Pedro, That was a really helpful organizational tool for the rest of us - Matt, I also hope you found it helpful. Thanks!
Margaret On Sun, Sep 14, 2008 at 2:48 PM, Pedro Paulo de Magalhães Oliveira Junior < [EMAIL PROTECTED]> 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]> > > 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 although it's evolved somewhat since then (unpublished).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 been superceded by the methodology in Neuroimage 23 (2004) 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 superseded, and which ones are totally cutting edge research, and not part 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 >>>>> >>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer@nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> >>>>> >>>>> >>>> >>> >>> >>> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > > > > -- > ----------------------------------------------------------- > Pedro Paulo de M. Oliveira Junior > Diretor de Operações > Netfilter & SpeedComm Telecom > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >
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