Surfers, Can someone please point me towards some detailed description of the algorithms that freesurfer uses to process the data.......maybe there are some papers that talk about this?? Anthony
Be careful what you ask for :)
-------------------------------------------------------------- if you use surface recons
Dale, A.M. and M.I. Sereno (1993) Improved localization of cortical activity by combining EEG and MEG with MRI cortical surface reconstruction: A linear approach. Journal of Cognitive Neuroscience 5:162-176.
Segonne F, Dale, AM, Busa E, Glessner M, Salvolini U, Hahn HK, Fischl B, A Hybrid Approach to the Skull-Stripping Problem in MRI. NeuroImage, 22, pp. 1160-1075, 2004
Dale, A.M., Fischl, Bruce, Sereno, M.I., (1999). Cortical Surface-Based Analysis I: Segmentation and Surface Reconstruction. NeuroImage 9(2):179-194
Fischl, Bruce, Sereno, M.I., Dale, A.M., (1999). Cortical Surface-Based Analysis II: Inflation, Flattening, and a Surface-Based Coordinate System. NeuroImage 9(2):195-207
Fischl, Bruce, Liu, Arthur, and Dale, A.M., (2001). Automated Manifold Surgery: Constructing Geometrically Accurate and Topologically Correct Models of the Human Cerebral Cortex. IEEE Transactions on Medical Imaging, 20(1):70-80
if you do inter-subject spherical averaging
Fischl, Bruce, Sereno, M.I., Tootell, R.B.H., and Dale, A.M., (1999). High-resolution inter-subject averaging and a coordinate system for the cortical surface. Human Brain Mapping, 8:272-284
if you do a thickness study
Fischl, Bruce, and Dale, A.M., (2000). Measuring the Thickness of the Human Cerebral Cortex from Magnetic Resonance Images. Proceedings of the National Academy of Sciences, 97:11044-11049.
if you use cortical parcellations
Fischl B, van der Kouwe A, Destrieux C, Halgren E, Ségonne F, Salat DH, Busa E, Seidman LJ, Goldstein J, Kennedy D, Caviness V, Makris N, Rosen B, Dale, AM Automatically Parcellating the Human Cerebral Cortex. Cerebral Cortex, 2004; 14:11-22.
there should be another one here by Desikan and Killiany - I'll have to add it.
if you do subcortical segmentation
Fischl B, Salat DH, van der Kouwe AJW, Makris N, Ségonne F, Dale AM. Sequence-Independent Segmentation of Magnetic Resonance Images. NeuroImage 23 Suppl 1, S69-84.
Fischl B, Salat D, Busa E, Albert M, Dieterich M, Haselgrove C, van der Kouwe A, Killiany R, Kennedy D, Klaveness S, Montillo A, Makris N, Rosen B, Dale A.M.. Whole brain segmentation. Automated labeling of neuroanatomical structures in the human brain. Neuron. 2002; 33(3): 341-355.
misc other ones
F. Segonne, E. Grimson and B. Fischl (2003). Topology Correction of Subcortical Segmentation", MICCAI 2003.
Salat DH, Buckner RL, Snyder AZ, Greve DN, Desikan RSR, Busa E, Morris JC, Dale AM, Fischl B. Thinning of the cerebral cortex in aging. Cerebral Cortex. Accepted with revision.
On Thu, 18 May 2006, anthony gallo wrote:
Surfers, Can someone please point me towards some detailed description of the algorithms that freesurfer uses to process the data.......maybe there are some papers that talk about this?? Anthony
btw, most of these are also listed at the end of:
recon-all -help
Bruce Fischl wrote:
Be careful what you ask for :)
if you use surface recons
Dale, A.M. and M.I. Sereno (1993) Improved localization of cortical activity by combining EEG and MEG with MRI cortical surface reconstruction: A linear approach. Journal of Cognitive Neuroscience 5:162-176.
Segonne F, Dale, AM, Busa E, Glessner M, Salvolini U, Hahn HK, Fischl B, A Hybrid Approach to the Skull-Stripping Problem in MRI. NeuroImage, 22, pp. 1160-1075, 2004
Dale, A.M., Fischl, Bruce, Sereno, M.I., (1999). Cortical Surface-Based Analysis I: Segmentation and Surface Reconstruction. NeuroImage 9(2):179-194
Fischl, Bruce, Sereno, M.I., Dale, A.M., (1999). Cortical Surface-Based Analysis II: Inflation, Flattening, and a Surface-Based Coordinate System. NeuroImage 9(2):195-207
Fischl, Bruce, Liu, Arthur, and Dale, A.M., (2001). Automated Manifold Surgery: Constructing Geometrically Accurate and Topologically Correct Models of the Human Cerebral Cortex. IEEE Transactions on Medical Imaging, 20(1):70-80
if you do inter-subject spherical averaging
Fischl, Bruce, Sereno, M.I., Tootell, R.B.H., and Dale, A.M., (1999). High-resolution inter-subject averaging and a coordinate system for the cortical surface. Human Brain Mapping, 8:272-284
if you do a thickness study
Fischl, Bruce, and Dale, A.M., (2000). Measuring the Thickness of the Human Cerebral Cortex from Magnetic Resonance Images. Proceedings of the National Academy of Sciences, 97:11044-11049.
if you use cortical parcellations
Fischl B, van der Kouwe A, Destrieux C, Halgren E, Ségonne F, Salat DH, Busa E, Seidman LJ, Goldstein J, Kennedy D, Caviness V, Makris N, Rosen B, Dale, AM Automatically Parcellating the Human Cerebral Cortex. Cerebral Cortex, 2004; 14:11-22.
there should be another one here by Desikan and Killiany - I'll have to add it.
if you do subcortical segmentation
Fischl B, Salat DH, van der Kouwe AJW, Makris N, Ségonne F, Dale AM. Sequence-Independent Segmentation of Magnetic Resonance Images. NeuroImage 23 Suppl 1, S69-84.
