External Email - Use Caution
Forgot to mention it but all the files seem nice and the WM segmentations are also good. I am using freesurfer 7.2
---------- Forwarded message --------- De: Carlos Estévez Fraga cefraga@alumni.unav.es Date: jue, 9 mar 2023 a las 17:32 Subject: Re: [Freesurfer] recon-all not parcellating To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu, < YHUANG43@mgh.harvard.edu>
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 (YHUANG43@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-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
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