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
[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
[log in to unmask]