Analysis of Brain Scans [was Re: Brain surface]

kenneth collins kenneth.p.collins at
Sat Nov 6 01:01:45 EST 2004

Hi Matthew. Your discussion is excellent. I'm 
going to comment
from NDT's perspective. No reply expected. [I'm 
really busy,
so I'm just going to comment, where I can add 
stuff that's of
value, and then get back to my own work.]

The other thing is, please do not take any of my 
as "criticism". As usual, I'm just communicating 
my under-
standing, using your thoughtful post as an 
opportunity to
do that -- adding stuff that I know it's useful to 

"Matthew Kirkcaldie" 
<m.kirkcaldie at> wrote in 
news:m.kirkcaldie-1C98BB.15542716102004 at
| In article <416fb952 at>,
| "John Hasenkam" <johnh at faraway.> wrote:
| > Thanks for the correction Matthew, like the 
original poster I was under the
| > impression that fMRI was limited. Perhaps you 
can help me with another
| > concern in relation to fMRI. I have noted in a 
number of articles that
| > images produced for a given task can vary 
quite considerably.
| I am by no means an fMRI expert, but the 
fundamental limitation of the
| technique is that it relies on changes in MRI 
density caused by changes
| in local blood oxygenation (often abbreviated 
BOLD fMRI - Blood Oxygen
| Level Dependent fMRI).  The technique, for those 
unfamiliar, involves
| making a scan of the brain while the subject 
does nothing, and then
| having the subject perform some kind of task or 
pay attention to a
| stimulus, and making the scan again. The 
"resting" scan forms a
| reference level, and at every point in the head, 
the "active" scan is
| compared to the reference.  If the "active" scan 
density is different at
| some points, it can be concluded that the local 
levels of blood
| oxygenation have changed, and the point is 
coloured according to how far
| off-baseline it is (calculated statistically 
based on the overall amount
| of change seen in the scan).
| This leads to several serious limitations of 
fMRI, which are
| particularly problematic when someone tries to 
treat an fMRI image as a
| picture of "nervous system activity":
| 1. fMRI is a map of changes in blood flow: 
nothing more, nothing less.
| It is conjectured, but not definitively proven, 
that active tissue in
| the CNS can modulate local blood flow to produce 
changes in density on
| an MRI scan.  fMRI advocates would say that the 
blood flow changes are
| produced by whatever processes contribute to the 
mental activity being
| performed, but that's rather a circular 
argument.  There's no proven
| causal chain between, say, a neuron firing more 
actively and a change in
| the amount of oxygenated blood flowing through 
the nearest capillary.

This problem is deep, but a 
analysis of the functional neuroanatomy allows it 
to be
resolved, to a first approximation.

First, the blood-flow considerations are 
constrained by cellular energy consumption. Com-
bustion is combustion, and oxygen is necessary in
rigorously-correlated quantities. So a neuron's
firing rate is directly-coupled to its oxygen use.

This said, I agree with the main point you make,
above, for reasons I discuss below.

| 2. As far as I know, the mechanism by which 
blood flow is altered is not
| understood. It is likely to be strongly mediated 
by astrocytes, whose
| processes wrap brain capillaries in continuous 
sheaths, and hence would
| be controlled by glial cells, rather than 
neurons.  Hence it seems
| likely that the needs of glia are more relevant 
to fMRI than the
| activity of neurons directly.

There's an extremely-integrated overall 
As I've discussed in long-former posts, glial 
changes actually enter into short-, intermediate- 
and long-
 term "addressing" ["memory"] dynamics, which 
leads into
your discussion immediately below.

| 3. There is no absolute scale for what 
constitutes "active" levels of
| difference on the fMRI image.  To a large extent 
they are set ad-hoc
| based on the levels observed in individuals. 
Hence it is difficult to
| compare between individuals and between studies. 
| co-ordinates such as the Talairach system can 
help adjust for the
| structural differences in individual brains, but 
there's no way to
| adjust for the real differences in regional 
function between
| individuals, which have been demonstrated 
anatomically and
| physiologically but don't show up on MRI.

There is a way, but it's exceedingly-arduous, 
several different forms of long-term analyses to 
carried out during the observational 'time'-frame. 
on this below.

| 4. Nobody has any idea if blood flow is 
modulated by the *type* of
| processing in a given region - aside from the 
ignorant people who
| believe we only use 10% of our brains, most 
neuroscientists would agree
| that even during "resting", there is sustained 
and large scale activity
| in the nervous system, and we are looking for 
fluctuations on a much
| smaller scale, which may or may not be relevant 
to what the region is
| doing.

Yeah, you've seen into the cruxt of the matter. 
More on
this below.

| For instance, active suppression of activity in 
a region is
| almost certainly more metabolically expensive 
than normal processing, so
| a strongly suppressed area would show up as more 
"active" on an fMRI
| scan.  Histological stains which show markers of 
high metabolic need are
| usually labelling inhibitory neurons, which 
tells us who the major
| "blood consumers" are in the brain.

