Hi Jodie

you can do this on the surface, then project the resulting label 1mm into the white matter if I understand what you want correctly. You might also check out the wmparc.mgz and see if it already does what you want.

cheers Bruce On Tue, 29 Jan 2013, Jodie Davies-Thompson wrote:

Dear Freesurfer users and experts,

We are attempting to grow a mask that we have created in FSL, to expand it into white matter.

At first, we tried this in FSL using the dilM command which dilated the size of the mask by n voxels. We then multiplied this by a  segmented white matter mask (again, created in FSL) so only the white matter voxels were included. However, a problem with this method, is that if a mask is over a gyri (as most of our masks are), then diluting the mask in a non-inflated brain causes some voxels from an adjacent gyri to be included.

What we would like to be able to do, is to dilute the mask using the inflated white matter brain created by Freesurfer, and then to take this back into FSL space; thereby, allowing us to create a mask of which includes the true surrounding white matter rather than white matter from adjacent gyri.

Hope this makes sense!? Does anyone know how to do this or could point us in the right direction?

Cheers,

Jodie

---

Jodie Davies-Thompson, Postdoctoral Fellow

Department of Ophthalmology & Visual Sciences

UBC/VGH Eye Care Centre

2550 Willow Street

Vancouver, BC, V5Z 3N9

Canada

Tel: 604-875-4111 ext 69003