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
m.clarkson@ucl.ac.uk Tel: 08451 555 000 ext. 723653 Fax: 020 7676 2066
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
m.clarkson@ucl.ac.uk 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
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 Or has it been superceded by the methodology in Neuroimage 23 (2004) "Sequence-independent segmentation of magnetic resonance imaging".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
m.clarkson@ucl.ac.uk 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
m.clarkson@ucl.ac.uk 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
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
m.clarkson@ucl.ac.uk 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
m.clarkson@ucl.ac.uk 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
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 fischl@nmr.mgh.harvard.edu
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
m.clarkson@ucl.ac.uk 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
m.clarkson@ucl.ac.uk 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,
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 < ppj@netfilter.com.br> 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 fischl@nmr.mgh.harvard.edu
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
m.clarkson@ucl.ac.uk 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
m.clarkson@ucl.ac.uk 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
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 <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu>
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 m.clarkson@ucl.ac.uk <mailto:m.clarkson@ucl.ac.uk> 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 m.clarkson@ucl.ac.uk <mailto:m.clarkson@ucl.ac.uk> Tel: 08451 555 000 ext. 723653 Fax: 020 7676 2066 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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@nmr.mgh.harvard.edu
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Bruce Fischl -
Margaret Sheridan -
Matt Clarkson -
Pedro Paulo de Magalhães Oliveira Junior