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Hi - it't not very clear from the JPGs that you sent what's going on; mostly the image looks like the -f threshold should be lowered. In general we would not recommend downsampling the data. If you would like to upload an example original image we can have a quick look. Please upload the files in a single compressed tarfile to http://www.fmrib.ox.ac.uk/cgi-bin/upload.cgi and then email me the upload ID. Cheers, Steve. On Fri, 16 Dec 2005, A Gouw wrote: > Dear all, we are trying to run SIENAX on T1-3D images (1x1x1mm) in a multi-center setting. However, we've run into several > problems. We hope that you could help us out. First, BET does not give satisfying results. Even after changing the options -f, -g > and -c and cutting off the neck, manual editing is still necessary (parts of the eyes and skull). We think that it could be caused > by a wrong scanning angle. Therefore, while manual editing is not feasible on 256 slices, we downsample the images to 4mm slices > before running BET. Then we combine the manual and automatic masks and run SIENAX without BET. For some centers, this works out > well. For other centers however, BET and segmentation still give bad results. For sagittal MPRAGES the temporal regions are not > properly segmented (see fig 1), and for coronal MPRAGES this is the case in the frontal and occipital regions. We believe that it > is a bias field problem, and we are trying to solve it with optimal N3-inhomogeneity correction. However, this has not been > satisfactory yet. Do you have any suggestions, or have suggestions using different FAST-options? Another problem is that for some > centres the FOV is too small and some parts of the skull are not included in the image. Therefore the skull image is distorted (see > fig 2 and 3). Do you have any ideas of how to solve this? Thank you in advance, best regards, Alida Gouw A.A. Gouw, MD VU Medical > Centre Amsterdam The Netherlands > -- Stephen M. Smith, Professor of Biomedical Engineering Associate Director, Oxford University FMRIB Centre FMRIB, John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222726 (fax 222717) [log in to unmask] http://www.fmrib.ox.ac.uk/~steve