You can do this using the paint tools in FSLView, a video tutorial is available here: https://www.youtube.com/watch?v=Fju5wlTAEOI&feature=youtu.be

and http://andysbrainblog.blogspot.be/2012/11/creating-masks-in-fsl.html

Make sure that the paint toolbar is visible. For that, select in the main menu of FSLView Tools > Toolbars > Pen/drawing palette. Then follow the video guide.

Good luck,

Pieter

Op 25/01/2017 om 16:11 schreef Mahmoud:

That's true. They end up in the background but I wanted to know if there is any way to fill let's say a square that has three sides connected to the brain tissue and just one side in the background?

On Wed, Jan 25, 2017 at 10:00 AM, Pieter Vandemaele <[log in to unmask]> wrote:

Are these really holes or are they connected to the background? If you see a hole, you can scroll through the 3D volume and "follow" the hole to see if you end up in the background.

Op 25/01/2017 om 15:52 schreef Mahmoud:

Dear experts,

I am using fslmaths -fillh -bin to create a binary mask of the brain tissue, however, I still see some holes in the mask when I am looking at the axial view. Is there any way to fill the holes even if they are not forming a completely closed boundary (volume)?

Thank you!

Mahmoud

--

Pieter Vandemaele, MSc-Ing
GIfMI Site Manager
Ghent Institute for Functional and Metabolic Imaging
MR Department -1K12
Ghent University Hospital
De Pintelaan 185
9000 Ghent - BELGIUM

[log in to unmask]	tel: +32 (0)9 332 48 20
http://gifmi.ugent.be	fax: +32 (0)9 332 49 69
ORCID ID	0000-0002-4523-2476

--

Pieter Vandemaele, MSc-Ing
GIfMI Site Manager
Ghent Institute for Functional and Metabolic Imaging
MR Department -1K12
Ghent University Hospital
De Pintelaan 185
9000 Ghent - BELGIUM

[log in to unmask]	tel: +32 (0)9 332 48 20
http://gifmi.ugent.be	fax: +32 (0)9 332 49 69
ORCID ID	0000-0002-4523-2476