Hi all
I would like to be certain about what are the algorithms that Freesurfer use for Segmentation of surfaces (brain-skull-skin), and after, what is the algorithm for surfaces construction and tessellation?. And moreover i would like to know if you have some papers about this topic.
Cheers.
here is a start in case you have insomnia....
Dale, A.M., Fischl, B., Sereno, M.I., 1999. Cortical surface-based analysis. I. Segmentation and surface reconstruction. Neuroimage 9, 179-194.
Dale, A.M., Sereno, M.I., 1993. Improved localization of cortical activity by combining EEG and MEG with MRI cortical surface reconstruction: a linear approach. J Cogn Neurosci 5, 162-176.
Desikan, R.S., Segonne, F., Fischl, B., Quinn, B.T., Dickerson, B.C., Blacker, D., Buckner, R.L., Dale, A.M., Maguire, R.P., Hyman, B.T., Albert, M.S., Killiany, R.J., 2006. An automated labeling system for subdividing the human cerebral cortex on MRI scans into gyral based regions of interest. Neuroimage 31, 968-980.
Fischl, B., Dale, A.M., 2000. Measuring the thickness of the human cerebral cortex from magnetic resonance images. Proc Natl Acad Sci U S A 97, 11050-11055.
Fischl, B., Liu, A., Dale, A.M., 2001. Automated manifold surgery: constructing geometrically accurate and topologically correct models of the human cerebral cortex. IEEE Trans Med Imaging 20, 70-80.
Fischl, B., Salat, D.H., 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., 2002. Whole brain segmentation: automated labeling of neuroanatomical structures in the human brain. Neuron 33, 341-355.
Fischl, B., Salat, D.H., van der Kouwe, A.J., Makris, N., Segonne, F., Quinn, B.T., Dale, A.M., 2004a. Sequence-independent segmentation of magnetic resonance images. Neuroimage 23 Suppl 1, S69-84.
Fischl, B., Sereno, M.I., Dale, A.M., 1999a. Cortical surface-based analysis. II: Inflation, flattening, and a surface-based coordinate system. Neuroimage 9, 195-207.
Fischl, B., Sereno, M.I., Tootell, R.B., Dale, A.M., 1999b. High-resolution intersubject averaging and a coordinate system for the cortical surface. Hum Brain Mapp 8, 272-284.
Fischl, B., van der Kouwe, A., Destrieux, C., Halgren, E., Segonne, F., Salat, D.H., Busa, E., Seidman, L.J., Goldstein, J., Kennedy, D., Caviness, V., Makris, N., Rosen, B., Dale, A.M., 2004b. Automatically parcellating the human cerebral cortex. Cereb Cortex 14, 11-22.
Han, X., Jovicich, J., Salat, D., van der Kouwe, A., Quinn, B., Czanner, S., Busa, E., Pacheco, J., Albert, M., Killiany, R., Maguire, P., Rosas, D., Makris, N., Dale, A., Dickerson, B., Fischl, B., 2006. Reliability of MRI-derived measurements of human cerebral cortical thickness: the effects of field strength, scanner upgrade and manufacturer. Neuroimage 32, 180-194.
Jovicich, J., Czanner, S., Greve, D., Haley, E., van der Kouwe, A., Gollub, R., Kennedy, D., Schmitt, F., Brown, G., Macfall, J., Fischl, B., Dale, A., 2006. Reliability in multi-site structural MRI studies: effects of gradient non-linearity correction on phantom and human data. Neuroimage 30, 436-443.
Reuter, M., Schmansky, N.J., Rosas, H.D., Fischl, B. 2012. Within-Subject Template Estimation for Unbiased Longitudinal Image Analysis. Neuroimage 61 (4), 1402-1418. http://reuter.mit.edu/papers/reuter-long12.pdf
Reuter, M., Fischl, B., 2011. Avoiding asymmetry-induced bias in longitudinal image processing. Neuroimage 57 (1), 19-21. http://reuter.mit.edu/papers/reuter-bias11.pdf
Reuter, M., Rosas, H.D., Fischl, B., 2010. Highly Accurate Inverse Consistent Registration: A Robust Approach. Neuroimage 53 (4), 1181–1196. http://reuter.mit.edu/papers/reuter-robreg10.pdf
Rosas, H.D., Liu, A.K., Hersch, S., Glessner, M., Ferrante, R.J., Salat, D.H., van der Kouwe, A., Jenkins, B.G., Dale, A.M., Fischl, B., 2002. Regional and progressive thinning of the cortical ribbon in Huntington's disease. Neurology 58, 695-701.
Segonne, F., Dale, A.M., Busa, E., Glessner, M., Salat, D., Hahn, H.K., Fischl, B., 2004. A hybrid approach to the skull stripping problem in MRI. Neuroimage 22, 1060-1075.
Segonne, F., Pacheco, J., Fischl, B., 2007. Geometrically accurate topology-correction of cortical surfaces using nonseparating loops. IEEE Trans Med Imaging 26, 518-529.
Sled, J.G., Zijdenbos, A.P., Evans, A.C., 1998. A nonparametric method for automatic correction of intensity nonuniformity in MRI data. IEEE Trans Med Imaging 17, 87-97.
On Fri, 15 Apr 2016, Gamaliel Huerta Urrea wrote:
Hi all I would like to be certain about what are the algorithms that Freesurfer use for Segmentation of surfaces (brain-skull-skin), and after, what is the algorithm for surfaces construction and tessellation?. And moreover i would like to know if you have some papers about this topic.
Cheers.
