Christopher Bailey wrote:

>Perhaps I shouldn't start this thread...but I'm so tempted...
>
No worry... I bite. As long as this don't start up a flame war that's
valid discussion. Please understand that I'm looking at it from an
engineer point of view.

By the way, I only focus on the subject of "Talairach vs MNI" and is
*NOT* commenting on why FSL is using MNI.

>
>Here's how I understand the Talairach VS MNI issue (most of it thanks to
>Matt Brett, see):
>
>http://www.mrc-cbu.cam.ac.uk/Imaging/Common/mnispace.shtml
>
>The brain sliced and diced by Talairach and Tournoux in the late 80s was
>that of a small elderly woman. The brain had been lying around in a jar
>of formaldehyde for some significant amount of time before the fellows
>started on the project. How well does this brain represent our typical
>(cognitive at least) FMRI subject population? How well does any single
>brain?
>
Its always a trade off. With only one brain, the results can be skewed
towards that brain's particularity. However, if you start averaging
brains, the brain regions become more fuzzy as there is a smoothing
effect. Not to mention that your transform parameter might matter.

Now, if you are worry about formadehyde distorting the brain (which as a
layman, I think it will), and I worry about averaging having a
detrimental effect, why not we try using the two brains from the
"Visiable Human Project". At least the male subject (god bless him), is
as "fresh" as you can get, and the resolution the best. Combining him
with her, we might have a very detail map with good labelling. At such
resolution, we might be able to introduce engineering principles such as
uncertainty measurement.

The biggest problem as I can see with any altas is the accuracy. I know
of people looking at areas 3mm across, but in imaging accept anything
6mm around the area of interest to be spot on the area. I even went into
a bitter discussion with somebody on it (I say 6mm is spot on, (s)he
says, no, its 3mm away and therefore on the wrong region). I think what
we need is a measure of confidence, say 3mm +/- 1mm at 90% confident
interval. That, together with good labelling on the template, will give
me more confident on my result.

>Another matter is their Brodmann labelling: they never performed
>/any/ histological examinations on their brain! Brodmann areas were
>written down on the basis of comparing their own drawings to those of
>Brodmann... A group in Germany presented progress on some some serious
>work on a Brodmann atlas at HBM04; we shall no doubt hear about that
>soon.
>
>The MNI 152 is the first "half" of a bigger average standard brain
>called prospectively something like the ICBM brain. [For some strange
>reason, the other half has never emerged...?] It is a linear average of
>152 "young adults". It's origin is defined to be at the AC, just like in
>the Talairach atlas. Not surprisingly, the MNI average differs from the
>Talairach brain (cf. ages, genders, no formaldehyde...). Basically, the
>further you go from AC, the less structures align.
>
>
That's probably true with any templates. It all depends on how the
averaging etc is done.

>mni2tal.m is a piecewise-linear (i.e. globally nonlinear) transformation
>from MNI "space" to Talairach "space". Different transformations are
>applied different parts of the brain to try to squeeze the MNI average
>into an old woman's brain...
>
So with transformation the other way round. The thing is, the more
transformation you do, the less accurate your result. Transforming from
subject space -> MNI ->Talairach is going to introduce more uncertainty,
then a direct subject space -> Talairach alone.

>
>Why are we so bent on giving coordinates relative to the AC of a single
>old woman? Because we want to use the atlas to give names to our blobs,
>even Brodmann-names?
>
Conversely, why so bent on giving corrdinates relative to a smooth (read
fuzzy) average brain image of 152 subjects? When transforming to a
single brain, although the brain is distorted (with or without
formadihyde), might be better if the actual brain coordinate can be
determine accurately. Ever consider this?

This are all trade-off. As I see it, engineering problems.

>Personally, after reading about the issue, I
>decided it would be more productive to spend some time learning
>neuroanatomy. Identifying structures in MRs isn't impossible, even for a
>computer-geek such as myself.
>
I suggest adding an extra dimension, since you claim to be a geek:
Understand the error introduce in the acquisition of data, how it
affects transformation etc. This is because in the end, it comes back to
how well can you trust the data.

>
>Don't get me wrong, coordinates are great. That way we can double-check
>each other, compare activations etc.
>
But you must understand the error in the measurement etc. This, I'm
afraid, most users do not.

>In principle, I mean, because the
>confusion around MNI/Talairach has been around for so long now that I
>don't know what to think when I read publications. Are they really
>Talairach coordinates (how did they get them?), or are they actually MNI
>and they just didn't realise (cf. the naming confusion even in FSL:
>img2talcoord)? I think the problem is that "Talairach space" has become
>a synonym for "standard space" and the distinction vanishes into the
>code of the software packages we use.
>
Let's just say Talairach is the de-facto standard. One way of seeing it
as the "standard space" is that it is the reference to wich all other
coordinate system can be compared to. It might or might not be the
lowest standard, but at least its a standard useful for comparing. As a
universal "standard", it is going to be much better then everyone
finding their own standard to compare to.

>
>I would advocate the use of the MNI average both as the registration
>standard (as is allways the case) and as the coordinate system when
>reporting activations. mni2tal just adds a layer of uncertainty to the
>whole process (can you imagine what a "piecewise linear" transformation
>does?). I also suggest that the FSL developers change their naming
>conventions, since when most of us see the word "Talairach", we
>instantly get a mental image of the atlas.
>
>
I'm neutral on the subject. As long as the user knows what they are
doing, that's fine.

The questions here is whatever everyone else is comfortable in doing
this. If everyone is using "Talairach" and you are using "MNI", your
coordinate system might be superior, but if others have to convert it
back to "Talairach", that makes discussion difficult.

Thanks,
Cinly