back from vacation. Thanks ever so much for this Pedro. It will keep me
on track.
Pedro Paulo de Magalhães Oliveira Junior wrote:
Matt,
I have a table I use sometimes. It contains 12 references I believe
are the most important and their role in recon-all process.
Regards,
PPJ
2008/9/12 Bruce Fischl <[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>>
Hi Matt,
the Segonne paper is the current skull stripping (the hybrid one),
although it's evolved somewhat since then (unpublished). The
segmentation is both those papers (the first one is the
segmentation methodology, the 2nd is the addition of a nonlinear
warp), plus the more recent one with Han as the 1st author
describing how we reestimate the atlas to account for sequence
differences. The surface stuff is similar in that the 93 paper is
still relevant as are the two 99 papers, then the parcellation,
spherical morphing, topology correction and more recent (Desikan)
parcellation.
cheers,
Bruce
On Fri, 12 Sep 2008, Matt Clarkson wrote:
Hi Bruce,
for sure, I didnt expect it to all be in one place!
For example, what I believe are the original papers
(Neuroimage 9 1999, and the 1993 Cognitive Neuroscience
paper), describe the first method, then we have all the other
subsequent papers. So for example, does the current
methodology use the brain stripping from Neuroimage 22 (2004),
(i believe it does, but I'm a newbie.), and is the volume
segmentation best described in the 2002 Neurotechnique paper
"Whole brain segmentation...."? Or has it been superceded by
the methodology in Neuroimage 23 (2004) "Sequence-independent
segmentation of magnetic resonance imaging".
I suppose, another way of phrasing the question is simply,
which methodology papers are in the current software version,
which ones have been superseded, and which ones are totally
cutting edge research, and not part of the software package?
I just wondered if anyone had a view on this, or compiled a
handy list that they would be willing to share?
Many thanks in advance.
Matt
Matt Clarkson
Senior Research Associate
Dementia Research Centre
UCL
Institute Of Neurology
Queen Square
London WC1N 3BG
[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>
Tel: 08451 555 000 ext. 723653
Fax: 020 7676 2066
Bruce Fischl wrote:
Hi Matt,
the methodologies are described in those papers. Sorry, I
don't think there's any one or two paper summary - it's
just too much stuff over the years (topology correction,
segmentation, surface analysis, morphing, etc....).
Bruce
On Fri, 12 Sep 2008, Matt Clarkson wrote:
Dear everyone,
Hopefully someone can help me. If I do "recon-all
--help" i can see a list of 31 steps for the main
cortical thickness pipeline. Does anyone have a list
that links each of the 31 steps to the most current
methodology paper?
I've been reading most of the methodology papers
referenced in the wiki, but the software has clearly
evolved over the years, and even though you can read
the wiki, and trawl through log files, I want to be
absolutely sure that for each step, I know exactly
what algorithm is applied. Has anyone gone through
this before?
Thanks in advance,
Matt
Matt Clarkson
Senior Research Associate
Dementia Research Centre
UCL
Institute Of Neurology
Queen Square
London WC1N 3BG
[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>
Tel: 08451 555 000 ext. 723653
Fax: 020 7676 2066
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