Have you looked at the T1.mgz?
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Julia Yang Sent: Wednesday, December 2, 2020 8:37 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] mri_watershed error: problem in the COG calcuation
External Email - Use Caution Hi,
While running the recon_all, I bumped into this error message below. \n mri_watershed -rusage /Users/Shared/PD-MCI/Freesurfer/PDMCI107/touch/rusage.mri_watershed.dat -T1 -brain_atlas /Applications/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz \n Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details The input file is T1.mgz The output file is brainmask.auto.mgz Weighting the input with atlas information before watershed *************************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. Darwin med-cr-mtm0xv 18.7.0 Darwin Kernel Version 18.7.0: Thu Jan 23 06:52:12 PST 2020; root:xnu-4903.278.25~1/RELEASE_X86_64 x86_64 recon-all -s PDMCI107 exited with ERRORS at Wed Nov
Recon_all failed without creating the brainmask.mgz. I have attached files for possible solution.
* Recon-all.log * Nu.mgz * Talairach_with_skull.log * Talairach.xfm
Any help would be much appreciated.
Kind Regards,
Julia Yang