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

*Phone*: +44 7788 926 982 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1M5H55_pSIYZRPYFNW-CsYxfE9o1dV1WkVKcnU7w3jBkjLm... 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 https://secure-web.cisco.com/165spvf4VWFE1ogju22P1fDwZzUOlB4fJIfy0bTpNU00Pjw... < https://secure-web.cisco.com/165spvf4VWFE1ogju22P1fDwZzUOlB4fJIfy0bTpNU00Pjw... . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

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 cefraga@alumni.unav.es Sent: Friday, March 10, 2023 7:39 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu; Huang, Yujing YHUANG43@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 <cefraga@alumni.unav.esmailto:cefraga@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 (<YHUANG43@mgh.harvard.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto: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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://secure-web.cisco.com/1w_KlYxiMObTTPgRwymBwN1eQ3S5tXbNnVhhtf1PpekN_RGCjGzMCrBgvburICnWmPSc9nkzkeDysWMf91kx6vYpZSQDimFaVLSafa5ktOjVaOEi3og9cbsOC3J5y2R1qrhapo6yAij5LLXahkzGeax1FJDdycSiRY8VWEsL7J1fQ0HVbUVGxGUMPddQ6M0MB7dAOa34TQmJA8gBc-M0BLcbZLL6EsQkRX-lYP5s_qvSbbm4Qo03P3qn417rcqg-UG99tCY7W2DD3CYCAlXdkWqS28xdn3ow0m23eKaklm0RQNq_oVB9dVconYdMzALAd/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer 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 https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/1N_NW3moDShsiszkPC18GU6T_r3oI3x_BH_gpoZZIURRlnorvz2E5FwhrLNqDZ5pvfYzhNjT4y8DgkzbosAF3QoS2_vkk2oLGuvomi3IE3Jv_47jj0JVQn8jUakd-6yHWJbAla9uX9h-ykimtPMEy9nfELjjm2tFRbDwDrRPRQHuvvgSDC0jqZvrDUW6yhiW4TtFUwxTvUcCCzOL48xUC7O4WOCMfW67dWq6RQdGcN1Q2zg5cQp6cdSPoRFDqg-LXuPlo-98-IeCiWV52XbV2wqBN6iE6kaHq6C0T7EfEs86t8N2H4an3avOwrfoXIhkG/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline <https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/1N_NW3moDShsiszkPC18GU6T_r3oI3x_BH_gpoZZIURRlnorvz2E5FwhrLNqDZ5pvfYzhNjT4y8DgkzbosAF3QoS2_vkk2oLGuvomi3IE3Jv_47jj0JVQn8jUakd-6yHWJbAla9uX9h-ykimtPMEy9nfELjjm2tFRbDwDrRPRQHuvvgSDC0jqZvrDUW6yhiW4TtFUwxTvUcCCzOL48xUC7O4WOCMfW67dWq6RQdGcN1Q2zg5cQp6cdSPoRFDqg-LXuPlo-98-IeCiWV52XbV2wqBN6iE6kaHq6C0T7EfEs86t8N2H4an3avOwrfoXIhkG/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

-- 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 <recon-all-status.log> <recon-all.log>