Hi Carlos,
Can you send recon-all.log as attachment? So, we can have a better understanding of what happened.
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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.fraga@ucl.ac.ukmailto:c.fraga@ucl.ac.uk Phone: +44 7788 926 982