Nick

I ran: recon-all -skullstrip -no-wsgcaatlas -clean-bm -s 3157

and got the exact same problem with brainmask.mgz

Darren

On Wed, Sep 5, 2012 at 3:37 PM, Nick Schmansky nicks@nmr.mgh.harvard.eduwrote:

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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