Can you also add '-gcareg' to your command line?
I'm not sure if any other steps are needed. If that doesn't work, can you run
the full recon-all pipeline? Use directive '-all' instead of '-autorecon1'.
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Ni, Zhen (NIH/NINDS) [C]
Sent: Wednesday, March 12, 2025 12:56 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] autorecon1_norm.mgz not found
External Email - Use Caution
Sorry,
I think I attached a wrong log moment ago. Please refer to this one.
Thanks
Zhen
From: Ni, Zhen (NIH/NINDS) [C]
Sent: Wednesday, March 12, 2025 12:46 PM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: RE: autorecon1_norm.mgz not found
Thanks a lot.
It moved a bit forward but new errors occurred, seems like co-registration to
Talairach space?
Zhen
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
Sent: Wednesday, March 12, 2025 11:58 AM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [EXTERNAL] Re: [Freesurfer] autorecon1_norm.mgz not found
Can you try to add '-canorm' to your 'recon-all -autorecon1' command line?
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 Ni, Zhen (NIH/NINDS) [C]
Sent: Wednesday, March 12, 2025 10:28 AM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] autorecon1_norm.mgz not found
External Email - Use Caution
Hello,
These two logs are from the same subject but with slightly different
preprocesses. The initial images are a 90 axial slides (512*512). I also have
her images with 30 slides (with 5mm gaps in between). All these got the same
error message with freesurfer. she has multiple lesions (but very small size)
in the cerebellum and cerebral cortex, and also in the white matter.
I hope these information may be useful.
Thanks
Zhen
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
Sent: Wednesday, March 12, 2025 8:09 AM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [EXTERNAL] Re: [Freesurfer] autorecon1_norm.mgz not found
Can you attach your recon-all.log?
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 Ni, Zhen (NIH/NINDS) [C]
Sent: Wednesday, March 12, 2025 7:56 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] autorecon1_norm.mgz not found
External Email - Use Caution
Hello,
I'm using the command "recon-all -autorecon1 -subjid $SUBJECTNAME".
After about 2 hours, there are a few mgz and other files generated in the /mri
directory, however, I got an error message:
WARNING: entowm has very low volumes so not using it to edit GA of cortex label
#--------------------------------------
#@# CC Seg Mon Mar 10 19:13:32 EDT 2025
\n seg2cc --s sub-002 \n
ERROR: cannot find /Applications/freesurfer/8.0.0/subjects/sub-002/mri/norm.mgz
Darwin nzs-MacBook-Air.local 23.6.0 Darwin Kernel Version 23.6.0: Fri Jul 5
17:54:20 PDT 2024; root:xnu-10063.141.1~2/RELEASE_X86_64 x86_64
recon-all -s sub-002 exited with ERRORS at Mon Mar 10 19:13:33 EDT 2025
I wonder if you have any idea to fix the problem.
Zhen
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