Dear morphometricians: Thanks to all who replied to my question last week on software solutions, which can be used to analyze 3D data plus published relevant case studies.
To summarize, I mix parts of the original replies of several people. Most people recommended Morphologika, which is downloadable from the following website http://www.york.ac.uk/res/fme/resources/software.htm. The help files & example datasets tell you everything you need to know, including how to format your data in textfiles, so that it is read in correctly. Morphologika will perform GPA, PCA, and visualization for you and can print relative warps into a log file. There is a tool for generating simple polygonal graphics also. It is worth spending time working out which landmarks you want to connect for illustration, in order to generate high quality illustrations. Indeed, I personally made the experience that this software is very easy to use and straightforward. If you have any questions about how to use it you can contact Prof. Paul O'Higgins directly (he and Nick Jones developed the software): http://www.york.ac.uk/res/fme/people/paul.htm Alternatively, people used Morpheus (D Slice) for visualization and basic realignement, or the old GRF-nd (D Slice) for doing basic analysis realignement with more options, and also the possibility of batch processing. The latter is an old program and you would need a "DOS box" to run it under windows. After realignement, you would need NTSYS (Rohlf) to get partial warps, relative warps and so on. Another option to use is the IMP software programmed by Dave Sheets, downloadable under http://www.canisius.edu/~sheets/morphsoft.html. This software is very useful, because you can ask the program to print partial or relative warps in a ASCII file for use in the statistical program of your choice, although the program can perform some routine statistics, like PCA. There are a lot of illustrative examples published, which can be of help, when you use these methods for 3D landmarks for the first time (see below). In addition, several people attached additional papers to their mails, I might forward to anybody, who is interested. Collard, M. and P. O'Higgins (2001). "Ontogeny and homoplasy in the papionin monkey face." Evol Dev 3(5): 322-31. O'Higgins, P. (2000). "The study of morphological variation in the hominid fossil record: biology, landmarks and geometry." J Anat 197 ( Pt 1): 103-20. Pan, R., F. Wei, et al. (2003). "Craniofacial variation of the Chinese macaques explored with Morphologika." J Morphol 256(3): 342-8. Free, S. L., P. O'Higgins, et al. (2001). "Landmark-based morphometrics of the normal adult brain using MRI." Neuroimage 13(5): 801-13. Klingenberg & Monteiro, 2005, Syst. Biol. Hennessy RJ, Moss JP. Facial growth: separating shape from size. European Journal of Orthodontics 23, 275-285, 2001. Hennessy RJ, Waddington JL and Moss JP. Localisation of Anatomical Features in the Human Face Using Differential Geometry. Proceedings of the Irish Machine Vision and Image Processing Conference, pp 21 – 28, ed Adam Winstanley, published by Department of Computer Science, National University of Ireland, Maynooth, Ireland, 2001. Ismail SFH, Moss JP and Hennessy RJ. Three-dimensional assessment of the effects of extraction and nonextraction orthodontic treatment of the face. American Journal of Orthodontic and Dentofacial Orthopedics 121(3), 244 - 256, 2002 Hennessy RJ and Stringer CB. Geometric morphometric study of the regional variation of modern human craniofacial form. American Journal of Physical Anthropology 117(1), 37 – 48, 2002. Hennessy RJ, Kinsella and Waddington JL. 3D laser surface scanning and geometric morphometric analysis of craniofacial shape as an index of cerebro-craniofacial morphogenesis : initial application to sexual dimorphism. Biological Psychiatry 51, 507 – 514, 2002. Moss JP and Hennessy RJ. Lasers in dental surgery - the uses of 3D images in dental surgery. Nederlands Tijdshrift voor Tandheelkunde 109, 378 – 383, 2002. Hennessy RJ, Lane A, Kinsella A, Larkin C, O’Callaghan E and Waddington JL. 3D morphometrics of craniofacial dysmorphology reveals sex-specific asymmetries in schizophrenia. Schizophrenia Research 67, 261-268, 2004. Hennessy RJ, McLearie S, Kinsella A, Waddington JL. “Facial shape and asymmetry by 3D laser surface scanning covary with cognition in a sexually dimorphic manner”, The Journal of Neuropsychiatry and Clinical Neurosciences, 18, pp 73 – 80, 2006. Hennessy RJ, McLearie S, Kinsella A, Waddington JL, “Facial surface analysis by 3D laser scanning and geometric morphometrics in relation to sexual dimorphism in cerebral-craniofacial morphogenesis and cognitive function”, Journal of Anatomy, 207, pp 283 – 295, 2005. My best wishes, Oliver Prof. Dr. Oliver Betz Zoologisches Institut Abt. Evolutionsbiologie der Invertebraten Auf der Morgenstelle 28E D-72076 Tübingen Germany phone: 0049-(0)7071-2972995 E-mail: [EMAIL PROTECTED] http:/www.uni-tuebingen.de/agbetz -- Replies will be sent to the list. For more information visit http://www.morphometrics.org
