Perhaps I shouldn't start this thread...but I'm so tempted...
Here's how I understand the Talairach VS MNI issue (most of it thanks to
Matt Brett, see):
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? 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
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.
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...
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? 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.
Don't get me wrong, coordinates are great. That way we can double-check
each other, compare activations etc. 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.
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.
But that's just me! All the best,
Christopher Bailey <[log in to unmask]>
PET Centre and
Center for Functionally Integrative Neuroscience
Aarhus University Hospital, Denmark
On Wed, 2004-09-29 at 21:08, Jason Craggs wrote:
> There is/was a mni2tal script used in SPM.
> I am not sure how 'portable' it is but you may want to look into it.
> -----Original Message-----
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On
> Behalf Of Mark Jenkinson
> Sent: Wednesday, September 29, 2004 4:03 AM
> To: [log in to unmask]
> Subject: Re: [FSL] Talairach space registration
> Our standard space images are in MNI space, not strict-Talairach
> space and I'm afraid we don't have any conversion available.
> As for relating the coordinates - the program tal2imgcoord
> and img2talcoord (although they work with MNI, not Talairach
> coordinates as they mis-leadingly suggest) give you the
> ability to relate any voxel coordinate in the image (pre-aligned)
> with the corresponding aligned coordinate given the images
> and the transformation matrix.
> Hope that does what you want.
> All the best,
> On 28 Sep 2004, at 18:39, Stamatis Sotiropoulos wrote:
> > Hi all,
> > I am using FLIRT and trying to register my T1 MRI scans in
> > space. I have a couple of questions:
> > -Is the "avg152T1..." template (which is available in fsl folders) the
> > right one? Is this a template for Talairach or for MNI coordinates? If
> > it
> > is an MNI template is there one available for Talairach space?
> > -Can I somehow get a relationship between the initial coordinate
> > (the one before alignment) and the final coordinate system? In other
> > words
> > can I relate the targeted coordinate system (Talairach or MNI) with
> > the
> > coordinate system of the scanner?
> > Thank you in advance,
> > Stamatis