Make sure it looks reasonable (that there is a brain in there, and the intensities look ok). You can send it to us if you want

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Julia Yang
Sent: Wednesday, December 2, 2020 10:27 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] mri_watershed error: problem in the COG calcuation

        External Email - Use Caution        

Hi,

What will you be looking in the T1.mgz?

I am quite new to this field so have a very basic understanding of it.

Much appreciated.

Julia Yang

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu>
Date: Thursday, 3 December 2020 at 12:39 pm
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] mri_watershed error: problem in the COG calcuation

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