Forwarding to the users list...  liz
 Original Message 
Subject:
Re: Forward ECG Problem
Date:
Wed, 30 Mar 2016 18:55:56 +0100
From:
Matthias Lange <m.lange@sheffield.ac.uk>
To:
Dana Brooks <brooks@ece.neu.edu>
CC:
Rob MacLeod <macleod@sci.utah.edu>,
"Alexjandro (Alex) Frangi" <a.frangi@sheffield.ac.uk>
Hi Dana, Hi
Rob
Thanks for
checking. Currently, I am working on using SCIRun to solve
the forward ECG problem. That way I
might be able to understand whether the problem is
with the activation pattern or with my numerical
solver of the forward ECG problem.
However, the
provided sample net needs a segmentations for the
torso. I struggle to generate this, as I work with
meshes. If you have a standard way of performing the
conversion from mesh to segmentation, it would be
helpful. Equal helpful would be if there is a sample
net which uses a surface or volume mesh as input.
Another
question: Does SCIRun support the
export of the standard ECG leads? This would be good
for comparison.
Best,
Matthias
On 29 March 2016 at 18:39, Dana
Brooks <brooks@ece.neu.edu>
wrote:
Matthias hi,
just checking in to see where you stand with all this
and if we can help in any way at this point ?
best,
Dana
On 3/17/16 4:51 AM, Matthias Lange wrote:
Dear Rob, Dear Dana
I like to thank you for fast answers!
Particular for mentioning the IBBM workshop,
for which I handed in an application on
Tuesday. >From both of your emails I
noticed, that I haven't gave you information
on my background. I studied physics with a
focus on general relativity. From there I
moved to my PhD, which started in 2012. The
PhD is about the impact of the fast conduction
system of the human heart, where I focus on
the largely unexplored false tendon. I started
with simulation based on the Eikonal equation
and then developed a monodomain solve for the
Purkinje system. The implementation used the
LifeV framework which also provides the
monodomain and bidomain formulation for the
myocardium. Furthermore, I made an effort to
move the solver of the electrophysiology
problem in the Purkinje to the GPU. My latest
work is to implement the forward ECG solver.
So far I haven't used SCIRun. This is because
I haven't spend the time to understand how the
GUI works. I hopeful I am lucky enough to be
awarded with the IBBM fellowship, and then get
a possibility to learn it. I know, that SCIRun
is in theory able solve the forward ECG
problem for a given transmembrane potential on
the epicardium. However, I haven't figured out
how to use a customised heart, which necessary
because a statistical atlas is used to
generate realistic heart shapes. Subsequently,
I like to solve the electrophysiology
problem and the forward ECG. This means the
torso will need to be modified for each heart.
ECGSim looks like a very interesting tool,
which I didn't know about. Currently, I am
going over the underlying publication, to
understand the generation of the source
potential. This seems to be of interest, as it
builds a positive potential. So far I haven't
understood where it comes from. Again, I like
to thanks' for your time and effort. Best
Matthias
On 14 March 2016 at
23:10, Rob MacLeod <macleod@sci.utah.edu>
wrote:
Hi
Matthias,
Sorry, I keep starting this email and
trying to find ways to keep it short,
then get distracted, then come back to
it, and now I really have to attend to
some other deadlines… So here is a
start and I will try to iterate soon.

What I really think you should do is
submit a fellowship application for our
summer course. The deadline in tomorrow
and the fellowship will cover most of
your expenses:
http://ibbm.sci.utah.edu/fellowship.html
I am not being facetious as this
course really is good and provides
answers to a lot of this background
material and to the use of all our
SCI/CIBC/MRL software. It is also a
great time! You can even see a video
about it
http://ibbm.sci.utah.edu/gallery.html
https://player.vimeo.com/video/104537720?portrait=0&title=0&byline=0
The short answer to your specific
question is that one must picture the
activation in the heart as a wave front
with polarized tissue in front and
depolarized behind. Under those
conditions, intracellular current flows
in one direction, extracellular in the
opposite, as you note. But one model at
the tissue level is a dipole surface
with sources and sinks split across the
wavefront. The size of the source is a
function of the current or dipole moment
of this source, i.e., the potential
gradient that appears in the equation
you included. From here, the path
diverges depending on which sort of
source formulation you want to pick, as
simple as a fixed dipole that change
direction and as complex and a full
bidomain.