TD E/I-minimization :-]

But the really-metabolically-expensive internal
condition occurs when neural activation becomes
relatively-random. All such instances can 
be "felt". The most-routine of these occurs during
the "startle response", when, if one works at
focussing internally, is experienced as an 
but highly-ordered flow, the end products of which
are the "orientation" behavioral manifestations 
are discussed in AoK, "Short Paper", Ap1 and Ap5,
in particular, and throughout AoK in general.

Long-term occurrences of elevated TD E/I [TD E/I
whose minimization cannot be successfully 
constitutes a relatively-random neural activation
dynamic which can be both observed in behavioral
manifestations and experienced internally, as con-
vergence 'time' courses increase in a way that 
orously reflects TD E/I. Further discussion below
[and in AoK].

| 5. Similarly, it is possible that changes in 
patterns of activity,
| rather than the overall amount of activity, 
could be far more relevant
| in processing tasks and stimuli.  The idea of 
synchronisation has been
| widely proposed as a way that processes could be 
"bound" together in
| consciousness, but that only involves altering 
the timing of spikes, not
| the overall number.  Presumably that wouldn't 
show up on fMRI at all,
| since the tissue's metabolic demands would be 

You're right, but some clarification is needed.

Given a stereotypical behavioral test, the nervous
system that can converge upon least activation
relatively rapidly will always meet the demands
of the behavioral test most successfully. This's
what, for instance, occurs within the nervous
systems of premiere athletes -- reflecting their
"genius". So overall amount of activity does
matter. Relatively-increased overall activation
always correlates to relatively-increased
randomness, which always shows up in energy-
consumption scans. But this can be a bit hard-
to-see because, as is discussed in AoK, nervous
systems 'blindly' and automatically work to
eliminate randomness, so when there's long-
term TD E/I(up), that virtually always leaves a
subject, at least temporarily with a structurally-
diminished neural architecture [hippocampal
stem cell stuff can overcome such loss].

[Sidebar on "synchronization":
The "synchronization" stuff is junk -- only
a meaningless artifact of neural activation's
being looked at without understanding the
functional neuroanatomy.

Within the "supersystem configuration"
dynamics that are discussed in AoK, Ap5,
myriad parallel processes are occurring
simultaneously. What has been considered
to constitute "synchronization" is nothing
but happenstance frequency-matching as
elements within these myriad processes are
=each= being TD E/I-minimized.

There is, of course, global integration, but
this global integration is, itself, just more
TD E/I-minimization -- TD E/I-(down) within
one dynamic can result in TD E/I(up) within
another dynamic, and TD E/I-minimization
within this second dynamic always imposes
TD E/I(up) back on the first dynamic. All
of this is commonly-observable in very-many
routine behavioral dynamics, such as hand-
eye coordination. Rather than "synchronization",
what's going on is mutual convergence upon
TD E/I(down).

The above is also flat-out-obvious in the
abstract. How can a behavioral dynamic, say,
correlate to "synchronization' when the behavioral
dynamic is, itself, everywhere-unique -- like
with respect to an arm's position in space?
Dance an arm in space, as if conducting an
orchestra. See what I mean? Everything in-
there is in a 'state' of flux. Even when an arm
is being held "perfectly still", the underpinning
neural dynamics must be always-changing
because of the physics involved. The accelera-
tion of 'gravity' must be counteracted by a
commensurate acceleration within neural
dynamics as muscular fatigue sets-in.

On top of all of this, the brain is always
doing myriad other information-processing
things in parallel with any particular thing
that's being observed, and, as above, these
myriad other information-processing dynamics
are underpinned by myriad neural activation
dynamics, all of which are being TD E/I-min-
imized in parallel, each imposing TD E/I-min-
imization adjustements upon the other.

[Side-bar to the side-bar:
I don't know if it was televised down under,
but, here in the U.S.A., PBS televised a
series on the brain back in the early 1980s.
In several of their segments "movies" of
scans were shown [I believe they were
PETs]. In these one can literally see this
mutual TD E/I adjustment =and= the
supersystem configuration dynamics that
are correlated to them. Flashes of activation,
traveling front-to-back, back-to-front, etc.
My jaw dropped down upon seeing the
"supersystem configuration" dynamics so
completely substantiated. What's more,
by working back from the old mappings
of Brodal, etc., one can analyze the dyn-
amics to =any= depth. But one has to,
first, understand "supersystem configuration"
as it's discussed in AoK, Ap5. This analysis
capability also maps directly into the "In-
ternal Frame of Reference" [IFR] simply
because of the way the great decussations
map the external environment into the nervous
system. There's one =BIG= problem inherent,
and I believe it's the one that you're ad-
dressing in your post. It is that myriad things
are happening in-parallel, and, when one
looks with a "flat" scan [which includes all
of the scanning techniques of which I'm aware],
one sees traces that correlate to =everything=
that's happening in-there. How does one go
about "separating" the 'individual' processes?
For instance, how does one "separate" activa-
tion that's best-correlated with maintenance
of proprioception with respect to the IFR?

