Hi Gabriel

the contrast probably isn't changed, just the display. Tkmedit tries to compute good window level settings based on the image content, and after stripping there will be far less bright fat, so the brain will probably look brighter. Check the actual voxel values.

cheers Bruce

On Mon, 9 Apr 2012, Gabriel Gonzalez Escamilla wrote:

Dear FreeSurfer experts

I'm using the command "recon-all -skullstrip -clean-bm -gcut -subjid name" to improve the skull stripping of my subjects, but after running this command the contrast looks so changed (bright), is it normal? Does this whitening somehow can change the later analyses?

Regards, Gabriel.