check the end of the recon-all.log file to see if it completed without error, then visually inspect the surfaces and such to see if they are reasonable
cheers Bruce On Sun, 7 Jul 2013, Lin, Richard Lee-Tsong wrote:
Thanks Bruce. I did run that particular analysis to completion, after which it sent me an email with the text "recon-all -s {subjid} finished with errors".
If I can just ignore that error message, I have a follow-up question - in the absence of an email stating that recon-all is completed without error, how can I confirm that my recon-all stages 2 and 3 ran successfully? Are there some files that, if generated in a subdirectory under {subjid}, can give me a final confirmation?
Thanks!
Richard
On Jul 6, 2013, at 8:34 PM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
p.s. I think that is a warning embedded in the depths of some open source numerical minimization code we use that seems benign On Sat, 6 Jul 2013, Lin, Richard Lee-Tsong wrote:
Attaching other log outputs from recon-all. Thanks. ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Lin, Richard Lee-Tsong [Richard_Lin@hms.harvard.edu] Sent: Saturday, July 06, 2013 3:35 PM To: free surfer Subject: [Freesurfer] Error after recon_all on pre-BETed image
Hi FS gurus,
For whatever reason, BET worked better on my structural image than mri_watershed, so I used a BET image with recon-all -autorecon1 -noskullstrip. Here is a summary of the codes that I used:
bet structural.nii structural_brain.nii.gz recon-all -i structural.nii -s {subjid} recon-all -autorecon1 -noskullstrip -s {subjid} mri_convert structural_brain.nii.gz {FS_directory}/{subjid}/mri/brainmask.mgz recon-all -autorecon2 -autorecon3 -subjid {subjid}
Stage 1 ran without errors. Stage 2 ran with errors, but when I checked the log (see attached), and the only message that resembled error to me was the following: IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH
Is there something I did wrong? Thanks.
Best, Richard
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