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:

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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
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