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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