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Thank you Eugene and Niels - after reading the page you linked to, I ended up using the -c option with the rough brain CoG coordinates that I eyeballed from one of the images. That seems to've worked well. Cheers, Tudor On 9 April 2018 at 13:18, Niels Bergsland <[log in to unmask]> wrote: > *Somehow "neck" got autocorrected to "new" :) > > On Mon, Apr 9, 2018 at 1:16 PM, Niels Bergsland <[log in to unmask]> > wrote: > >> Hi - you should try running robustfov on your images beforehand as they >> contain a considerable amount of new in the FOV. >> >> On Mon, Apr 9, 2018 at 1:11 PM, Tudor Popescu <[log in to unmask]> wrote: >> >>> Dear all, >>> >>> The fslvbm_1_bet command is producing unsatisfactory results with my T1 >>> images. Namely, there is always too much non-brain tissue left in the the >>> output (_brain) images (sample screenshot attached). >>> >>> I played around with the f value, increasing it in 0.1 steps, but I >>> haven't found any value for which the extraction is neither too much nor >>> too little. I also tried calling the fslvbm_1_bet command with several >>> other options, including -R, -F, and -N, but the results don't change much. >>> >>> What else can I try? Many thanks! >>> >>> Tudor >>> >> >> >> >> -- >> Niels Bergsland >> Integration Director / Research Assistant Professor of Neurology >> Buffalo Neuroimaging Analysis Center / University at Buffalo >> 100 High St. Buffalo NY 14203 >> <https://maps.google.com/?q=100+High+St.+Buffalo+NY+14203&entry=gmail&source=g> >> [log in to unmask] >> > > > > -- > Niels Bergsland > Integration Director / Research Assistant Professor of Neurology > Buffalo Neuroimaging Analysis Center / University at Buffalo > 100 High St. Buffalo NY 14203 > <https://maps.google.com/?q=100+High+St.+Buffalo+NY+14203&entry=gmail&source=g> > [log in to unmask] >