Bruce:

Thank you for looking. I have uploaded the files: I uploaded them in Dicom Format. This is a T1, MPRAGE, image, acquired with GRAPPA, resolution 1x1x1. Name: 3157.tar.gz

Darren

On Wed, Sep 5, 2012 at 11:27 AM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:

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:

...

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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