Fischl B, Salat D, Busa E, Albert M, Dieterich M, Haselgrove C, van der Kouwe A, Killiany R, Kennedy D, Klaveness S, Montillo A, Makris N, Rosen B, Dale A.M.. Whole brain segmentation. Automated labeling of neuroanatomical structures in the human brain. Neuron. 2002; 33(3): 341-355.
misc other ones
F. Segonne, E. Grimson and B. Fischl (2003). Topology Correction of Subcortical Segmentation", MICCAI 2003.
Salat DH, Buckner RL, Snyder AZ, Greve DN, Desikan RSR, Busa E, Morris JC, Dale AM, Fischl B. Thinning of the cerebral cortex in aging. Cerebral Cortex. Accepted with revision.
On Thu, 18 May 2006, anthony gallo wrote:
Surfers, Can someone please point me towards some detailed description of the algorithms that freesurfer uses to process the data.......maybe there are some papers that talk about this?? Anthony
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Anthony,
See the references section at the bottom of the main wiki page, where most of the papers themselves can be downloaded:
https://surfer.nmr.mgh.harvard.edu/fswiki
On Thu, 2006-05-18 at 17:02 -0400, Doug Greve wrote:
btw, most of these are also listed at the end of:
recon-all -help
Bruce Fischl wrote:
Be careful what you ask for :)
if you use surface recons
Dale, A.M. and M.I. Sereno (1993) Improved localization of cortical activity by combining EEG and MEG with MRI cortical surface reconstruction: A linear approach. Journal of Cognitive Neuroscience 5:162-176.
Segonne F, Dale, AM, Busa E, Glessner M, Salvolini U, Hahn HK, Fischl B, A Hybrid Approach to the Skull-Stripping Problem in MRI. NeuroImage, 22, pp. 1160-1075, 2004
Dale, A.M., Fischl, Bruce, Sereno, M.I., (1999). Cortical Surface- Based Analysis I: Segmentation and Surface Reconstruction. NeuroImage 9(2):179-194
Fischl, Bruce, Sereno, M.I., Dale, A.M., (1999). Cortical Surface- Based Analysis II: Inflation, Flattening, and a Surface-Based Coordinate System. NeuroImage 9(2):195-207
Fischl, Bruce, Liu, Arthur, and Dale, A.M., (2001). Automated Manifold Surgery: Constructing Geometrically Accurate and Topologically Correct Models of the Human Cerebral Cortex. IEEE Transactions on Medical Imaging, 20(1):70-80
if you do inter-subject spherical averaging
Fischl, Bruce, Sereno, M.I., Tootell, R.B.H., and Dale, A.M., (1999). High-resolution inter-subject averaging and a coordinate system for the cortical surface. Human Brain Mapping, 8:272-284
if you do a thickness study
Fischl, Bruce, and Dale, A.M., (2000). Measuring the Thickness of the Human Cerebral Cortex from Magnetic Resonance Images. Proceedings of the National Academy of Sciences, 97:11044-11049.
if you use cortical parcellations
Fischl B, van der Kouwe A, Destrieux C, Halgren E, Ségonne F, Salat DH, Busa E, Seidman LJ, Goldstein J, Kennedy D, Caviness V, Makris N, Rosen B, Dale, AM Automatically Parcellating the Human Cerebral Cortex. Cerebral Cortex, 2004; 14:11-22.
there should be another one here by Desikan and Killiany - I'll have to add it.
if you do subcortical segmentation
Fischl B, Salat DH, van der Kouwe AJW, Makris N, Ségonne F, Dale AM. Sequence-Independent Segmentation of Magnetic Resonance Images. NeuroImage 23 Suppl 1, S69-84.
Fischl B, Salat D, Busa E, Albert M, Dieterich M, Haselgrove C, van der Kouwe A, Killiany R, Kennedy D, Klaveness S, Montillo A, Makris N, Rosen B, Dale A.M.. Whole brain segmentation. Automated labeling of neuroanatomical structures in the human brain. Neuron. 2002; 33(3): 341-355.
misc other ones
F. Segonne, E. Grimson and B. Fischl (2003). Topology Correction of Subcortical Segmentation", MICCAI 2003.
Salat DH, Buckner RL, Snyder AZ, Greve DN, Desikan RSR, Busa E, Morris JC, Dale AM, Fischl B. Thinning of the cerebral cortex in aging. Cerebral Cortex. Accepted with revision.
On Thu, 18 May 2006, anthony gallo wrote:
Surfers, Can someone please point me towards some detailed description of the algorithms that freesurfer uses to process the data.......maybe there are some papers that talk about this?? Anthony
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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