Dear all
I put a T1w image through the recon-all process and it completed without errors, but the segmentation output (aparc.a2009s+aseg) does not line up with the subjects own brain.mgz or orig.mgz. I have had a similar problem with other T1w images that I've used. Any ideas why this might be and how to correct?
Many thanks for your help Rumana
really? No, we've never seen anything like that. Can you send us a snapshot? What version are you using? On Fri, 23 Jul 2010, Rumana Chowdhury wrote:
Dear all
I put a T1w image through the recon-all process and it completed without errors, but the segmentation output (aparc.a2009s+aseg) does not line up with the subjects own brain.mgz or orig.mgz. I have had a similar problem with other T1w images that I've used. Any ideas why this might be and how to correct?
Many thanks for your help Rumana
Hi Rumana, have you gone through the troubleshooting steps that we describe on our wiki?
doug
Rumana Chowdhury wrote:
Dear all
I put a T1w image through the recon-all process and it completed without errors, but the segmentation output (aparc.a2009s+aseg) does not line up with the subjects own brain.mgz or orig.mgz. I have had a similar problem with other T1w images that I've used. Any ideas why this might be and how to correct?
Many thanks for your help Rumana
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Douglas N Greve -
Rumana Chowdhury