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.uk

Phone: +44 7788 926 982