Forgot to include the message:
Skull Stripping Thu Apr 6 10:09:25 PDT 2006 /subject12/mri mri_mask -xform /subject1/mri/transforms/Subject1_to_Subject12.lta T1 /subject1/mri/brain brain transform file name is /subject1/mri/transforms/Subject1_to_Subject12.lta corRead(): can't open file /subject1/mri/brain/COR-.info mri_mask: could not read mask volume T1 --------------------------------------------- Segmentation Thu Apr 6 10:09:28 PDT 2006 ERROR: cannot find brain/COR-.info recon-all exited with errors at Thu Apr 6 10:09:28 PDT 2006
-----Original Message----- From: Nguyen, Thang Q Sent: Thursday, April 06, 2006 10:27 AM To: 'freesurfer@nmr.mgh.harvard.edu' Subject: recon-all problem: skull stripping asks for COR-.info files that do not exist
Hello all, I'm not sure if this is a problem with the incorporation of the mgz format or not but when I run recon-all, the skull stripping step requests for COR-.info files. The only format that I have in the mri folder is the mgz format. Is there an override option that tells recon-all that I am using mgz format that I don't see? Thank you for your help, Thang Nguyen