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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
Date: Thursday, 3 December 2020 at 12:39 pm
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
<freesurfer@nmr.mgh.harvard.edu<mailto: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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
On Behalf Of Julia Yang
Sent: Wednesday, December 2, 2020 8:37 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto: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
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