Hi,

 

While running the recon_all, I bumped into this error message below and failed to create a brainmask.

I could not attach the T1.mgz and log file because the file were too big.

 

When I looked through, the white matter intensity were only between 70-90. 

It is pretty much an entire white matter intensity that I think it may be difficult to manually add control points. 

 

What would be your suggestions? 

I have added screenshots of the freeview. 

 

\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

 

 

 

 

 

Kind Regards,

 

Julia Yang