Re: [Freesurfer] recon-all not parcellating

[Carlos Estévez Fraga]

External Email - Use Caution         Sure!  I’ll run it and let you know. I’ve also contacted the support team from the cluster in case there is any issue with the script Many thanks Best regards Carlos  Enviado desde mi iPhone El 10 mar 2023, a la(s) 14:47, Huang, Yujing <yhuan...@mgh.harvard.edu> escribió:  Hi Carlos,   I’m not sure what happened. There are no errors reported in recon-all.log. Can you try running it again without ‘-parallel’?   Best,   Yujing   From: Carlos Estévez Fraga <cefr...@alumni.unav.es> Sent: Friday, March 10, 2023 7:39 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>; Huang, Yujing <yhuan...@mgh.harvard.edu> Subject: Re: [Freesurfer] recon-all not parcellating           External Email - Use Caution         Sorry just wanted to follow up on this as not sure the email was received   Many thanks    Best regards    Carlos Enviado desde mi iPhone El 9 mar 2023, a la(s) 17:32, Carlos Estévez Fraga <cefr...@alumni.unav.es> escribió: Sure I am attaching the recon-all file.    Below is the output I get in the mri/ folder   I have also tried running recon-all -autorecon1 -autorecon2 -autorecon3 and it stops at the same place.    Many thanks,   Best regards,    Carlos         antsdn.brain.mgz aseg.auto.mgz aseg.auto_noCCseg.label_intensities.txt aseg.auto_noCCseg.mgz aseg.presurf.mgz brain.finalsurfs.mgz brainmask.auto.mgz brainmask.mgz brain.mgz ctrl_pts.mgz mri_nu_correct.mni.log mri_nu_correct.mni.log.bak norm.mgz nu.mgz orig orig.mgz orig_nu.mgz rawavg.mgz segment.dat T1.mgz talairach.label_intensities.txt talairach.log talairach_with_skull.log transforms wm.asegedit.mgz wm.mgz wm.seg.mgz         El jue, 9 mar 2023 a las 17:04, Huang, Yujing (<yhuan...@mgh.harvard.edu>) escribió: Hi Carlos,   Can you send recon-all.log as attachment? So, we can have a better understanding of what happened.   Best,   Yujing   From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Carlos Estévez Fraga Sent: Thursday, March 9, 2023 9:33 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] recon-all not parcellating           External Email - Use Caution         Dear Freesurfer team,   I am trying to run recon-all -all in the cluster but unfortunately I am unable to obtain the parcellated images (exact command is  recon-all -parallel -openmp $NSLOTS -s ${j} -i ${j}_corrected.nii.gz -all -cw256)   I have run the script different times with different subjects and it just stops abruptly always in the same point, after WM segmentation, see below the recon-all-status.log for one subject (same in all of them, it stops after WM segmentation)   I tried it on my laptop and in my desktop computer and it works, but not in the cluster...   Any chance you know why this may be happening?    Best regards,    Carlos   #@# MotionCor Tue Mar  7 22:10:08 GMT 2023 #@# Talairach Tue Mar  7 22:10:18 GMT 2023 #@# Talairach Failure Detection Tue Mar  7 22:13:37 GMT 2023 #@# Nu Intensity Correction Tue Mar  7 22:13:37 GMT 2023 #@# Intensity Normalization Tue Mar  7 22:16:54 GMT 2023 #@# Skull Stripping Tue Mar  7 22:18:15 GMT 2023 #@# EM Registration Tue Mar  7 22:20:49 GMT 2023 #@# CA Normalize Tue Mar  7 22:22:45 GMT 2023 #@# CA Reg Tue Mar  7 22:23:44 GMT 2023 #@# SubCort Seg Tue Mar  7 23:07:13 GMT 2023 #@# CC Seg Wed Mar  8 00:00:24 GMT 2023 #@# Merge ASeg Wed Mar  8 00:03:01 GMT 2023 #@# Intensity Normalization2 Wed Mar  8 00:03:01 GMT 2023 #@# Mask BFS Wed Mar  8 00:04:47 GMT 2023 #@# WM Segmentation Wed Mar  8 00:04:48 GMT 2023 #@# Fill Wed Mar  8 00:07:28 GMT 2023     -- Dr Carlos Estevez-Fraga, MD, PhD Senior Clinical Research Fellow Department of Neurodegenerative Diseases UCL Queen Square Institute of Neurology London, UK Mail: c.fr...@ucl.ac.uk Phone: +44 7788 926 982 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed.  If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/complianceline <MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/complianceline> . 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