Re: [Freesurfer] Corrupted T1 file (?) but segmentation look fine

2018-11-21 Thread Bruce Fischl
Hi Anneliis freeview tries to guess the right window levels to display a volume, but sometimes fails. Try changing the min/max or window/level with the T1.mgz highlighted and see if it looks better. Alternatively, load the norm.mgz, which will probably look better with freeview's default algor

[Freesurfer] Corrupted T1 file (?) but segmentation look fine

2018-11-21 Thread Anneliis Sartin-tarm
External Email - Use Caution Hello all, I have been running into a curious problem with a couple brains (8 out of 150 seem to have this problem) running through the recon-all pipeline. Upon loading brainmask.mgz, T1.mgz, and corresponding white matter and pial surfaces in Free