One does this by cumulative analyses,
carrying-through each thing, working from
environment to IFR, and from the mappings
of the stereotypical functional neuroanatomy
back to the environment.

And that's the analyses that have been in AoK
all along.]

So all the "synchronization" stuff is just art-
ifactual, meaningless happenstance within
global TD E/I-minimization dynamics.

And, as you point out in your last sentence,
above, the various TD E/I(ups and downs)
tend to mask what's actually going on in-there.
It's extremely important to understand this
particular point you make. It's resolvaple
through resort to the rigorous mappings that
have been worked out by the Neuroanatomists
and the whole body of the neurophysiological
experimental literature.]

| 6. An allied argument is that changes in blood 
flow are a cumulative
| result of sustained activity, such that only the 
| changes are going to show up as changes to blood 
flow.  The blood flow
| changes necessarily lag whatever processes cause 
them, and that may take
| place over a much longer time scale than the 
processing itself takes.
| The longest-duration processes are not 
necessarily the most relevant to
| the ability under study.

And, without analyses, as I discussed above,
all one "sees" is the =sum= of myriad under-
pinning neural dynamics, flowing into each
other. This's like a surface plot. It's oblivious
to the supersystem configuration dynamics
that are active within it and which determine
everything within it.

| Finally, the major problem with fMRI is that it 
produces pretty images,
| at great expense, but really tells us very 
little about how the brain
| does what it does.  Ask yourself whether our 
knowledge of face
| recognition and how the brain does it is 
enhanced by knowing it's done
| on the fusiform gyrus, instead of knowing it 
happens in the head
| "somewhere".   Its illusion of specificity, 
combined with a lack of any
| real insight to processing, produces the 
dangerous illusion of
| understanding phenomena which in reality have 
only been *described*
| slightly more accurately.

Yeah, scans, taken alone, are insufficient.

| These and other reservations have led to fMRI 
being characterised by
| some hard-core physiologists of my acquaintance 
as "phrenology with
| coloured lights." A harsh assessment, but one 
which I have found quite
| hard to escape after hearing it.

This shortcoming is eliminated by viewing the
scans through the "lens" of NDT. [Geese! Does
that ever sound "self-serving. But it's True :-]

| Of course there are insights to be gained from 
fMRI applied with regard
| for its limitations, but there is a growing body 
of "soft" science which
| appears to regard it as a kind of x-ray vision 
where you can watch
| people thinking.  Sorry, not even close!
| > This concern was heightened recently when I 
| > an unpublished paper citing that replicability 
in PET and fMRI is difficult
| > to achieve. The author asserted that 
replicability was all but absent. When
| > I found his web page he had posted various 
editor responses and none of
| > these indicated a challenge to his paper, 
rather that he needed to do more
| > work, or it was not appropriate for that 
particular journal. The only reason
| > I read this paper is because I had noted this 
lack of replicability
| > mentioned in quite a few other papers, though 
only in passing.
| I'd love to read the paper you mention - these 
kind of views are not
| very fashionable at the moment, and it would be 
great to hear what
| others say.

The difficulty of "replicability" results, simply,
from the facts that nervous systems are always
working on myriad problems simultaneously,
and they learn -- they undergo plasticity. The
former requires that the "background" be always
different, and the latter requires that the 
different "background" always occurs within
a physically-different mapping. How can any-
thing be "replicable"?

Via the extremely-arduous way I've discussed 
Basically, it requires a thorough databasing of
both scan data and behavioral-history data [a
mapping of learning], and differential 'time'-span
analyses within these two data realms, all cross-
correlated to the full body of experiment [which
is what allows the myriad sub-processes to be

When this's done, everything is seen to reduce
to one thing: TD E/I-minimization.

This matters, because absence of understanding
of this one thing has folks killing one another 
otherwise, 'moving away from' Truth].

[Forgive me, please, Matthew [all]. No matter
where I start, I always end-up at the same 
As I said at the outset, allI'm doing is adding 
insights gained over the course of the past 34
'years' of hammering on this stuff -- in the hope
that folks'll get it. No reply expected. It's 
stuff. Just wish I could get the gist of it to the

| > Your opinion on these matters would be 
| Please bear in mind it's only an opinion, many 
others know way more than
| I do about it, and I would appreciate 
corrections, refutations and
| amplifications from others.
| Sorry to go on at such length - all this has 
been brewing at the back of
| my mind for several months.  How do I know it 
was at the BACK of my
| mind?  Well, there's this type of brain scanning 
called fMRI, and ...
| Cheers,
| Matthew.
| > ps, hope you get some rain down there soon, 
here in SE QLD dry as dust ... .
| Hope so for all of us, but if the CO2 continues 
to rise it might be an
| academic question.

Thanks for posting your thoughtful discussion, 

Cheers, ken [k. p. collins] 

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