Hi Darren
can you describe your input data? What format, resolution, etc... is it?
If you upload it we'll take a look
cheers
Bruce
On Wed, 5 Sep 2012, Darren Gitelman
wrote:
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> Nick, List:
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> Still no luck with this data. See attached as an example.
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> To get to this point I had run:
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> recon-all -all
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> This ran to the error: mri_watershed Error: GLOBAL region of the brain empty !
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> Then I followed your recommendation below
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> recon-all -s <subjid> -skullstrip -no-wsgcaatlas, which had no errors and then
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> recon-all -s <subjid> -autorecon2 -autorecon3
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> This produced the result attached.
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> I then deleted this directory and re-imported all the dicom data for this subject. Looked at the images, which look fine.
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> Then I ran recon-all -s <subjid> -autorecon1
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> This fails with the mri_watershed error.
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> Then I ran recon-all -s <subjid> -skullstrip -no-wsgcaatlas.
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> This runs without error but when I look at the brainmask.mgz it looks just like the attached image.
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> Is there some way to set the thresholds differently? The T1 image looks fine to me although perhaps the intensity is slightly
> less than usual, but it doesn't seem particularly noisy.
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> Darren
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