It is not clear what is going wrong as there is not really an error message.Was there anything printed to the terminal that is not in the log file? The last thing it did was to write out mri/aparc.DKTatlas+aseg.mgz. Can you check that and see if it looks ok? Did you run out of space on the disk?
On 9/10/2022 4:06 PM, Estephan Moana Filho wrote:
External Email - Use Caution
Hello, I am using QuNex to process MRI data with the HCP pipelines. I was able to complete the hcp_pre_freesurfer without problems, but I am having trouble completing the hcp_freesurfer step. I tried processing 10 participants, and they all fail after several hours of processing. The qunex log reports the error "ERROR: recon-all command failed with return_code: 1". The recon-all.log is not clear about what went wrong (at least to me). See attached the log file.
Please let me know your thoughts on this. Thank you.
Estephan
-- Estephan J. Moana-Filho, DDS, MS, PhD Assistant Professor Division of TMD, Orofacial Pain and Dental Sleep Medicine Graduate Faculty in Oral Biology Department of Diagnostic and Biological Sciences UMN School of Dentistry moana004@umn.edu
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-- Estephan J. Moana-Filho, DDS, MS, PhD Assistant Professor Division of TMD, Orofacial Pain and Dental Sleep Medicine Graduate Faculty in Oral Biology Department of Diagnostic and Biological Sciences UMN School of Dentistry moana004@umn.edu
6-320d Moos Tower 515 Delaware St. SE Minneapolis, MN 55455-0329 Office: (612) 624-3338 Clinic: (612) 626-0140 Fax: (612) 626-0138
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