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Hi, It is easy to run bet2 (and most other utilities) at the command line and this is a useful skill to master. To start with, open up a terminal window. Then go to the directory that your image is in using "cd" e.g. cd subj001_analysis/ Say there is an image called structural in this directory (either structural.hdr and structural.img or structural.nii.gz, it doesn't matter which) Then you can run bet2 by typing the following command: bet2 structural structural_bet -e -v It will then show you some output as it is going, and when it is finished the results will be in that directory with filenames starting with "structural_bet" If you then want to generate meshes or images for the skull and scalp surfaces, you need to run "betsurf" e.g. betsurf -m structural structural_t2 structural_bet_mesh.off struct2standard.mat struct_surf Note that we recommend you have a T1 and T2 weighted image and that you need to have run registration to standard space to generate the struct2standard.mat file. If you are having trouble with the basics, try looking at the fslcourse lectures, practicals or any of the many online tutorials for using unix and the command line. All the best, Mark On 9 Aug 2005, at 14:36, farzaneh s.mostafaie wrote: > Hello all > How can I use BET2 because it has no visual option in BET section > working with FSL 3.2 > and in command window I can not run it. > If it's possible pleas guide me how I should specify my files > ,and what I should type to run it (or where I can download it). > Thanks for your guides so far . > Best wishes > Farzaneh > > Send instant messages to your online friends > http://uk.messenger.yahoo.com