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Signal intensity in air cavities tend to be pretty close to that of bone, which makes them pretty hard to actually see. Separating air from bone using the segmentation in SPM is therefore highly dependent on the tissue priors. I tried to generate tissue priors that vaguely represented the location of air cavities, but to do this a bit more accurately would probably require good quality CT and MR of the same subjects. This sort of data is not usually so easy to get hold of (although I haven't yet tried with scans from The Retrospective Image Registration Evaluation Project). There are other approaches that could also be helpful. You're probably familiar with Clare Poynton's work with Sandy Wells, which should contain something you could use: Atlas-based improved prediction of magnetic field inhomogeneity for distortion correction of EPI data. Poynton C, Jenkinson M, Wells W. Med Image Comput Comput Assist Interv (MICCAI), 12(2):951-9, 2009. Another related approach is this one: Hofmann, Matthias, Florian Steinke, Verena Scheel, Guillaume Charpiat, Jason Farquhar, Philip Aschoff, Michael Brady, Bernhard Schölkopf, and Bernd J. Pichler. "MRI-based attenuation correction for PET/MRI: a novel approach combining pattern recognition and atlas registration." Journal of Nuclear Medicine 49, no. 11 (2008): 1875-1883. Best regards, -John On 23 January 2013 15:50, Kevin Chen <[log in to unmask]> wrote: > Hi all, > > I have been using the "New Segment" tool in trying to segment tissue > classes, including bone and air cavities, but it seems that the air > cavities are constantly underestimated (for example, in the nasal cavity). > Is there a way to improve segmentation of air, such as orienting the head > in a specific way or doing some preprocessing of the MR images? Thanks in > advance! > > Best, > Kevin Chen > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in error > but does not contain patient information, please contact the sender and properly > dispose of the e-mail.