One key that I cannot find in the
description is what sort of sequence of
activation you have (or came out of the
simulations). This is key and without
it, you will generate strange ECGs.
Another approach to test your code is
to pick a static point in time, assign
potentials in the heart to what we know
to be at least approximately right, and
then see how your potentials distribute
on the torso surface. There are lots of
textbook examples of the sequence of
activation that can guide you in setting
the transmembrane potentials in
different regions of the heart.
I need to wrap up now but we can
certainly iterate more. I cannot tell
where to jump into the derivation as I
also cannot tell the extent of your
previous training or background in
electrophysiology and bioelectricity.
Best (for now),
Rob
Matthias hi,
I am going to bring Rob
MacLeod in on this
discussion. Although I
might be able to get some
of this figured out, I
suspect Rob will do so
with much more accuracy
and much more rapidity too
!
BTW Alex mentioned that
you are using SCIRun and
some of the figures looked
familiar  can you tell
us a bit about if/ / how
you are using SCIRUn ?
and have you looked at
ECGSIM ? Although it uses
a surface transmembrane
potential source model
rather than a bidomain
source, it is a very
useful standard to compare
TMPs and surface
potentials against and
allows very nice
examination of details of
how a forward model is
working.
Rob hi,
please see below. Looking
forward to your
explanation :)
best,
Dana
 Original Message

Subject:
Forward ECG
Problem
Date:
Mon, 14 Mar 2016
09:42:42 +0000
From:
Matthias Lange <m.lange@sheffield.ac.uk>
To:
brooks@ece.neu.edu
CC:
Alejandro Frangi
<a.frangi@sheffield.ac.uk>,
Toni Lassila <t.lassila@sheffield.ac.uk>
Dear Prof. Brooks
I am a PhD student of
Prof Alejandro Frangi
working on cardiac
simulations. Alejandro
told me that you
kindly agreed to have
a look at a problem I
have with the forward
ECG.
We are developing a
solver for the
uncoupled bidomain
equations in three
dimensions. The
problem is that we
observe an inverted
ECG in our
simulations.
Furthermore, I do not
understand why the
real ECG has the
opposite orientation.
To generate realistic
orientated ECGs, the
left leg lead needs to
be positive against
the right arm lead. In
simulations reported
in the literature this
happens because of two
charge accumulations.
The left side of the
body becomes positive
compared to the
resting state, while
the right hand side
becomes negative
compared to the
resting state. To
generate this surface
charge distribution
the extracellular
potential at the heart
apex needs to turn
positive, while at the
base it should become
negative. All this
would need to happen
during depolarisation.
At this point I get
confused. My
understanding is that
the action potential
arises because
positive charge from
the extracellular
space is entering the
intracellular space,
i.e. Na+. This should
result in a lower
extracellular
potential compared
against the resting
potential. This
contradicts the
assumption of a
positive charged apex
as stated in the first
paragraph.
In our simulation, we
observe a negative
extracellular
potential during
depolarisation.
Solving the forward
problem with a
negative extracellular
potential at the heart
apex results in a
negative body surface
potential on the left
side of the body. This
potential distribution
is in line with the
ECG we observed.
However, it is
inverted with respect
to a real ECG and what
others report for
their simulations.
Obviously, some of
the assumptions or
conclusions have to be
invalid. To me it is
not clear where I made
the mistake.
Attached is a
document describing
the mathematical
formulation we used,
including a few images
of the heart
activation and the
torso potentials. If
you need the 3D
simulation results let
me know and I will
share them with you in
Google Drive.
Any thought are
highly appreciated,
and I would like to
thank you very much
for your effort.
Best wishes,
Matthias
<ForwardECG.pdf><Mlange_R9_2016.pdf>
