Creating masks using FSL and applying it

Creating masks using FSL and applying it

FSL has a very useful feature of creating and applying masks easily to large number of images. The first step is to create a mask. FSL-eyes provides one method to do that, but I would not go in to details of it. Another method to create masks is by indicating the coordinates of the region of interest and defining the radius, in pixels, of the circle around it. Below are quick commands to do that





Once the mask is created, one can easily apply it to the desired image using the following command





An important tip if you are making masks using FSLeyes. Don’t close your FSLeyes in which you are editing your mask until and unless you are completely satisfied with your mask results. If is much easier to edit your mask if the original file is still open.

Why I started writing blog?

I had the opportunity to learn things in life that most people do not get. That’s why I feel obliged to return a favor to my fellow human beings by sharing what I learnt. These are my personal opinions of life and I understand that many people may not agree with my take on these issues, but that’s perfectly normal, we all may have differences of opinion

“Noble laureates are also normal people like us” – Terry Sejnowski

Neuroscience blog and background

After my Masters, I decided to move to the emerging field of Neuroscience. With time, I learnt that having computational skills in this field is of my great advantage, and even though I had to learn many new things, I was able to solve most problems rather easily than my peers in the field. This motivated me to write some hacks and tutorials for use in neuroimaging analysis and processing. If you find these useful, please do let me know too at

Following are the most common neuroimaging analysis softwares and most of my blog posts would be using these softwares
1. SPM
2. FSL
4. ANTs
5. Freesurfer
6. Nipype
7. Openfmri tools (heudiconv and fmriprep)