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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@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: laure...@stanford.edu<mailto:laure...@stanford.edu>
P: (650)-725-1716
________________________________
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Huang, Yujing
<yhuan...@mgh.harvard.edu<mailto:yhuan...@mgh.harvard.edu>>
Sent: Wednesday, September 13, 2023 11:05 AM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto: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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
On Behalf Of Lauren Stephens
Sent: Wednesday, September 13, 2023 2:02 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto: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: laure...@stanford.edu<mailto:laure...@stanford.edu>
P: (650)-725-1716
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