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it's evolved somewhat since then (unpublished).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superceded by the methodology in Neuroimage 23 (2004) "Sequence-independent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papers are in the current software version, which ones have been superseded,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]
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]
Tel: 08451 555 000 ext. 723653
Fax: 020 7676 2066
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