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 <fis...@nmr.mgh.harvard.edu>wrote: > 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 > > > > > > > > > > > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > -- Darren Gitelman, MD Northwestern University 710 N. Lake Shore Dr. Abbott 11th Floor Chicago, IL 60611 Ph: (312) 908-8614 Fax: (312) 908-5073
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