Hi Anthony
we included the tracts that we found that we could segment reliably, under
the guidance of a trained neuroanatomist. Certainly we can only do as well
as the information contained in the diffusion data, but we have found that
we can automated what someone with neuroanatomical expertise could obtain
by following the Wakana protocol. I don't think we make any claims beyond
that, but in and of itself it seemed like a worthy goal, opening up the
field of tractography to a bigger potential user pool. Certainly that
comes with potential problems, as it does in fMRI. I don't see it being
significantly different than people guessing Brodmann areal identity based
on visual inspection of folding patterns and presumed homology with the
macaque. It's a useful tool, but like all tools you can overintepret the
results if you are not cautious.
cheers
Bruce
On Wed, 15 Jun 2011, Anthony Dick wrote:
> Hello Anastasia,
>
> This just reinforces my point. Tracts #7 and #8 of that paper are the
> inferior longitudinal fasciculus and the inferior occipitofrontal
> fasciculus, respectively. But you have chosen to leave one out
> (incidentally, both appear in the Oishi atlas). Note that in this paper,
> the authors recommend manual intervention for certain tracts.
>
> When a tool like this is developed, it gets referenced in papers which
> gives it a kind of legitimacy. What we want to avoid here is giving
> legitimacy to fiber pathways that may not actually exist, or missing
> ones that do because the tool left them out. So what is the rule for how
> pathways are added or removed from this tool? It seems that simply
> requesting that they be added can potentially result in such an
> addition, or that deciding not to include a tract for whatever reason
> can result in its disappearance. This gives any pathway identified by
> this tool a legitimacy it might not otherwise have.
>
> I am not necessarily against the tool (I think it is better for
> exploratory analysis), but I am against the idea, from the Wiki, that
> Tracula "obviates the need for manual intervention for tract solutions
> and thus facilitates the application of tractography to large datasets".
> This seems to me to be a horrible idea. Tractography is not at this
> point a completely data driven procedure.
>
> Anthony
>
> On 6/15/11 12:44 PM, Anastasia Yendiki wrote:
> >
> > Hi Anthony - The labeling was done based on Wakana et al 2007. We did
> > not include the IFOF exactly b/c of the controversy surrounding it.
> >
> > a.y
> >
> > On Wed, 15 Jun 2011, Anthony Dick wrote:
> >
> > > Hello all,
> > >
> > > Is there any atlas to which these tracs are referenced? For cortical
> > > anatomical boundaries there is broad consensus and a published
> > > referenced
> > > atlas, which makes Freesurfer's automatic parcellation of cortical
> > > regions
> > > an excellent tool. But there is not (as is often assumed) as broad a
> > > consensus on white matter tracts (e.g., there is no middle
> > > longitudinal
> > > fasciculus in the recent Oishi et al. white matter atlas and many
> > > would
> > > argue it doesn't exist; the existence of separate inferior
> > > longitudinal
> > > fasciculus and inferior occipitofrontal fasciculus is disputed;
> > > Catani's
> > > arcuate fasciculus is based on one paper etc.). Is it such a good
> > > idea to go
> > > automatically identifying white matter tracts without saying how
> > > they
> > > are
> > > identified?
> > >
> > > Anthony
> > >
> > > On 6/15/11 12:07 PM, Seán Froudist Walsh wrote:
> > > Hi Anastasia,
> > >
> > > Thanks for getting back to me and well done on making a very
> > > nice program. The first tracts I would like to have are the
> > > optic radiations, but there are others that would be nice to
> > > include: a three part arcuate fasiculus (a la Catani et al.,
> > > 2005) rather than a 2 part one, Fornix, anterior commissure.
> > >
> > > If I were to manually do the dissections for the 33 subjects,
> > > what would be the most Tracula compatible way of doing it? I
> > > normally use TrackVis but I figure making all of the file
> > > conversions might be a nightmare. Which program was used in
> > > the
> > > original virtual dissections?
> > >
> > > Any further suggestions? Perhaps some of these tracts are
> > > included but I've missed them.
> > >
> > > Sean
> > >
> > >
> > >
> > > On 15 June 2011 08:37, Anastasia Yendiki
> > > <[email protected]> wrote:
> > >
> > > Hi Seán - Which tracts do you want to add? Our
> > > existing tracts have been labeled on 33 healthy
> > > subjects. It's certainly possible to include new
> > > tracts in the atlas but someone has to do the
> > > labeling on the same or a similar set of subjects.
> > >
> > > a.y
> > >
> > > On Wed, 15 Jun 2011, Seán Froudist Walsh wrote:
> > >
> > > Hi FreeSurfing Gurus,
> > >
> > > I would like to add some new tracts to
> > > the Tracula pipeline using my own
> > > regions of interest. What would be the
> > > best way to do this?
> > >
> > > All the best and many thanks in advance,
> > >
> > > Seán
> > >
> > >
> > >
> > >
> > >
> > >
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