Thank you very much Michael. Dr Fatemeh Geranmayeh Wellcome Trust Clinical Research Fellow The Computational, Cognitive and Clinical Neuroimaging Laboratory Imperial College London Telephone : 020 7594 7994 From: Michael Dwyer <[log in to unmask]<mailto:[log in to unmask]>> Reply-To: FSL - FMRIB's Software Library <[log in to unmask]<mailto:[log in to unmask]>> Date: Thursday, 9 January 2014 17:50 To: "[log in to unmask]<mailto:[log in to unmask]>" <[log in to unmask]<mailto:[log in to unmask]>> Subject: Re: [FSL] Artifact on ROI Hi, if I understand correctly, you are trying to get a 10mm binary spherical mask (ROI) centered around a given point. I just tried your approach, and I think the trouble you're having is floating point error, given that you end up working with tiny values that are quite close to zero. When you open it in fslview, it defaults to an extremely narrow intensity range. For your purpose, I would suggest to use maximum dilation rather than mean filtering (although it IS a bit slower), and to use integer output. E.g.: fslmaths /Users/fg00/fsl/data/standard/MNI152_T1_1mm -mul 0 -add 1 -roi 81 1 141 1 127 1 0 1 -kernel sphere 10 -dilF rSFG10mm -odt int That will leave the output as 0's and 1's, rather than near-zeros (e-13) and 0.00024 in the mask. On Thu, Jan 9, 2014 at 8:46 AM, Fatemeh Geranmayeh <[log in to unmask]<mailto:[log in to unmask]>> wrote: Dear Experts. I am using fslmaths to create ROIs using the following command: fslmaths /Users/fg00/fsl/data/standard/MNI152_T1_1mm -mul 0 -add 1 -roi 81 1 141 1 127 1 0 1 -kernel sphere 10 -fmean rSFG10mm -odt float However the output has an unusual artifact with streaks radiating away from the ROI and a a few other mirror ROIs are also created elsewhere. I have previously used the same script (as far as I can tell) and managed to create the ROI with no problem. Can you help me with figuring out where I am going wrong please? I am happy to upload the images if you would like to see it. Best wishes Fatemeh -- Michael G. Dwyer, Ph.D. Assistant Professor of Neurology Director of Technical Imaging Development Buffalo Neuroimaging Analysis Center University at Buffalo 100 High St. Buffalo NY 14203 [log in to unmask]<mailto:[log in to unmask]> (716) 859-7065