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Hi - see http://www.fmrib.ox.ac.uk/fsl/bet2/ If you have t1 and t2, you can just use betall - to get usage just type "betall". If you have just t1 you can use betsurf with the second set of options when you just type "betsurf". Hopefully this is clear - if not, you might be interested in the first 5 or 6 sections of the unix intro: http://www.isu.edu/departments/comcom/unix/workshop/unixindex.html Cheers, Steve. On Sun, 14 Aug 2005, farzaneh s.mostafaie wrote: > Hi , > I 'm sorry but I couldn't run betsurf correctly when I type the line: > betsurf -m structural structural_t2 structural_bet_mesh.off > struct2standard.mat struct_surf > > it says :unable to open struct2standard.mat > what is this error ?,and the other problem if I want to use just T1 images > how should I use betsurf? > > thanks ,specially Mark for the guide. > best, > Farzaneh > --------------------------------------------------------------------- > 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 > > Send instant messages to your online friends http://uk.messenger.yahoo.com -- Stephen M. Smith DPhil Associate Director, FMRIB and Analysis Research Coordinator Oxford University Centre for Functional MRI of the Brain 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