-- Gamaliel Huerta Ingeniero Civil Biomédico HealthCare Analytics Centro Interdisciplinario de Innovación en Salud Universidad de Valparaíso
joajoajojoa Thanks, chers from Chile
2016-04-15 9:46 GMT-03:00 Bruce Fischl fischl@nmr.mgh.harvard.edu:
here is a start in case you have insomnia....
Dale, A.M., Fischl, B., Sereno, M.I., 1999. Cortical surface-based analysis. I. Segmentation and surface reconstruction. Neuroimage 9, 179-194.
Dale, A.M., Sereno, M.I., 1993. Improved localization of cortical activity by combining EEG and MEG with MRI cortical surface reconstruction: a linear approach. J Cogn Neurosci 5, 162-176.
Desikan, R.S., Segonne, F., Fischl, B., Quinn, B.T., Dickerson, B.C., Blacker, D., Buckner, R.L., Dale, A.M., Maguire, R.P., Hyman, B.T., Albert, M.S., Killiany, R.J., 2006. An automated labeling system for subdividing the human cerebral cortex on MRI scans into gyral based regions of interest. Neuroimage 31, 968-980.
Fischl, B., Dale, A.M., 2000. Measuring the thickness of the human cerebral cortex from magnetic resonance images. Proc Natl Acad Sci U S A 97, 11050-11055.
Fischl, B., Liu, A., Dale, A.M., 2001. Automated manifold surgery: constructing geometrically accurate and topologically correct models of the human cerebral cortex. IEEE Trans Med Imaging 20, 70-80.
Fischl, B., Salat, D.H., 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., 2002. Whole brain segmentation: automated labeling of neuroanatomical structures in the human brain. Neuron 33, 341-355.
Fischl, B., Salat, D.H., van der Kouwe, A.J., Makris, N., Segonne, F., Quinn, B.T., Dale, A.M., 2004a. Sequence-independent segmentation of magnetic resonance images. Neuroimage 23 Suppl 1, S69-84.
Fischl, B., Sereno, M.I., Dale, A.M., 1999a. Cortical surface-based analysis. II: Inflation, flattening, and a surface-based coordinate system. Neuroimage 9, 195-207.
Fischl, B., Sereno, M.I., Tootell, R.B., Dale, A.M., 1999b. High-resolution intersubject averaging and a coordinate system for the cortical surface. Hum Brain Mapp 8, 272-284.
Fischl, B., van der Kouwe, A., Destrieux, C., Halgren, E., Segonne, F., Salat, D.H., Busa, E., Seidman, L.J., Goldstein, J., Kennedy, D., Caviness, V., Makris, N., Rosen, B., Dale, A.M., 2004b. Automatically parcellating the human cerebral cortex. Cereb Cortex 14, 11-22.
Han, X., Jovicich, J., Salat, D., van der Kouwe, A., Quinn, B., Czanner, S., Busa, E., Pacheco, J., Albert, M., Killiany, R., Maguire, P., Rosas, D., Makris, N., Dale, A., Dickerson, B., Fischl, B., 2006. Reliability of MRI-derived measurements of human cerebral cortical thickness: the effects of field strength, scanner upgrade and manufacturer. Neuroimage 32, 180-194.
Jovicich, J., Czanner, S., Greve, D., Haley, E., van der Kouwe, A., Gollub, R., Kennedy, D., Schmitt, F., Brown, G., Macfall, J., Fischl, B., Dale, A., 2006. Reliability in multi-site structural MRI studies: effects of gradient non-linearity correction on phantom and human data. Neuroimage 30, 436-443.
Reuter, M., Schmansky, N.J., Rosas, H.D., Fischl, B. 2012. Within-Subject Template Estimation for Unbiased Longitudinal Image Analysis. Neuroimage 61 (4), 1402-1418. http://reuter.mit.edu/papers/reuter-long12.pdf
Reuter, M., Fischl, B., 2011. Avoiding asymmetry-induced bias in longitudinal image processing. Neuroimage 57 (1), 19-21. http://reuter.mit.edu/papers/reuter-bias11.pdf
Reuter, M., Rosas, H.D., Fischl, B., 2010. Highly Accurate Inverse Consistent Registration: A Robust Approach. Neuroimage 53 (4), 1181–1196. http://reuter.mit.edu/papers/reuter-robreg10.pdf
Rosas, H.D., Liu, A.K., Hersch, S., Glessner, M., Ferrante, R.J., Salat, D.H., van der Kouwe, A., Jenkins, B.G., Dale, A.M., Fischl, B., 2002. Regional and progressive thinning of the cortical ribbon in Huntington's disease. Neurology 58, 695-701.
Segonne, F., Dale, A.M., Busa, E., Glessner, M., Salat, D., Hahn, H.K., Fischl, B., 2004. A hybrid approach to the skull stripping problem in MRI. Neuroimage 22, 1060-1075.
Segonne, F., Pacheco, J., Fischl, B., 2007. Geometrically accurate topology-correction of cortical surfaces using nonseparating loops. IEEE Trans Med Imaging 26, 518-529.
Sled, J.G., Zijdenbos, A.P., Evans, A.C., 1998. A nonparametric method for automatic correction of intensity nonuniformity in MRI data. IEEE Trans Med Imaging 17, 87-97.
On Fri, 15 Apr 2016, Gamaliel Huerta Urrea wrote:
Hi all
I would like to be certain about what are the algorithms that Freesurfer use for Segmentation of surfaces (brain-skull-skin), and after, what is the algorithm for surfaces construction and tessellation?. And moreover i would like to know if you have some papers about this topic.
Cheers.
-- Gamaliel Huerta Ingeniero Civil Biomédico HealthCare Analytics Centro Interdisciplinario de Innovación en Salud Universidad de Valparaíso
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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freesurfer@nmr.mgh.harvard.edu
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Gamaliel Huerta Urrea