hmmm, that's interesting. If you send us the data we'll take a look. In any case, you can run, if you create an orig_stripped.mgz you can run:

mri_mask T1.mgz orig_stripped.mgz brain.mgz

then you should be able to run from after the skull stripping forward (check the recon-all help. You'll need to run a couple of steps before autorecon2-wm and autorecon3).

cheers Bruce

On Fri, 8 Aug 2008, Vina Goghari wrote:

Hi all, I get this error for one subject: mri_watershed Error: GLOBAL region of the brain empty !

I check the talairach transformation and it looked good. I also tried just scripting the orig.mgz and I get a wonderful strip. How can I move forward with the recon-all process?

Thanks, Vina

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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Vina,

Can you check the FOV value for the orig.mgz file? That is:

cd subj/mri mri_info orig.mgz

Is it greater than 256? Are the dimensions >256?

I have just recently been looking into this error for someone else, and the source of the problem was improper handling by mri_convert of data that has a FOV > 256. But I don't know if this is the source of your problem. A fix for the problem I am working on is forthcoming.

Nick

On Fri, 2008-08-08 at 19:35 -0500, Vina Goghari wrote:

Hi all, I get this error for one subject: mri_watershed Error: GLOBAL region of the brain empty !

I check the talairach transformation and it looked good. I also tried just scripting the orig.mgz and I get a wonderful strip. How can I move forward with the recon-all process?

Thanks, Vina

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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer