Good morning, Recon-all finished without error, but no aseg.mgz file was created. I cannot find any errors in the recon-all.log (attached) to indicate what may have happened. Any suggestions on how to troublshoot this? Thank you, Sarah
Hi Sarah,
It doesn't look like your recon-all is done processing yet from the attached recon-all.log.
You should also have these two files: recon-all-status.log recon-all.done
What did they report?
Thanks.
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of O'Dor, Sarah,PhD Sent: Tuesday, November 15, 2022 9:31 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] aseg.mgz not created
Good morning, Recon-all finished without error, but no aseg.mgz file was created. I cannot find any errors in the recon-all.log (attached) to indicate what may have happened. Any suggestions on how to troublshoot this? Thank you, Sarah
Hi Sarah
I think you didn't give it any flags other than the subject and input. You need to specify -all if you want it to run all the steps it knows how to
Cheers Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of O'Dor, Sarah,PhD Sent: Tuesday, November 15, 2022 9:31 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] aseg.mgz not created
Good morning, Recon-all finished without error, but no aseg.mgz file was created. I cannot find any errors in the recon-all.log (attached) to indicate what may have happened. Any suggestions on how to troublshoot this? Thank you, Sarah
freesurfer@nmr.mgh.harvard.edu
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Fischl, Bruce R.,PHD -
Huang, Yujing -
O'Dor, Sarah,PhD