Hi Abby
can you check the T1.mgz and see if it was normalized properly? Most of the WM should have an intensity around 110. If it doesn't, adding a couple of control points and rerunning may do the trick.
If you can't figure it out feel free to ftp us the tarred and gzipped subject dir.
cheers Bruce
On Mon, 21 Jan 2019, Abby tang wrote:
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Hello FreeSurfer Developers,
I'm attempting to recon-all subjects but for some of my subjects I get the following error when I run recon-all comm and:
*************************WATERSHED************************** Sorting... mri_watershed Error: Problem in the COG calculation: T1.mgz may not contain properly normalized white-matter. Confirm that T1.mgz has enough white-matter voxels of value 110. If white-matter contains few if any voxels of value 110, try adding wm control-points to nu.mgz, and re-run recon-all.
Linux abby-virtual-machine 4.15.0-43-generic #46-Ubuntu SMP Thu Dec 6 14:45:28 UTC 2018 x86_64 x86_64 x86_64 GNU/Lin ux
recon-all -s 0078 exited with ERRORS at Sun Jan 20 20:16:12 CST 2019
I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-sho ot this one? Also, Ive attached the recon-all.log in case it's of any use.
Thank you!