External Email - Use Caution
Hi Freesurfers,
I am attempting to run recon-all on a set of .nii.gz files. Each file is in our subject directory and has run through recon-all. Recon-all only takes 10 seconds to run and says it was completed without errors. When I go to the folder recon-all creates, the folders are empty.
Here is the code we ran:
recon-all -s 967 -i /Users/corpuscallosum/Desktop/subjects/sR0391178-0002-00001-000208-01.nii.gz
Here is the output message:
Started at Wed Sep 13 10:52:44 PDT 2023
Ended at Wed Sep 13 10:52:54 PDT 2023
#@#%# recon-all-run-time-hours 0.003
recon-all -s 967 finished without error at Wed Sep 13 10:52:54 PDT 2023
done
We are using an iMac Pro 2017 running Ventura 13.5.2 and FreeSurfer version 7.3.2.
I have attached the recon-all.log file and would appreciate any suggestions. We have previously run many successful recon-all's and have not encountered any issues.
Thank you,
Lauren Stephens
Lauren Stephens, MS
Assistant Clinical Research Coordinator
Department of Psychiatry and Behavioral Science
Stanford University School of Medicine
E: laurenss@stanford.edu
P: (650)-725-1716
External Email - Use Caution
Hi Lauren,
You will also need to specify '-all' to recon-all.
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Lauren Stephens Sent: Wednesday, September 13, 2023 2:02 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Recon-all completed without error in 10 seconds
External Email - Use Caution Hi Freesurfers,
I am attempting to run recon-all on a set of .nii.gz files. Each file is in our subject directory and has run through recon-all. Recon-all only takes 10 seconds to run and says it was completed without errors. When I go to the folder recon-all creates, the folders are empty.
Here is the code we ran:
recon-all -s 967 -i /Users/corpuscallosum/Desktop/subjects/sR0391178-0002-00001-000208-01.nii.gz
Here is the output message:
Started at Wed Sep 13 10:52:44 PDT 2023
Ended at Wed Sep 13 10:52:54 PDT 2023
#@#%# recon-all-run-time-hours 0.003
recon-all -s 967 finished without error at Wed Sep 13 10:52:54 PDT 2023
done
We are using an iMac Pro 2017 running Ventura 13.5.2 and FreeSurfer version 7.3.2.
I have attached the recon-all.log file and would appreciate any suggestions. We have previously run many successful recon-all's and have not encountered any issues.
Thank you,
Lauren Stephens
Lauren Stephens, MS
Assistant Clinical Research Coordinator
Department of Psychiatry and Behavioral Science
Stanford University School of Medicine
E: laurenss@stanford.edumailto:laurenss@stanford.edu
P: (650)-725-1716
External Email - Use Caution
Hi Yujing,
Thank you, that did work!
Follow up question: Why would the code I used above, successfully generate the recon-all outputs for our other files?
Thanks,
Lauren Stephens
Lauren Stephens, MS
Assistant Clinical Research Coordinator
Department of Psychiatry and Behavioral Science
Stanford University School of Medicine
E: laurenss@stanford.edu
P: (650)-725-1716
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Huang, Yujing YHUANG43@mgh.harvard.edu Sent: Wednesday, September 13, 2023 11:05 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Recon-all completed without error in 10 seconds
External Email - Use Caution
Hi Lauren,
You will also need to specify ‘-all’ to recon-all.
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Lauren Stephens Sent: Wednesday, September 13, 2023 2:02 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Recon-all completed without error in 10 seconds
External Email - Use Caution
Hi Freesurfers,
I am attempting to run recon-all on a set of .nii.gz files. Each file is in our subject directory and has run through recon-all. Recon-all only takes 10 seconds to run and says it was completed without errors. When I go to the folder recon-all creates, the folders are empty.
Here is the code we ran:
recon-all -s 967 -i /Users/corpuscallosum/Desktop/subjects/sR0391178-0002-00001-000208-01.nii.gz
Here is the output message:
Started at Wed Sep 13 10:52:44 PDT 2023
Ended at Wed Sep 13 10:52:54 PDT 2023
#@#%# recon-all-run-time-hours 0.003
recon-all -s 967 finished without error at Wed Sep 13 10:52:54 PDT 2023
done
We are using an iMac Pro 2017 running Ventura 13.5.2 and FreeSurfer version 7.3.2.
I have attached the recon-all.log file and would appreciate any suggestions. We have previously run many successful recon-all's and have not encountered any issues.
Thank you,
Lauren Stephens
Lauren Stephens, MS
Assistant Clinical Research Coordinator
Department of Psychiatry and Behavioral Science
Stanford University School of Medicine
E: laurenss@stanford.edumailto:laurenss@stanford.edu
P: (650)-725-1716
External Email - Use Caution
Hi Lauren,
You need to tell recon-all what to run. These are the options:
" Fully-Automated Directive: -all : performs all stages of cortical reconstruction -autorecon-all : same as -all
Manual-Intervention Workflow Directives: -autorecon1 : process stages 1-5 (see below) -autorecon2 : process stages 6-23 after autorecon2, check white surfaces: a. if wm edit was required, then run -autorecon2-wm b. if control points added, then run -autorecon2-cp c. proceed to run -autorecon3 -autorecon2-cp : process stages 12-23 (uses -f w/ mri_normalize, -keep w/ mri_seg) -autorecon2-wm : process stages 15-23 -autorecon2-inflate1 : 6-18 -autorecon2-perhemi : tess, sm1, inf1, q, fix, sm2, inf2, finalsurf, ribbon -autorecon3 : process stages 24-34 if edits made to correct pial, then run -autorecon-pial "
Without passing one of options, I don't think it will run.
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Lauren Stephens Sent: Wednesday, September 13, 2023 2:11 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Recon-all completed without error in 10 seconds
External Email - Use Caution Hi Yujing,
Thank you, that did work!
Follow up question: Why would the code I used above, successfully generate the recon-all outputs for our other files?
Thanks,
Lauren Stephens
Lauren Stephens, MS
Assistant Clinical Research Coordinator
Department of Psychiatry and Behavioral Science
Stanford University School of Medicine
E: laurenss@stanford.edumailto:laurenss@stanford.edu
P: (650)-725-1716
________________________________ 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 Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> Sent: Wednesday, September 13, 2023 11:05 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Recon-all completed without error in 10 seconds
External Email - Use Caution
Hi Lauren,
You will also need to specify '-all' to recon-all.
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 Lauren Stephens Sent: Wednesday, September 13, 2023 2:02 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Recon-all completed without error in 10 seconds
External Email - Use Caution
Hi Freesurfers,
I am attempting to run recon-all on a set of .nii.gz files. Each file is in our subject directory and has run through recon-all. Recon-all only takes 10 seconds to run and says it was completed without errors. When I go to the folder recon-all creates, the folders are empty.
Here is the code we ran:
recon-all -s 967 -i /Users/corpuscallosum/Desktop/subjects/sR0391178-0002-00001-000208-01.nii.gz
Here is the output message:
Started at Wed Sep 13 10:52:44 PDT 2023
Ended at Wed Sep 13 10:52:54 PDT 2023
#@#%# recon-all-run-time-hours 0.003
recon-all -s 967 finished without error at Wed Sep 13 10:52:54 PDT 2023
done
We are using an iMac Pro 2017 running Ventura 13.5.2 and FreeSurfer version 7.3.2.
I have attached the recon-all.log file and would appreciate any suggestions. We have previously run many successful recon-all's and have not encountered any issues.
