Hi Pablo

I would guess this just a display problem - that freeview is incorrectly setting the initial window levels. Try changing them. One nice feature of freeview is that if you highlight the intensity volume in the "volumes" list in the pane on the left, you can do shift-middle-mouse and select a region in the image that freeview uses to set the window levels. Try selecting a big area that includes mostly or all brain

cheers Bruce

On Thu, 24 Jul 2014, pablo najt wrote:

FreeSurfer experts,I have a question about one of my scans after running recon-all -all. When I open the image with freeview for inspecting brain mask volume. To give you a better idea of the problem I have attached a screenshot of the T1 volume. All my other images did not show the coloured black background that observed here, so I am wondering what might be the problem. To open T1 I have used the suggested command:

freeview -v pial_edits_before/mri/T1.mgz \ pial_edits_before/mri/brainmask.mgz \ -f pial_edits_before/surf/lh.white:edgecolor=yellow \ pial_edits_before/surf/lh.pial:edgecolor=red \ pial_edits_before/surf/rh.white:edgecolor=yellow \ pial_edits_before/surf/rh.pial:edgecolor=red My scans have been processed in nifti format. Also I have previously run nu_correct for correction of artefacts in the top of the brain. I also opened this particular scan and it looks very similar to the others. Thank you in advance for your attention. Pablo