,
         '-gregion[0].g_en', ge,
         '-gregion[0].g_mult', gm_bl,
         '-gregion[1].num_IDs ', 1,
         '-gregion[1].ID[0]', 2, #2=non-conducting element
         '-gregion[1].g_il ', 0.0000001,
         '-gregion[1].g_it ', 0.0000001,
         '-gregion[1].g_in ', 0.0000001,
         '-gregion[1].g_el ', 0.0000001,
         '-gregion[1].g_et ', 0.0000001,
         '-gregion[1].g_en ', 0.0000001,
         '-gregion[1].g_mult', gm_bl]
After creating element files 'f_fib' and 'f_slow conductive' (i haven't added in changes to imp for the fibrotic region for the moment). The two element files look like they have been created successfully. But yes, i end up with a mesh where a subset of the elements in the fibrotic region are completely removed, rather than having their conductance changed.
Any tips or help would be grealty appreciated!

1 Answer

+1 vote
by (3.5k points)

Could you please provide more information of your parameter.par file? What is the fiber direction of these regions? What are the physics regions defined in your experiment?


by (130 points)
HI Jorge,

In gathering the information to respond I realized I made a simple mistake and simply used the original mesh, and not the retagged mesh, in the simulation. Thanks for your help!

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