Darren,
I forgot to mention that you'll need to add
-clean-bm
after the -no-wsgcaatlas flag, otherwise the prior brainmask.mgz will be
retained and the new one will be saved as brainmask.auto.mgz.
Nick
On Wed, 2012-09-05 at 09:54 -0500, Darren Gitelman wrote:
> Nick, List:
>
>
>
> Still no luck with this data. See attached as an example.
>
>
>
> To get to this point I had run:
>
>
>
> recon-all -all
>
>
>
> This ran to the error: mri_watershed Error: GLOBAL region of the
> brain empty !
>
>
>
> Then I followed your recommendation below
>
>
>
> recon-all -s <subjid> -skullstrip -no-wsgcaatlas, which had no errors
> and then
>
> recon-all -s <subjid> -autorecon2 -autorecon3
>
>
>
> This produced the result attached.
>
>
>
> I then deleted this directory and re-imported all the dicom data for
> this subject. Looked at the images, which look fine.
>
> Then I ran recon-all -s <subjid> -autorecon1
>
>
>
> This fails with the mri_watershed error.
>
>
>
> Then I ran recon-all -s <subjid> -skullstrip -no-wsgcaatlas.
>
>
>
> This runs without error but when I look at the brainmask.mgz it looks
> just like the attached image.
>
>
>
> 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.
>
>
>
> Darren
>
>
>
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