External Email - Use Caution
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
[A picture containing calendar Description automatically generated]
Kind Regards,
Julia Yang
What kind of scan is that? It looks like the skull is very bright, which will cause watershed to fail
On 12/16/2020 8:41 PM, Julia Yang wrote:
External Email - Use Caution
Hi,
We had MP2RAGE UNI images which had background noise. So we had to mask with INV2 images. To do so we put threshold of -5 to INV2 and multiply with T1_UNI.
Maybe the skull became very bright on this process? What could you do to fix this up?
Kind Regards,
Julia From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Greve, Douglas N.,Ph.D. Sent: Thursday, 24 December 2020 3:22 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Recon_all: COG calculation error
What kind of scan is that? It looks like the skull is very bright, which will cause watershed to fail On 12/16/2020 8:41 PM, Julia Yang wrote:
External Email - Use Caution 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
[A picture containing calendar Description automatically generated]
Kind Regards,
Julia Yang
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External Email - Use Caution
Hi,
We had MP2RAGE UNI images which had background noise. So we had to mask with INV2 images. To do so we put threshold of -5 to INV2 and multiply with T1_UNI.
Maybe the skull became very bright on this process? What could you do to fix this up?
Kind Regards,
Julia
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@MGH.HARVARD.EDU Date: Thursday, 24 December 2020 at 3:28 am To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Recon_all: COG calculation error What kind of scan is that? It looks like the skull is very bright, which will cause watershed to fail On 12/16/2020 8:41 PM, Julia Yang wrote:
External Email - Use Caution 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
[A picture containing calendar Description automatically generated]
Kind Regards,
Julia Yang
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Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
https://secure-web.cisco.com/1x7m6lNjtOh9H5q-Mq_da-KWeiqnXd99sbcsei3mBkxPag7...
You can try running INV2 through recon-all (at least until it creates the brain mask), then mask with that brain mask
On 1/20/2021 11:24 PM, Julia Yang wrote:
External Email - Use Caution
Hi,
We had MP2RAGE UNI images which had background noise.
So we had to mask with INV2 images. To do so we put threshold of -5 to INV2 and multiply with T1_UNI.
Maybe the skull became very bright on this process?
What could you do to fix this up?
Kind Regards,
Julia
*From: *freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@MGH.HARVARD.EDU *Date: *Thursday, 24 December 2020 at 3:28 am *To: *freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Subject: *Re: [Freesurfer] Recon_all: COG calculation error
What kind of scan is that? It looks like the skull is very bright, which will cause watershed to fail
On 12/16/2020 8:41 PM, Julia Yang wrote:
* External Email - Use Caution * 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 A picture containing calendar Description automatically generated Kind Regards, Julia Yang _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/1x7m6lNjtOh9H5q-Mq_da-KWeiqnXd99sbcsei3mBkxPag7cVi3RPT1iho23B-XbaYvyXypIqv2A_RAf_4TkDndKBaSegls6M-b4P0X8OwTMFsVEIFTqZrvHNeEg_yBLaQz_UlEV8dwtEovibRGj-4ytfH3T1RYPgm8kGNa5h1L7YvdPr8Ks9yW3svdUDqFGMVZ6sD_STfv9BISy7m4VyANmu7727FjF4BgR9V674-LPbeEhXgUlxhuQIKgtRzzb7Giu82cDACvJx-BZEVI539Q/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
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Douglas N. Greve -
Greve, Douglas N.,Ph.D.
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Julia Yang