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Hi, I agree with Wolf that it may well be a registration issue, with images in the wrong spaces. It would be helpful if you could post the exact commands that you were running. All the best, Mark wolf zinke <[log in to unmask]> wrote: Hi, Maybe this is a problem with the transformation into the individual subject brain space? Otherwise it might be a good idea to mask the spherical ROI with a brain mask to ensure that it is not exceeding the brain. good luck, wolf On 04/16/2013 08:28 PM, Nucleos P wrote: > Hi Wolf - > > This helps...however, when I run fslmeants using the ROI sphere mask > it shows all zeros for individual subjects. I've done more constrained > analysis on the same image (e.g. less than 8mm radius) and gotten > values. > > Thank you, > Cat > > > On 4/15/13, wolf zinke <[log in to unmask]> wrote: >> Hi, >> >> fslroi uses voxel, but would not be the right tool for your purpose >> anyway, since it changes the image size, cropping it to the defined region. >> >> If you want to create a cubic mask you can use the -roi option of >> fslmaths. This option uses voxel coordinates, so you have to adjust the >> values according to your voxel dimension. >> >> If you want to create a more sphere-like ROI you can do follow this >> description in a recent post: >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=FSL;6ce4bff3.1301 >> >> I hope this helps, >> wolf >> >> On 04/16/2013 12:52 AM, Nucleos P wrote: >>> Hello Experts - >>> >>> When using fslroi it is unclear if the x size, y size, and z size >>> refer to mm or # of voxels around the coordinates? >>> >>> For instance, if I wanted to create a mask at ROI 125, 97, 107 MNI 152 >>> voxel coordinates and then extend to points outside (e.g. 8mm) how >>> would I set this up? >>> >>> Thank you, >>> Cat