Dear all,

I am running recon-all on few SPGR T1s and few MPRAGE T1s. However most of my dataset, may it be SPGR or MPRAGE has some artifacts and poor wm/gm contrast. Have attached a screen shot of bad pial and wm error (going beyond dura). Even gcut did not do a good job of cutting of all the dura, and I had to manually edit voxels in all the slices. I feel even after that if I run recon-all, it will not give me any reliable cortical thickness measures.

Can anyone please suggest me if I should still manually edit all other subjects for all the slices throughout the volume or exclude them from analysis?

PS: attached image FOV is 260 and I used -cw256 flag to restrict FOV to 256. For other images FOV is within 256, but still there is lot of dura in the brainmask.

Thanks, Sneha