Hi Doug,

Thanks for looking over that file. It is the correct recon-all file for one of the problem brains. I discovered that there was a system reboot of some sort when the recon-all was processing for these problem brains, so that is likely what caused the process to stop. How can I restart the recon-all process for these brains? I have tried just rerunning the recon-all command but the process exits within a few moments each time. I am wondering if there is something I need to delete that was partially processed during the first attempt.

Thanks,

Laurel 

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu>
Sent: Friday, January 24, 2020 9:34 AM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] recon-all errors - mri_segstats and mri_relabel_hypointensities

It did not look like there was an explicit error in that log file, it just stops at mris_volmask. Is that the right recon-all? Also, please just send the text file so that we don't have to unzip it.

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Hi FS Support,

I have two brains for which recon-all exited with errors after I edited the wm.mgz volume. It seems that the problem occurs during the mri_segstats and mri_relabel_hypointensities steps (if I'm reading the output of the command "tail scripts/recon-all.log" correctly). I attached one of the recon-all.log files as a zipped txt file. Please let me know if you have troubleshooting suggestions.

Thank you for your help!  

Laurel Quinlan

Research Specialist

Center for Healthy Minds

University of Wisconsin-Madison

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