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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

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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

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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