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
Hi Carlos,
Can you send recon-all.log as attachment? So, we can have a better understanding of what happened.
Best,
Yujing
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?
#@# 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
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-- 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 <recon-all-status.log> <recon-all.log>
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