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
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
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
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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> Date: Thursday, 3 December 2020 at 12:39 pm To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Julia Yang Sent: Wednesday, December 2, 2020 8:37 PM To: freesurfer@nmr.mgh.harvard.edumailto: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
External Email - Use Caution
Hi Brunce,
The T1 files were too big that I couldn’t attach. When I looked through the T1.mgz, the white matter intensity were only between 70-90 in majority of the area. Is there any way that I can adjust the intensity?
Kind Regards,
Julia
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu Date: Friday, 4 December 2020 at 4:54 am To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_watershed error: problem in the COG calcuation 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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> Date: Thursday, 3 December 2020 at 12:39 pm To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Julia Yang Sent: Wednesday, December 2, 2020 8:37 PM To: freesurfer@nmr.mgh.harvard.edumailto: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
freesurfer@nmr.mgh.harvard.edu
-
Fischl, Bruce -
Julia Yang