Hi Anthony
we are trying to get that piece of it published :) Hopefully soon!
Bruce
On Wed, 15 Jun 2011,
Anthony Dick wrote:
Good points Bruce. I guess I am more worried about the people using it, who
will not be as cautious for large datasets. Also--one thing that was a huge
benefit for the cortical parcellation was a quantification of the manual vs.
automated parcellation differences, but this does not appear to be published
yet (unless I missed it). Any added pathways should have to meet the same
standards.
Anthony
On 6/15/11 1:07 PM, Bruce Fischl wrote:
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
<ayend...@nmr.mgh.harvard.edu> 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
The information in this e-mail is intended only for the person
to whom it is
addressed. If you believe this e-mail was sent to you in error
and the e-mail
contains patient information, please contact the Partners
Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent
to you in error
but does not contain patient information, please contact the
sender and properly
dispose of the e-mail.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to
whom it is
addressed. If you believe this e-mail was sent to you in error and
the e-mai
l
contains patient information, please contact the Partners Compliance
HelpLin
e at
http://www.partners.org/complianceline . If the e-mail was sent to
you in er
ror
but does not contain patient information, please contact the sender
and prop
erly
dispose of the e-mail.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