Thank you,
Lauren Stephens
Lauren Stephens, MS
Assistant Clinical Research Coordinator
Department of Psychiatry and Behavioral Science
Stanford University School of Medicine
E: laurenss@stanford.edumailto:laurenss@stanford.edu
P: (650)-725-1716
External Email - Use Caution
I think you need to pass the flag ‘-all’ in the command line.
recon-all -s 967 -i /Users/corpuscallosum/Desktop/subjects/sR0391178-0002-00001-000208-01.nii.gz -all
Nárlon Cássio
Nárlon Cássio Boa Sorte Silva PhD (He, Him, His) CIHR and MSHR BC/CLEAR Postdoctoral Research Fellow Aging, Mobility, and Cognitive Health Lab Djavad Mowafaghian Centre for Brain Health Department of Physical Therapy, Faculty of Medicine University of British Columbia Vancouver, Canada Twitter: @BoaNarlon
On Sep 13, 2023, at 2:01 PM, Lauren Stephens laurenss@stanford.edu wrote:
[CAUTION: Non-UBC Email] External Email - Use Caution
Hi Freesurfers,
I am attempting to run recon-all on a set of .nii.gz files. Each file is in our subject directory and has run through recon-all. Recon-all only takes 10 seconds to run and says it was completed without errors. When I go to the folder recon-all creates, the folders are empty.
Here is the code we ran:
recon-all -s 967 -i /Users/corpuscallosum/Desktop/subjects/sR0391178-0002-00001-000208-01.nii.gz
Here is the output message:
Started at Wed Sep 13 10:52:44 PDT 2023 Ended at Wed Sep 13 10:52:54 PDT 2023 #@#%# recon-all-run-time-hours 0.003 recon-all -s 967 finished without error at Wed Sep 13 10:52:54 PDT 2023 done
We are using an iMac Pro 2017 running Ventura 13.5.2 and FreeSurfer version 7.3.2.
I have attached the recon-all.log file and would appreciate any suggestions. We have previously run many successful recon-all's and have not encountered any issues.
Thank you,
Lauren Stephens
Lauren Stephens, MS Assistant Clinical Research Coordinator Department of Psychiatry and Behavioral Science Stanford University School of Medicine E: laurenss@stanford.edumailto:laurenss@stanford.edu P: (650)-725-1716
<recon-all.log>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/18cN-c8_vQxcaAMABP4EWOqTAtg-0ja1ftsBN7Glspegdgb... 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.
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Hello Lauren:
Open the sR0391178-0002-00001-000208-01.nii.gz file using freeview and see if the whole 3D brain is in place. This should give you a clue as to why this occurred.
best,
Alan
On Wed, Sep 13, 2023 at 1:02 PM Lauren Stephens laurenss@stanford.edu wrote:
External Email - Use CautionHi Freesurfers,
I am attempting to run recon-all on a set of .nii.gz files. Each file is in our subject directory and has run through recon-all. Recon-all only takes 10 seconds to run and says it was completed without errors. When I go to the folder recon-all creates, the folders are empty.
Here is the code we ran:
recon-all -s 967 -i /Users/corpuscallosum/Desktop/subjects/sR0391178-0002-00001-000208-01.nii.gz
Here is the output message:
Started at Wed Sep 13 10:52:44 PDT 2023
Ended at Wed Sep 13 10:52:54 PDT 2023
#@#%# recon-all-run-time-hours 0.003
recon-all -s 967 finished without error at Wed Sep 13 10:52:54 PDT 2023
done
We are using an iMac Pro 2017 running Ventura 13.5.2 and FreeSurfer version 7.3.2.
I have attached the recon-all.log file and would appreciate any suggestions. We have previously run many successful recon-all's and have not encountered any issues.
Thank you,
Lauren Stephens
*Lauren Stephens, MS *
Assistant Clinical Research Coordinator
Department of Psychiatry and Behavioral Science
*Stanford University School of Medicine*
E: laurenss@stanford.edu
P: (650)-725-1716
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1FAb5I8xYlPAgBt9HJQcYvRJa1vFCwIguqkaqurJoq_3eDr...
freesurfer@nmr.mgh.harvard.edu