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I just noticed my critical typo. They are hyperintensities (high). The images do have some white matter hypointensities (MS lesions), but I've masked them out (in reality, sienax -lm has masked them out for me). On Mon, Feb 28, 2011 at 11:38 AM, Mark Jenkinson <[log in to unmask]> wrote: > Dear Mishkin, > Could you let me know whether the areas what are > excluded from the white matter correspond to high > intensities (hyper) or low intensities (hypo)? I struggled > to see what it was from your images and description, > and they would represent really very different problems. > All the best, > Mark > > > On 25 Feb 2011, at 19:32, Mishkin Derakhshan wrote: > > Hi, > Like a few others on the list I've had problems with FAST v4.1 leaving > holes in the segmentation ie. classifying parenchyma as CSF. > > http://i.imgur.com/7KLqh.png > > Looking at the data (see above link for examples), it seems like this > might be related to white matter hypointensities that are not disease > related, and is present at the mixeltype stage. > > I've tried varying f, H, R, capital i and lower case L and N, but I've > had little success. > My best attempts have been lowering the bias field smoothing kernel to > a FWHM of 4, but this still leaves/creates many small holes, and it > drastically changes the results of the GM segmenation. > > Any tips on what flags I should vary and in what direction (ie. > bigger/smaller than the default) to help this? > > thanks, > mishkin > > >